From 953541b8737ca85b0225c9f69483538f6542feaf Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 14 Aug 2024 08:02:49 +0000 Subject: [PATCH] Jenkins update build 205. --- automated_tool_installation_log.tsv | 58 ++++ staging.gvl.org.au/annotation.yml | 122 ++++---- staging.gvl.org.au/assembly.yml | 247 ++++++++-------- staging.gvl.org.au/bacterial_typing.yml | 6 +- staging.gvl.org.au/bb_tools.yml | 4 +- staging.gvl.org.au/bed.yml | 16 +- staging.gvl.org.au/blast.yml | 16 +- staging.gvl.org.au/chemicaltoolbox.yml | 60 ++-- staging.gvl.org.au/chip_seq.yml | 8 +- staging.gvl.org.au/collection_operations.yml | 6 +- staging.gvl.org.au/convert_formats.yml | 40 +-- staging.gvl.org.au/deeptools.yml | 130 ++++----- staging.gvl.org.au/dna_metabarcoding.yml | 10 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 4 +- staging.gvl.org.au/fastafastq.yml | 106 +++---- staging.gvl.org.au/fastq_quality_control.yml | 30 +- staging.gvl.org.au/filter_and_sort.yml | 5 +- staging.gvl.org.au/gemini_tools.yml | 22 +- staging.gvl.org.au/genome_editing.yml | 6 +- staging.gvl.org.au/get_data.yml | 41 +-- staging.gvl.org.au/graphdisplay_data.yml | 55 ++-- staging.gvl.org.au/hca_single_cell.yml | 38 +-- staging.gvl.org.au/hicexplorer.yml | 24 +- staging.gvl.org.au/imaging.yml | 64 ++--- staging.gvl.org.au/ivar.yml | 76 ++--- .../join_subtract_and_group.yml | 4 +- staging.gvl.org.au/machine_learning.yml | 48 ++-- staging.gvl.org.au/mapping.yml | 46 +-- staging.gvl.org.au/metabolomics.yml | 22 ++ staging.gvl.org.au/metagenomic_analysis.yml | 131 +++++---- staging.gvl.org.au/mothur.yml | 6 +- staging.gvl.org.au/multiple_alignments.yml | 60 ++-- staging.gvl.org.au/nanopore.yml | 54 ++-- staging.gvl.org.au/none.yml | 66 ++--- staging.gvl.org.au/phylogenetics.yml | 89 +++--- staging.gvl.org.au/picard.yml | 6 +- staging.gvl.org.au/proteomic_ai.yml | 14 +- staging.gvl.org.au/proteomics.yml | 200 ++++++------- staging.gvl.org.au/qiime_2.yml | 2 +- staging.gvl.org.au/rad_seq.yml | 80 +++--- staging.gvl.org.au/rna_seq.yml | 168 +++++------ staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 62 ++-- staging.gvl.org.au/send_data.yml | 8 +- staging.gvl.org.au/single_cell.yml | 159 ++++++----- staging.gvl.org.au/statistics.yml | 30 +- staging.gvl.org.au/text_manipulation.yml | 40 +-- staging.gvl.org.au/variant_calling.yml | 40 +-- staging.gvl.org.au/vcfbcf.yml | 266 +++++++++--------- usegalaxy.org.au/annotation.yml | 118 ++++---- usegalaxy.org.au/assembly.yml | 252 ++++++++--------- usegalaxy.org.au/bacterial_typing.yml | 12 +- usegalaxy.org.au/bb_tools.yml | 6 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 16 +- usegalaxy.org.au/chemicaltoolbox.yml | 46 +-- usegalaxy.org.au/chip_seq.yml | 16 +- usegalaxy.org.au/collection_operations.yml | 10 +- usegalaxy.org.au/convert_formats.yml | 32 +-- usegalaxy.org.au/deeptools.yml | 124 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 10 +- usegalaxy.org.au/emboss.yml | 2 +- usegalaxy.org.au/epigenetics.yml | 6 +- usegalaxy.org.au/fastafastq.yml | 88 +++--- usegalaxy.org.au/fastq_quality_control.yml | 28 +- .../fetch_alignmentssequences.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 24 +- usegalaxy.org.au/genome_editing.yml | 6 +- usegalaxy.org.au/get_data.yml | 40 +-- usegalaxy.org.au/graphdisplay_data.yml | 61 ++-- usegalaxy.org.au/hca_single_cell.yml | 34 +-- usegalaxy.org.au/hicexplorer.yml | 20 +- usegalaxy.org.au/imaging.yml | 54 ++-- usegalaxy.org.au/ivar.yml | 74 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 8 +- usegalaxy.org.au/machine_learning.yml | 42 +-- usegalaxy.org.au/mapping.yml | 50 ++-- usegalaxy.org.au/metabolomics.yml | 22 ++ usegalaxy.org.au/metagenomic_analysis.yml | 135 ++++----- usegalaxy.org.au/mothur.yml | 4 +- usegalaxy.org.au/multiple_alignments.yml | 54 ++-- usegalaxy.org.au/nanopore.yml | 56 ++-- usegalaxy.org.au/none.yml | 58 ++-- usegalaxy.org.au/phylogenetics.yml | 99 +++---- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 12 +- usegalaxy.org.au/proteomics.yml | 216 +++++++------- usegalaxy.org.au/qiime_2.yml | 2 +- usegalaxy.org.au/rad_seq.yml | 70 ++--- usegalaxy.org.au/rna_seq.yml | 160 +++++------ usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 82 +++--- usegalaxy.org.au/send_data.yml | 10 +- usegalaxy.org.au/single_cell.yml | 153 +++++----- usegalaxy.org.au/statistics.yml | 30 +- usegalaxy.org.au/text_manipulation.yml | 32 +-- usegalaxy.org.au/variant_calling.yml | 42 +-- usegalaxy.org.au/vcfbcf.yml | 216 +++++++------- usegalaxy.org.au/viral_tools.yml | 2 +- 100 files changed, 2798 insertions(+), 2665 deletions(-) diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 2dcb35b55..6b1acafe9 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7572,3 +7572,61 @@ Install 1578 10/08/24 22:06:59 waveica True Installed recetox bf32ae95a06f lates Install 1578 10/08/24 22:14:36 xcms_plot_eic True Installed workflow4metabolomics 51015f22fcb7 latest 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1578/install_log.txt Install 1578 10/08/24 22:18:14 xcms_plot_raw True Installed workflow4metabolomics 520448a32548 latest 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1578/install_log.txt Install 1578 10/08/24 22:27:40 xtb_molecular_optimization True Installed recetox 6e1ef071fffc latest 4/4 ChemicalToolBox toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1578/install_log.txt +Update 205 14/08/24 11:43:12 agat False Tests failed bgruening e7449b2c14bf e7449b2c14bf Staging Testing 14/15 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 11:47:29 bakta False Tests failed iuc ba6990f72184 ba6990f72184 Staging Testing 0/6 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 11:53:28 bcftools_mpileup False Tests failed iuc bf533509c5b6 bf533509c5b6 Staging Testing 6/7 VCF/BCF toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 11:57:25 biotransformer False Tests failed recetox e5fcba090b10 e5fcba090b10 Staging Testing 0/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:01:01 cat_bins False Tests failed iuc 0e63d03c8790 0e63d03c8790 Staging Testing 0/4 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:03:13 data_manager_gtdbtk_database_installer False Installed iuc 6ab422fba1a3 6ab422fba1a3 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:04:04 data_manager_metaphlan_database_downloader False Installed iuc d8dc037e3c13 d8dc037e3c13 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:07:27 dorado False Tests failed galaxy-australia 99c9427219d3 99c9427219d3 Staging Testing 0/3 Nanopore toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:09:55 encyclopedia_encyclopedia False Tests failed galaxyp eac99effe86f eac99effe86f Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:12:20 encyclopedia_walnut False Tests failed galaxyp 0d2e93e01e68 0d2e93e01e68 Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:21:34 fastp False Installed iuc d60c3f704da0 d60c3f704da0 12/12 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:25:13 fastqe False Tests failed iuc c1a33f603da2 c1a33f603da2 Staging Testing 0/2 FASTQ Quality Control toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:28:34 funannotate_compare False Tests failed iuc 0418d28136de 0418d28136de Staging Testing 0/3 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:32:14 funannotate_predict False Tests failed iuc 4b96ced19f75 4b96ced19f75 Staging Testing 0/4 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:38:47 matchms_convert False Installed recetox c990df6afc24 c990df6afc24 6/6 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:45:50 matchms_filtering False Installed recetox 00e66c401366 00e66c401366 7/7 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 12:50:24 matchms_fingerprint_similarity False Installed recetox d7b517f2c5fe d7b517f2c5fe 3/3 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:12:35 matchms_formatter False Installed recetox 9e3c83d2afc3 9e3c83d2afc3 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:16:48 matchms_metadata_export False Installed recetox b576ed720711 b576ed720711 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:23:24 matchms_metadata_match False Installed recetox 1d443ed476a1 1d443ed476a1 6/6 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:31:40 matchms_networking False Installed recetox 1d74ae228df3 1d74ae228df3 9/9 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:35:43 matchms_spectral_similarity False Installed recetox 7627b40601f6 7627b40601f6 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:40:16 matchms_split False Installed recetox 500f473df7e4 500f473df7e4 3/3 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 13:46:38 metaphlan False Tests failed iuc 1a037928504c 1a037928504c Staging Testing 1/9 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:00:17 msconvert False Tests failed galaxyp 545054b15d7c 545054b15d7c Staging Testing 0/34 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:24:29 msmetaenhancer False Installed recetox b5467dead5b1 b5467dead5b1 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:27:00 openms_decoydatabase False Tests failed galaxyp 06cca574e337 06cca574e337 Staging Testing 0/4 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:29:36 openms_targetedfileconverter False Tests failed galaxyp 43b9ed22e8ce 43b9ed22e8ce Staging Testing 0/30 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:32:05 openms_xmlvalidator False Tests failed galaxyp ad2ba3a95a02 ad2ba3a95a02 Staging Testing 0/2 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:35:50 pear False Installed iuc 037f0acc7830 037f0acc7830 2/2 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:52:04 picrust2_add_descriptions False Installed iuc 2f47a294ef49 2f47a294ef49 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 14:57:03 picrust2_hsp False Installed iuc 3b133b8d578a 3b133b8d578a 3/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:03:17 picrust2_metagenome_pipeline False Installed iuc 709adbfcf308 709adbfcf308 4/4 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:07:48 picrust2_pathway_pipeline False Installed iuc f53beb324696 f53beb324696 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:27:08 picrust2_pipeline False Installed iuc d6bb2e3febda d6bb2e3febda 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:32:39 picrust2_place_seqs False Installed iuc 73b56418e7f4 73b56418e7f4 3/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:35:58 picrust2_shuffle_predictions False Installed iuc 677f3c8db525 677f3c8db525 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:43:46 plotly_ml_performance_plots False Installed bgruening f234e2e59d76 f234e2e59d76 5/5 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:50:50 ramclustr False Installed recetox da7722f665f4 da7722f665f4 6/6 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 15:54:07 ramclustr_define_experiment False Installed recetox f2c1d0bbb074 f2c1d0bbb074 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:09:26 recetox_aplcms_align_features False Installed recetox 79ad928a0dae 79ad928a0dae 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:12:11 recetox_aplcms_compute_clusters False Installed recetox f3a18e020cdd f3a18e020cdd 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:14:53 recetox_aplcms_compute_template False Installed recetox dfebc82ba1f0 dfebc82ba1f0 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:17:47 recetox_aplcms_correct_time False Installed recetox 9064aecc78a7 9064aecc78a7 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:35:30 recetox_aplcms_generate_feature_table False Installed recetox b3413f335327 b3413f335327 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:38:28 recetox_aplcms_merge_known_table False Installed recetox 17a48d0a80f4 17a48d0a80f4 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:41:11 recetox_aplcms_recover_weaker_signals False Installed recetox d7f5878a98c3 d7f5878a98c3 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:46:17 recetox_aplcms_remove_noise False Installed recetox ffbabefbd2e2 ffbabefbd2e2 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 16:56:16 recetox_xmsannotator_advanced False Installed recetox 6b5dec818827 6b5dec818827 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:00:42 rmassbank False Installed recetox 5a6bb93ec656 5a6bb93ec656 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:25:13 roary False Installed iuc 9b2b122d0415 9b2b122d0415 2/2 Phylogenetics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:36:15 sample_seqs False Tests failed peterjc bdaefd241921 bdaefd241921 Staging Testing 12/16 Filter and Sort toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:39:38 scanpy_cluster_reduce_dimension False Installed iuc 64ff3ef24fae 64ff3ef24fae 0/0 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:46:48 scanpy_filter False Tests failed iuc aa0059118fb9 aa0059118fb9 Staging Testing 5/9 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:49:47 scanpy_inspect False Installed iuc ca086f24422f ca086f24422f 0/0 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:52:46 scanpy_plot False Installed iuc 70fa84e99463 70fa84e99463 0/0 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 17:56:47 uniprot_rest_interface False Tests failed bgruening 95fb5712344f 95fb5712344f Staging Testing 1/4 Get Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt +Update 205 14/08/24 18:02:27 yahs False Tests failed iuc ff4031bfaa22 ff4031bfaa22 Staging Testing 5/7 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_205/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 162349d9e..e1be21996 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -3,17 +3,17 @@ tools: owner: iuc revisions: - 6e9aea89e388 - - c2ef298da409 - 4efdca267d51 - - 3f3e247c053d - 78c75f134c16 + - c2ef298da409 + - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -40,39 +40,39 @@ tools: - name: annotatemyids owner: iuc revisions: - - a79ee60b6926 - - 1aae04680c4b - - cd2480f35935 + - 4f2967b27e67 - 133f36c29579 - 3e1f6f6d557e + - cd2480f35935 - b5d8e5475247 + - fe3ca740a485 + - a79ee60b6926 - 44018dd6b447 + - 1aae04680c4b - f29602ae449e - - fe3ca740a485 - - 4f2967b27e67 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: + - 7be22100e5e1 - dc027fa56d55 - 6519ebe25019 - - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: + - 28433faa6e42 - ca6d970d931c - 09855551d713 - - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -86,8 +86,8 @@ tools: - name: barrnap owner: iuc revisions: - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -100,24 +100,24 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - - 1ac12c0cc7a0 - 8e9e228c54c4 + - 1ac12c0cc7a0 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - 63662ae295d6 - - 9d1fbff733cf - d9c3016f7283 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -141,47 +141,47 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 756376aeb1ae - - 3bbe70fef6df - 14f588312c56 - - 9f2455341fac - - b6b5cd37f2a2 - 582fd74dc2a1 - 9c15ca7e764e + - b6b5cd37f2a2 + - 3bbe70fef6df + - 756376aeb1ae + - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 8e1ace8f77c6 + - 0ffe5be70caf - 1691af4a0d17 - - 30fb23d4c31c + - 73428a792541 - 989f7c061f35 - - 0ffe5be70caf + - 8e1ace8f77c6 + - 30fb23d4c31c - a230ea445788 - - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - e94187d661df - - 57c6718cbfcc - - 30f08d74024f - 5a5ae61da69c - - 494f0bb4a993 + - 57c6718cbfcc - 563a19373357 + - e94187d661df + - 494f0bb4a993 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - d6c7106b7b2e - f31125bb85ea - - 7abc5f6dd595 + - 1bc5a03faf2e - f77d7b685bb3 + - d6c7106b7b2e - 2bba2ff070d9 - - 1bc5a03faf2e + - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort @@ -189,11 +189,11 @@ tools: revisions: - 520e30695ec3 - d77fdcca400e - - 54961e026fe4 + - fed64e676186 - b3cf4684e9c7 - 52af33194019 + - 54961e026fe4 - d3af38b9c7e1 - - fed64e676186 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -205,9 +205,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - - 07d7991bf205 - 79261884facd + - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -220,9 +220,9 @@ tools: owner: iuc revisions: - ef2ad746b589 - - 602de62d995b - - 8b3e3657034e - 43798b4caee0 + - 8b3e3657034e + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -246,16 +246,16 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - 98cafcbd2578 - - 74810db257cc - c55643c3d813 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -273,26 +273,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - 370c210d9541 - - d46d803ca6cc - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - b815ec682418 + - e95d52d295d7 - 624606f7c996 - c8ac28e8ac44 - 033755194fe9 - - e95d52d295d7 - - b815ec682418 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -322,11 +322,11 @@ tools: - name: prokka owner: crs4 revisions: - - eaee459f3d69 - - a17498c603ec - - d643e3b03500 - 8a22554cdde2 + - a17498c603ec - bf68eb663bc3 + - d643e3b03500 + - eaee459f3d69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -358,21 +358,21 @@ tools: - name: snpeff owner: iuc revisions: - - cfcf33df7fc0 - - 5b80f544c67f - 5c7b70713fb5 - - 8f92c2b26e6d - - 9473cd297a76 + - 268d162b9c49 + - cfcf33df7fc0 - 68693743661e - 5a29ab10dba6 - - 268d162b9c49 + - 9473cd297a76 + - 5b80f544c67f + - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - 5fab4f81391d + - 09d6806c609e - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -385,8 +385,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -398,24 +398,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - ac8250086ac3 - - 037a11682176 - - 51dd22484644 - e1a9d6fd258d - - ba6f87115e13 + - 200c378d85f3 - 4839e590cb26 - - d03af1c7002c + - ac8250086ac3 + - 51dd22484644 + - 37213cf56392 + - 037a11682176 - 809dfc93d593 - - 200c378d85f3 - 45083d070fb8 - - 37213cf56392 + - d03af1c7002c + - ba6f87115e13 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 165b05a33..d6fbf11fe 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -3,25 +3,25 @@ tools: owner: iuc revisions: - a929ce596a34 - - 0e93176640ac - 7547fcab5d19 - - 890b794c997d - - 8f1b150a2487 - - fa5259cc561b - - 841084c5fc46 - 553bfe8bd0b5 + - 841084c5fc46 + - 0e93176640ac - 0124fce4654a + - 890b794c997d + - fa5259cc561b + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - 21e491ad532a - - b2860df42e16 - - b9e31c5c01c7 + - 94fe43e75ddc - ddddce450736 + - b2860df42e16 - 067592b6b312 - - 94fe43e75ddc + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -34,47 +34,47 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - faee8629b460 - - 3371c5bdc17a - - 22286dab5aa1 - a7f16f24e9a1 + - 22286dab5aa1 + - 3371c5bdc17a + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 8c2167481e72 - 53dd00a4ab68 + - 8c2167481e72 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - 94170eee0ad8 - - 46ae58b1d792 + - 1e62c28ba91d + - 0d243f458b53 - cf13a1e03e5b - 1440ae06552f - - 2dd755c1c6ff - - 5ecdeca79a0d - - 602fb8e63aa7 - - ea8146ee148f - - 0d243f458b53 - - 4048d82f0c88 - - 41030a6c03b7 - e4bd1e99bacf + - 41030a6c03b7 + - 46ae58b1d792 - f18f0b887c31 - e824f5d958d0 + - 602fb8e63aa7 - bb935709506a - - 1e62c28ba91d + - 4048d82f0c88 + - 5ecdeca79a0d + - 2dd755c1c6ff + - ea8146ee148f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - c5b7390290b1 - 86f150c8019d - 5732f959936a - - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -86,30 +86,30 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 + - 1ce9b1d72ec3 - 3ee0ef312022 - - 291923e6f276 - - cb8dfd28c16f + - 276f5d8712d5 - e27815e82dd4 - - 1ce9b1d72ec3 - 8d4f03b5fe9d + - cb8dfd28c16f + - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - 01210c4e9144 - - 460fad600dce - 3169a38c2656 - b2f674562a18 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 - 06bcf65179fb - 8b330a577046 + - 7348b69e5109 - ba88bc5a6446 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,9 +117,9 @@ tools: owner: bgruening revisions: - 3fba9c77550a - - 690c2caa367e - 3ef480892a9f - 5127a713de83 + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -131,23 +131,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 6505bd37670d - - 3f7be05a1597 - - df25d4fb79b7 - - 41cea2aa2dce - - 045c7c3d8e59 - - 60024a528cbd - - 0ee0c3089254 - - 284a1cb82b61 - - da9d8bf98802 - - 2061fb3b81b4 - 9ef6920c3089 - - 366a11d316a7 - - 5f625c63b8bc - - ec9e21e9c71b - 71740308d412 - 5bec28269d95 + - 3f7be05a1597 + - 60024a528cbd + - 045c7c3d8e59 - f3c89da3af16 + - ec9e21e9c71b + - 6505bd37670d + - 2061fb3b81b4 + - da9d8bf98802 + - 5f625c63b8bc + - 0ee0c3089254 + - 366a11d316a7 + - 41cea2aa2dce + - df25d4fb79b7 + - 284a1cb82b61 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -166,42 +166,42 @@ tools: owner: iuc revisions: - 14ddfc8ffb93 - - 7518ee87b53d - de387b2b2803 + - 7518ee87b53d - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae + - 9d79beb19ac3 - eb7b00ec347d - - f8113c25bc6b - 09c589057ee8 - d7edbc9c3a07 - - 9d79beb19ac3 + - 39edec572bae + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - 29dabd8db6f2 - eadfd71dde37 - 51c2360aa807 - - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 99ecfdafc64f + - 3ca2d2a9068c + - eb7a370f6588 - f338e9942b27 + - 99ecfdafc64f - f369ef5f210b - - fd128c111ab0 - - 2ecf5a570907 - - 3ca2d2a9068c - e731ea24e48d + - 2ecf5a570907 + - fd128c111ab0 - 606b09cc9860 - - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -213,10 +213,10 @@ tools: - name: miniasm owner: iuc revisions: - - b799a615995d - - 8b6d0d85252b - 73a3846701e1 - 8dee0218ac7d + - b799a615995d + - 8b6d0d85252b - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -235,8 +235,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 15200570e926 + - 7c2f5268d01c - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -249,69 +249,69 @@ tools: - name: pretext_map owner: iuc revisions: + - 8fef980d48b5 - dfb8a4497339 - - 2b16ba799da9 - 79b48f02db49 + - bbe19ef04a74 - d256a51a656b + - 2b16ba799da9 - 02831bf9e95f - - bbe19ef04a74 - - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - a315c25dc813 - 76d4cbefff85 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 675488238c96 - 72472698a2df - - 3061c8b029e5 - - ebb0dcdb621a + - 7594365c546b + - 342a1d1fed7b + - 675488238c96 - 6fcbee531de6 - - 875d0f36d66f - 59db8ea8c845 - - 342a1d1fed7b - - 7594365c546b + - ebb0dcdb621a + - 3061c8b029e5 + - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - a199cd7ac344 - - 39bed8de8017 - - aa39b19ca11e - d865b62f501c - cd06929b224b + - 39bed8de8017 + - aa39b19ca11e - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - f11b994b7eb2 - 5c55448d0f33 - - 33b7d8481a76 + - f11b994b7eb2 + - f8564b2d7f63 - 2b2a352488fa + - 33b7d8481a76 - 3edba9afc9bc - - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 28189050e437 + - 5fc94b3a4704 + - 1d06c8b38e77 - 378e55aeeb25 + - e122f9101584 - 53c2bc8c2ae3 - - 5fc94b3a4704 - ef69617ecb42 - - 28189050e437 - - e122f9101584 - - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -324,148 +324,148 @@ tools: owner: iuc revisions: - 865119fcb694 + - 196a599ec43d - ee17a294d3a3 - - f698c7604b3b - - d9f6a00b6db7 - ad80238462c1 - 83ead2be47b2 - - 196a599ec43d + - d9f6a00b6db7 + - f698c7604b3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 24e471d13fe9 + - 5e0825476fb7 - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 - - 1bb12736175c - 7490b213baa9 - - c33a476f4001 - 1fc82fe7ebef - - 604782a8a53a + - 1bb12736175c + - c33a476f4001 + - 051fd2db8a27 - 904bf932cf78 + - 604782a8a53a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 9678993ca5bd - 655fa188c3cc - - 808b3a0a6716 - d6e617c4e338 - - 34305b013402 - - ad8b536d1caa - fee85957cebe + - ad8b536d1caa + - 34305b013402 + - 808b3a0a6716 + - 9678993ca5bd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 21da31ed41a1 + - b8002c3f7141 + - 7e27faaad80e + - 037f9927c4ff - 6b5a5842531e - 8d4b90bf9caf - - 037f9927c4ff - - 7e27faaad80e + - 21da31ed41a1 - e5a3b75a271f - - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 7922870efcca - f1532cb33c75 + - 2a10645aeadd - 9de69775f512 - 86f66ab58e14 - - 2a10645aeadd - - 328aa71f0f3c - 5b26685e5d3b + - 7922870efcca + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 340bc17f49cf - - 8cc856b935ee + - 1708851f8804 - e41dcb0e913b - 85fb02c43042 - 6aad515a5270 - - 1708851f8804 + - 8cc856b935ee tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b3490b036c5a - - b65a43f70b99 - - d159735a6a9f + - 249f6a28c751 - d5fb354f745d - de1260f8a300 + - d159735a6a9f + - b65a43f70b99 - 6357b127161e - - 249f6a28c751 + - b3490b036c5a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d5887ace0dd4 - 9006e5836729 - - d2d1df21dfb9 + - dd7ad84f3943 - 7897763d14ec - - a90db5dbaaf3 - 33368fec3b70 - - dd7ad84f3943 + - d5887ace0dd4 + - a90db5dbaaf3 - b7829778729f + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - 189e837009c9 - - 505a9833ab5d + - 8f631679571f + - ced385aa976d - 6f4c8ad6ea01 + - 505a9833ab5d - ed2425b9fd27 - - ced385aa976d - - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - 9ded6109434a - - 356afed970b4 - - f31d376ce725 - d40ed4eb0c0e + - f31d376ce725 - 19bdfd1e6fe3 - e59bee4565b3 + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - af40e971a8cc + - b23249f81bc4 + - ebd801e712bc - 4688ae3b49b5 - 80a17897564d - - ebd801e712bc - - af40e971a8cc - 6dd935e4984b - - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b5e35a2ca4f3 - - 59bd28f6265d - - cb1e3db43020 - - b64696992ee9 - 937ea677d437 + - cb1e3db43020 + - 59bd28f6265d - bb11fefb23a3 + - b64696992ee9 + - b5e35a2ca4f3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample @@ -473,22 +473,22 @@ tools: revisions: - 6bfab4a4a988 - 05bd7504fdb2 + - cb4768eeca3b + - 6015aa0303f2 - 383bb5ad32e2 - 2628f6790eda - - 6015aa0303f2 - - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - 3e44ef016b45 - 6e26c9afd301 - 8f9f06995f98 + - e92675014ac9 - 0a3a602cd1e3 - - 3e44ef016b45 - - e022dff952df - 9e3e80cc4ad4 - - e92675014ac9 + - e022dff952df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet @@ -496,17 +496,17 @@ tools: revisions: - 8d09f8be269e - 08256557922f - - 920677cd220f - 5da9a0e2fb2d + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 37d88f41c810 + - 4a53b89fa703 - 0e2b4e3f9ca1 - d81360ea69d8 - - 4a53b89fa703 - - 37d88f41c810 - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -514,5 +514,6 @@ tools: owner: iuc revisions: - 39495e107274 + - ff4031bfaa22 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 27e37646f..3fb786aad 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,9 +2,9 @@ tools: - name: integron_finder owner: iuc revisions: + - 4768f7f8e93f - 392f100eebcd - bfd290fe1588 - - 4768f7f8e93f - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,16 +18,16 @@ tools: owner: iuc revisions: - 1f5641a52664 - - ded48b36f3b7 - 31812e7a1315 - 8e8dc9a1e3e5 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 17fcac7ddf54 + - 5c8ff92e38a9 - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 6fb7d4f8b..98225b452 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - d1f62024a08b - - 204a131e47db - a9c9d768b751 + - 159b04e36791 - 0840ba83860c - 1c427e24fb79 - - 159b04e36791 + - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index f79c6c956..bdfdd5b9f 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 64e2edfe7a2c - - 589e7e57fd6d - - 87ee588b3d45 - - a68aa6c1204a - - ce3c7f062223 - a8eabd2838f6 - - b28e0cfa7ba1 - - a1a923cd89e8 + - 87ee588b3d45 + - 07e8b80f278c - dde39ba9c031 + - 64e2edfe7a2c - 0a5c785ac6db + - b28e0cfa7ba1 + - a1a923cd89e8 + - a68aa6c1204a - e19bebe96cd2 - - 07e8b80f278c + - ce3c7f062223 + - 589e7e57fd6d tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 87e71fd98..a9c0ee888 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: + - 62c9df8382c2 - f921014aba5a - - 54f751e413f4 - e8ac2b53f262 - - 62c9df8382c2 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - acf4e47b734c - - 6f386c5dc4fb - cbf3f518b668 + - 5edc472ec434 - 2889433c7ae1 - - 0e3cf9594bb7 - e25d3acf6e68 - - d999e774072a - - 5edc472ec434 - a52d2d93e595 + - acf4e47b734c + - 6f386c5dc4fb + - d999e774072a + - 0e3cf9594bb7 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus @@ -43,8 +43,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index af2ebbcb4..a613685de 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - f4230f116196 - - 27ee142314a9 + - 6ca543ec1bf8 + - 710301bc46fa - da6bd1975a71 - c8cdde00b105 - - 710301bc46fa - - 6ca543ec1bf8 - 095ad4d096d1 + - 27ee142314a9 + - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_rxn_maker @@ -124,74 +124,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - 88076940fa94 - 3b8a9d5ced85 + - 79cfd9ead848 - bfb65cb551d8 + - 88076940fa94 - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - d532b7e5f64b - - b46d4b4d995c - - 55918daa5651 - f5d979cb4b54 - 715cd0e87781 + - b46d4b4d995c + - 55918daa5651 + - d532b7e5f64b - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 97872d87ba80 - 5579659312e6 - d2f955aea23a - - fdf2cc80adb5 - f26afd1b7104 + - fdf2cc80adb5 + - 97872d87ba80 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - - 319a28774da9 - d1d0efda35c0 + - 319a28774da9 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - ed736e6eee39 - - cac1886249a2 - - 4da9ee404eab - 2c349b027a01 + - 4da9ee404eab + - 070e3ecc3fda + - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - f197e34c33a9 - d1f803b5943c - - c0c9a5024177 + - f197e34c33a9 - 73008ef1f487 - - 807aa4c9293d + - 525ca7c8065f - da8753545526 + - 807aa4c9293d + - c0c9a5024177 - 2e219a2d9327 - - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - 27ea4e1a3f95 - - 2c8ed1b52bf7 + - c4fbab8e03c5 - 61094e01eff9 - 7568ae18908a - - c4fbab8e03c5 + - 1809414a9454 + - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -203,11 +203,11 @@ tools: - name: md_converter owner: chemteam revisions: - - ccfbd956a2d3 + - 79e8ab8f1e81 - d7ec25187599 - - 730ef07b90ae - ba83f0923369 - - 79e8ab8f1e81 + - ccfbd956a2d3 + - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -256,9 +256,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - b59c91adeac1 - 1400d1977e7b - e6011617c748 - - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -318,10 +318,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - bf99565cec1f - - d4c67ced6abc - 9b48456a96fe + - d4c67ced6abc - 85fad59f8168 + - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 91218c84e..1303e0c0c 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -3,9 +3,9 @@ tools: owner: bgruening revisions: - 163688bb8f73 - - f907216064f6 - fa56d93f7980 - c97a786e8fb5 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -30,11 +30,11 @@ tools: - name: macs2 owner: iuc revisions: + - 640d3af5d833 - f5d67c722d67 - - 86e2413cf3f8 - 495a4173006f + - 86e2413cf3f8 - 424aefbd7777 - - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -53,9 +53,9 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 4a14714649b4 - 5c2cc3b58c7d + - 74c9214cc8e6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index a416373e0..482c18a72 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -10,16 +10,16 @@ tools: owner: nml revisions: - 830961c48e42 + - 90981f86000f - 25136a2b0cfe - 33151a38533a - - 90981f86000f tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -32,8 +32,8 @@ tools: owner: bgruening revisions: - 2dae863c8f42 - - 0046692724f9 - 6cbe2f30c2d7 + - 0046692724f9 - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index cf3ca151e..42742b3a8 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -14,39 +14,39 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 6ef0b5664c69 - - 5e1240a87bcb - - ab9350a8ab4d - - a3b86937ead6 - - f3a19509108a - - 4a6ee918c13a - - e3cbd2287f63 - 3b6f97e7094c + - e3cbd2287f63 + - 4a6ee918c13a - 0b3c3ad92827 + - ab9350a8ab4d + - f3a19509108a + - 5e1240a87bcb + - a3b86937ead6 - 367b1ed91207 + - 6ef0b5664c69 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 54ccb7e1f49a - - 584008e574b2 - - 33c99804a32f - e177a8ea0bf1 - - 501c21cce614 + - d4d4e9febf5c + - 584008e574b2 + - e525f9ffb9ac - 72ed72122deb - 1b5fc03380d4 - - d4d4e9febf5c - - 091bb5922a82 - bd46669113b9 - - e525f9ffb9ac + - 501c21cce614 + - 33c99804a32f + - 091bb5922a82 + - 54ccb7e1f49a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - 11c3eb512633 - a0d092f27fdf + - 11c3eb512633 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -65,9 +65,9 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 8979c288aefb - 77b41c89d856 - 186b8d913e6c + - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -86,8 +86,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -132,24 +132,24 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 92ac8e086317 - 26c6706bfb07 - 63769c4217a7 - 19e45916daf9 + - 92ac8e086317 - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index f803233ed..703907f33 100644 --- 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deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 - - 167788df3b46 + - fd1275e01605 - 514fa53b5efb - - a60c359ec43c - - fb9cf9c97ec4 + - 167788df3b46 - 9470f29702f8 - - fd1275e01605 + - d9a637e83828 - b73e213add0c + - a60c359ec43c + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - a02cfa31e9cb + - 86febdcc4283 - c34d11ea4ba6 - 5bffaa8354a1 - - a02cfa31e9cb - e479c7ca5570 - - ca0616bb2cdf - - 86febdcc4283 - 2c37ce318bc3 + - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 78f405266706 + - 2d466b530754 + - 004aea905d4d - 1fcb7adc39b8 - - 192ef85c0b0b - 69a8621ca2f0 + - 192ef85c0b0b + - 78f405266706 - 01fb6a7654e6 - - 2d466b530754 - - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 137c4beed34b - db940c262830 + - d580d6acd1df + - d9ce4897dbb2 - 9ecba5e225a6 - 2f9e4843f480 - - 137c4beed34b - 3c9f0c486cca - - d580d6acd1df - 459cfa861f0b - - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - bd7db9e2f2cb - bad3ca889618 - - fbe773640707 - - 2c66e43f1c86 - fd408d755394 + - 2c66e43f1c86 + - bd7db9e2f2cb - 32e451def88c + - f264afa9fa6f + - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 231994413f89 - - 3b9d990a0a0e - - 7fda5607e777 - 9368fbc49c8b - - 56bce3c82278 + - 7fda5607e777 + - 231994413f89 - 7e361d147872 + - 56bce3c82278 - 4e12ea27f788 + - 3b9d990a0a0e tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 - - b1779366c8e9 - d9114ef1c8a5 - - e65d16fb2724 - - 4431f39ede55 - 94ca68515826 + - 4431f39ede55 + - b1779366c8e9 - ce4ce3316f74 + - e65d16fb2724 + - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - b88ebb3672a1 + - d57251071381 - 4ed32329e0ed - - f8fc4e5aff9d - - 23f7c5f1fdaf - 793665fff0f8 - - d57251071381 + - b88ebb3672a1 - 2da482e408b8 + - 23f7c5f1fdaf + - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - e4c7985d4585 - - 010e58e9d822 - a4dfb122e52b + - e4c7985d4585 + - 512155688d98 - 25d830337d31 + - ba6efa77fb79 - a7849312d328 - - 512155688d98 - c60570fa602f - - ba6efa77fb79 + - 010e58e9d822 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - aa200e4f3939 - - 443d9a9d6d11 - 38e3f226248b + - 4d678170d29b - 00d869ea03a1 + - 443d9a9d6d11 - c899e0ccff8c - - 4d678170d29b - 69264da0ce77 + - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - a2d70c4fd406 - - c361b12d207a + - 6662b1a8d326 + - 10301d137111 - d806504e96d9 - aac8444d6681 - - 10301d137111 - - 6662b1a8d326 + - a2d70c4fd406 + - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index 5f8621846..bea5d79d0 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,22 +23,22 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - 02bab5ff7c37 + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 91a1ed0b486f + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - d4bea99366f9 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index e9a6db869..83e65c370 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 + - 832c20329690 - dba489bfcd62 + - ce385837c160 - 63dd26468588 - - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index cb2fa1505..fe563a179 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -9,9 +9,9 @@ tools: owner: iuc revisions: - 62f5fab76dfb - - cf1322aeb137 - d82648ad25a3 - 6da3972210ee + - cf1322aeb137 - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 0e6b99013..af4deedf8 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8c0175e03cee - - c4b82dce8335 + - c5e2e5902201 - 64172f1c1202 - - 48f587c13075 - - 4e5056fefd88 - - 5eb7e84243f2 - 660cffd8d92a - - de6cebe3c043 - - b1c926deaa2d - - 135b80fb1ac2 - - 44e2cc14f75b - 8665bcc8b847 - - 5915ea1ec9b1 - - c5e2e5902201 - - 288f97432497 - c053d4cad713 - e4691e1589d3 - - 093678460093 + - b1c926deaa2d + - 288f97432497 + - c4b82dce8335 + - de6cebe3c043 + - 135b80fb1ac2 + - 4e5056fefd88 + - 44e2cc14f75b - fe74900d6dc7 + - 5915ea1ec9b1 - 49370cb85f0f + - 5eb7e84243f2 + - 48f587c13075 + - 8c0175e03cee + - 093678460093 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -53,8 +53,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -73,16 +73,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - e626b3ff9922 - 8cacfcf96a52 + - e626b3ff9922 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: + - 9457a20156db - 516b97a23d7e - 859422bcb689 - - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -102,8 +102,8 @@ tools: owner: devteam revisions: - ec0b5076173a - - f773e98b26cf - f81d4362b6c1 + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -115,9 +115,9 @@ tools: - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a - 56022eb50bbd - cd0874854f51 + - 9c620a950d3a - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -131,29 +131,30 @@ tools: owner: iuc revisions: - c59d48774d03 + - d60c3f704da0 - 1d8fe9bc4cb0 - - dbf9c561ef29 - 65b93b623c77 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - c59d48774d03 + - d60c3f704da0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -173,22 +174,22 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -201,9 +202,9 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - - 35e38452bb3f - 249c8393f2d4 + - 35e38452bb3f + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -215,9 +216,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 045f0e1043f7 - 74db4cffab1f - 54053ea6c77e - - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -249,10 +250,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - 09070cacefd8 - d5e9e83cd3d8 - 529bccd5e4a1 - 567d5b3c52b1 - - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -265,8 +266,8 @@ tools: owner: devteam revisions: - 8abdedf55101 - - 4bedca26c133 - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -279,9 +280,9 @@ tools: owner: devteam revisions: - bdf1ce174e39 - - cb1e251cac37 - - 736b8f6ee456 - 90858c306551 + - 736b8f6ee456 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -293,9 +294,9 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 07497255281e - 7ce1891db6f5 - 421f0af4ee95 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -307,10 +308,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - f984bb114520 - 02f8a17a4ebd - b29d37ca9e41 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -322,10 +323,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - - 177f0621c266 - 0c2907307ba4 + - 177f0621c266 - e246088b6e34 + - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -337,10 +338,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: + - 73194cdd4f57 + - 547e8d00f11c - 377ac2829eac - 61b4cedc8934 - - 547e8d00f11c - - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -364,21 +365,22 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd + - 037f0acc7830 - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear owner: iuc revisions: - - b4c6f054210a + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort @@ -391,15 +393,15 @@ tools: - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 3da72230c066 - 4b494533146a + - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -417,15 +419,15 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - 71f649c23021 + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -437,10 +439,10 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 - - 8250ea3a1501 - - b557acca0b56 - 24013bf85a6f + - b557acca0b56 + - 8250ea3a1501 + - e654095ab143 - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -459,12 +461,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 9fa7803d1c51 - - 6a675c3aa610 - - 828dba98cdb4 - - 7accf7407811 - 27ac32a22ad2 - f3759eec3018 + - 828dba98cdb4 + - 6a675c3aa610 + - 9fa7803d1c51 + - 7accf7407811 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 5020cdfcf..9b370be6b 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,29 +3,29 @@ tools: owner: devteam revisions: - 64e9a6afdd0c + - 7b4468117008 - ce9cd02d5b88 - e41385662e5e - - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - e7b2202befea - - ff9530579d1f - - 5ec9f6bceaee - - 9da02be9c6cc + - 2c64fded1286 + - f2e8552cf1d0 - 2b0c9d9fc6ca - 3d0c7bdf12f5 - - f2e8552cf1d0 - - 2c64fded1286 + - 9da02be9c6cc + - ff9530579d1f + - 5ec9f6bceaee + - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -39,8 +39,8 @@ tools: owner: devteam revisions: - 18a51655db17 - - b6b54ba71bd8 - ad116ae3f4d9 + - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics @@ -54,23 +54,23 @@ tools: - name: filtlong owner: iuc revisions: + - 8880fb74ef56 - a72af9de6bf5 - 1f296803dfa3 - - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - 9a913cdee30e - 1c2db0054039 - - abfd8a6544d7 - f7985e0479b9 - - 5e33b465d8d5 - - 75c93c70d094 - - 9a913cdee30e - - bf675f34b056 + - abfd8a6544d7 - b2f1f75d49c4 + - bf675f34b056 - 3d93dd18d9f8 + - 75c93c70d094 + - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index 0060ed139..1dc6b6ca8 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,21 +2,22 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs owner: peterjc revisions: + - bdaefd241921 - 7c40a1fbc82e tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id owner: peterjc revisions: - - 141612f8c3e3 - 83a19df00eab - 85ef5f5a0562 + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index aa3266fd0..2b448c6dc 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -24,29 +24,29 @@ tools: - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: - - 45296e47d565 - - b2c25142267e - cf61daf064fe + - b2c25142267e + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -101,8 +101,8 @@ tools: - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -137,15 +137,15 @@ tools: - name: gemini_region owner: iuc revisions: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 3fed957fb..6e2bcd639 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,15 +2,15 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 01f668d72..e81e3a2a8 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,9 +2,9 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee - 983bf725dfc2 - b39347891609 + - c1b437242fee - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,51 +18,52 @@ tools: owner: iuc revisions: - 28587613264f - - 1c58de56d587 - e063168e0a81 + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: + - 4317d3cb6cba + - c441583adae5 - 7068f48d0ef9 + - aad3885b3216 + - f5ea3ce9b9b0 + - 653e89d73fc4 + - e08a7ad4378b + - 5e6237d58b0c - 69ebb7f46e45 + - 1ec814014652 + - 1790dcf3c32d + - e407b9da183a + - 516a54ddf218 + - 83c7d564b128 + - 6ea73833cf67 - 734abc7ac21d - - c441583adae5 - - 6591f049cf7e - - 653e89d73fc4 - ba931a59dd59 - - 516a54ddf218 + - f8054ea1c365 - 9a776b080193 - - f5ea3ce9b9b0 + - 6591f049cf7e - 4df8de2d0e48 - - f8054ea1c365 - - e407b9da183a - - 5e6237d58b0c - - 4317d3cb6cba - - aad3885b3216 - - 83c7d564b128 - - 1ec814014652 - - e08a7ad4378b - - 6ea73833cf67 - - 1790dcf3c32d tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 75b3b3d0adbf - - 9aaa46d45472 - 21a560af5913 + - 9aaa46d45472 - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a + - 95fb5712344f - af5eccf83605 - - 468c71dac78a - 054483e27a35 + - bfdc6a7ffd3a + - 468c71dac78a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 57b67e1f3..a50a3e3e8 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - c4bde687c846 - - df7356989ac1 - 740057a5126d - - 290a11559985 - 4b519282a05b - fd59d783248a - - 7f13dc906cb9 - ae9994cf526f + - df7356989ac1 - a64dc31ab7f2 + - 290a11559985 + - c4bde687c846 + - 7f13dc906cb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,8 +34,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - 7cf5b1d072b5 + - 867ab348287d - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,21 +48,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - '566197475670' - - 3b37b1b1c3a7 - ca7cb0eaad62 + - 53460afd5115 + - 3b37b1b1c3a7 - 374e9062d874 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - - 391a4cc45fea - - d3a9e32672ec - 10515715c940 + - d3a9e32672ec + - da4c086cff5b - 3d059e9c2fba + - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -81,11 +81,11 @@ tools: owner: iuc revisions: - 299307abd804 - - e3a675da7fd0 - d0fc8b746d57 - - 1acf88921176 - 5fe1dc76176e + - 1acf88921176 - 3b12bf9b4b87 + - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -103,22 +103,22 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram owner: devteam revisions: - - 6f134426c2b0 - cdb9e89e2970 + - 6f134426c2b0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -130,17 +130,17 @@ tools: - name: jbrowse owner: iuc revisions: + - 2bb2e07a7a21 + - 112eb40ba6cf - a6e57ff585c0 + - 836d1aa3e89a - 1cfc579079a6 - 4542035c1075 - - 836d1aa3e89a - 667e17248bfe - - 2bb2e07a7a21 - ca2def38369c - 6cd09d7b5f37 - 17359b808b01 - fd5dbf0f732e - - 112eb40ba6cf tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -159,8 +159,8 @@ tools: owner: iuc revisions: - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -172,9 +172,10 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb + - 1c5dcef5ce0f + - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -193,9 +194,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: + - 44c66e8d21e6 - 7c9417381ad5 - 6c571966cfb9 - - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -208,20 +209,20 @@ tools: owner: iuc revisions: - 360df4999907 - - 7dd841a32245 - - a1abfa420d9d - - 2824d77cd8f8 - 4ac4e7083b7e - 14e7c35f3d00 - - 326a3db8d9d1 - 36b848d5f3ec + - 2824d77cd8f8 + - a1abfa420d9d + - 7dd841a32245 + - 326a3db8d9d1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd - 2f557f6abbfb + - 73b8cb5bddcd - 83c573f2e73c - 44608d0193ed tool_panel_section_label: Graph/Display Data diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 573bafe25..c32121c47 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,15 +21,15 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -56,8 +56,8 @@ tools: - name: scanpy_find_markers owner: ebi-gxa revisions: - - d8f5224005bb - 0a8e527d1517 + - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes @@ -70,37 +70,37 @@ tools: - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - 9d76c3d6dff6 - c9da9192eee5 + - 9d76c3d6dff6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - ff6decc0f432 - 94697510d55f + - ff6decc0f432 - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 53ce0e336840 - 70cb0596ffef + - 53ce0e336840 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data @@ -113,29 +113,29 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - d4c9061c8fef - 73d43034c860 + - d4c9061c8fef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 7d5c97823f8b - 1be0fc4d8654 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -155,22 +155,22 @@ tools: - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 79cc06a557b0 - 6a6364b488db + - 79cc06a557b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt owner: ebi-gxa revisions: - - 12f67b0c1a94 - 03921aa8b29c + - 12f67b0c1a94 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_fdg owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -190,22 +190,22 @@ tools: - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - - ea91cfd0444e - 0f98603d0116 + - ea91cfd0444e + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index e61b782db..a6d2778bb 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -4,49 +4,49 @@ tools: revisions: - 921a2da49a0c - 29f66c353bcb - - ed2cca6b5de4 - a4c13ddcc8ee + - ed2cca6b5de4 - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - ec4b948dc6f0 - 5746d61f0a91 + - d404277cc87a - 78fb5e286609 + - ec4b948dc6f0 - 755df866ad0c - - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 4d511437b1e5 - 11fa44ee0603 - - 9e357a8b2ec3 - 977dc15add20 + - 4d511437b1e5 + - 9e357a8b2ec3 - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - - 41dbf4d162a2 - 0ba4f56a3613 - - c3e5e2cf12b7 + - 41dbf4d162a2 - 77919cc3618e + - c3e5e2cf12b7 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 12d51d7be66f - - b63363075c2e - - 7babd8a46fe0 - - 5308ca68ef3d - 9939786dd9c9 + - 5308ca68ef3d + - 7babd8a46fe0 + - b63363075c2e + - 12d51d7be66f tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 7f1017eb8..9d176b6cc 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,55 +2,55 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 81f0cbca04a7 - 0c777d708acc - - 699a5e9146b3 - - 8bccb36e055a - 7db4fc31dbee + - 81f0cbca04a7 + - 8bccb36e055a - 3df9f0a4bf34 + - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - - 2436a8807ad1 - 5bc8cdc17fd0 - 0a53256b48c6 + - 2436a8807ad1 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: + - 6ad1d3cfdea1 - e576b73a2e2f - 9d47aabda459 - - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - b1c2c210813c - - 70316d792fc9 - 77f7159d775a + - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - d51310ab328a + - dba87c4b32d3 - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - b07f4839ca77 - 85edbb7a436b - - 10eed33aa9b2 - - f3360fbeda64 - fcadded98e61 + - f3360fbeda64 + - 10eed33aa9b2 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -71,9 +71,9 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - - e917a2424690 - eb6c08714244 + - e917a2424690 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -86,9 +86,9 @@ tools: - name: cp_common owner: bgruening revisions: + - 6070780813d9 - e7273daa5ae2 - 670975e92458 - - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image @@ -103,8 +103,8 @@ tools: owner: bgruening revisions: - 2484086dee41 - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -118,64 +118,64 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - - f8fa0f6718a3 - d0178bdcd00e + - f8fa0f6718a3 + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - - 3245681b2f6d - ad271f78a87a + - 3245681b2f6d + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: + - b6eec6087271 - 993faa34333b - 87d4d92d7487 - - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - 6100a22bf4f2 - ff1a86a87364 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - - 667a513e67e4 - b178453ea8d1 + - 667a513e67e4 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - ac5bea85a391 - - 2564f461de62 - a1a961c46d4b + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - a32c3f810ade - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -183,15 +183,15 @@ tools: owner: bgruening revisions: - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 980aed9e8fd5 - 407925835dd9 + - 980aed9e8fd5 - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 27edbb90ab2b - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -263,7 +263,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index da0651e1c..121e37813 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: + - e4ee04da1c19 + - 1069f6db0a0e + - 40737febe339 - 78bbd17d0703 + - a38934e303b9 - 3e4f434a69c6 - 3a72fede57ce - - 40737febe339 - - e4ee04da1c19 - e319b5b65879 - - a38934e303b9 - - d6e72da3ec35 - f362150bef41 - - 1069f6db0a0e + - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 618297d23022 - - 72ddd32392cd - - f91cfb73d369 - - 2b95d5c04908 - - c88553ec696e - 7fe36019c073 + - f91cfb73d369 - fcbeda41d0ac - - 9537184d421f - - 0135f1d487a0 + - 2b95d5c04908 - 8f8df367470d + - 618297d23022 + - 0135f1d487a0 + - 72ddd32392cd + - 9537184d421f + - c88553ec696e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - 2cf4a1cafc16 - fafb3d685fa9 - d7e79eb3bcb3 - ad0dc9f4c9e2 - - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee2beb764a7b - - bd2a7d1316b9 - - 5dc33613c288 - 43aac8d29685 - - 8d36959b000d - - a1c2aecd7a0d - - 6a1515bb0687 + - 5dc33613c288 - ee29337f905c - - 7f1cfa4c0e32 - - 8c05afb547fa - - 3d18f8c3c0f6 - 9eaadf03e0df + - ee2beb764a7b + - 7f1cfa4c0e32 - 28a6f1908fcc + - 8d36959b000d + - 3d18f8c3c0f6 + - a1c2aecd7a0d + - bd2a7d1316b9 + - 8c05afb547fa - 94df24c6bc00 + - 6a1515bb0687 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - db536ad45f28 + - c092052ed673 - bcaa0d571ce2 - - 5d6ed46cc101 + - e3bb03cf207a + - 8858fa037a15 + - 5671e1d3d5ee - cb903c9dc33d + - 86a20ae274fc + - 5d6ed46cc101 - a250929be21b - - c092052ed673 + - 9f978da6528a - 364f4ffec275 - d37ede8589b2 - - 86a20ae274fc - - 5671e1d3d5ee - - db536ad45f28 - - e3bb03cf207a - - 8858fa037a15 - - 9f978da6528a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 3b6a16d82c1b - - f95f403841ad - - 230b05597996 - - abbc8041e8ec - - 38b91a3190cd - 49236b03e4fd - 194e3ceee923 - - 584beffa972b - - 12d66d0d05ac + - e1a015876aa9 + - abbc8041e8ec + - f95f403841ad + - 230b05597996 - c5c9f02b6167 - ed28dd32141c - - e1a015876aa9 + - 584beffa972b + - 12d66d0d05ac + - 38b91a3190cd + - 3b6a16d82c1b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index 597912d87..da49c626b 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - b8a457820315 - - 0f1724dd59d2 - f198773344e4 + - 0f1724dd59d2 - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu @@ -14,7 +14,7 @@ tools: - ba0c40780ecf - 22c2a1ac7ae3 - a513e3fbb4c5 - - 374cb875d38a - ac092723240d + - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index 71b700cd9..04e9a106c 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,9 +2,9 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 522137aaa9c4 - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config @@ -18,20 +18,20 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: + - b6ef6d0cb6b7 - 818f9b69d8a0 - - f1b9a42d6809 - - e1317b5502fa - 2af1346e68c9 - - b6ef6d0cb6b7 + - e1317b5502fa + - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 8334dc98c48e + - 1588f9076e32 - 947c2eacccb8 - 05143043ca13 - - 1588f9076e32 + - 8334dc98c48e - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,62 +39,62 @@ tools: owner: bgruening revisions: - 9991c4ddde14 - - 29e4122c90de - - 1552b8cb4a94 - - 83228baae3c5 - 25b46af53232 + - 83228baae3c5 + - 1552b8cb4a94 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - 53616c8b0865 - - 841a6cc5fc58 - - f3dfa4bdf87e - - 1a53edc4b438 - 060ca94ac049 + - 1a53edc4b438 + - f3dfa4bdf87e + - 841a6cc5fc58 - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 - - 927586a18553 - - 91c4e3331208 - d4808d5b83da - - 40f4447733b2 + - dc4b5fd604a6 - 2fc89dcd41c8 + - 40f4447733b2 + - 91c4e3331208 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: + - 7626ea9c2e1b - 301e07345c93 + - 25ab6b4e376e - 36e8d6d5d01b - - c6ae57f774c6 - - 7626ea9c2e1b - e5a5ad882f1f - - 25ab6b4e376e + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - - 02d2be90dedb + - f9639b488779 - 4ed102b922cb - 80852884053f - - f9639b488779 - b7c3e9a3b954 + - 02d2be90dedb + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - - ec69cbe34b73 - 14180f9c831e + - ec69cbe34b73 - 61634a87efc7 + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index a4b05af34..d5b253805 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - cd659e8cc5fa - - 749c918495f7 - - 0d4acadabb04 - - 017aba02828d + - 17062a0decb7 - d5ceb9f3c25b - a6d65b0c67af - - 17062a0decb7 - f6877ad76b00 - - 3ba8d4563129 + - 017aba02828d + - 749c918495f7 - 03e9b2fbc005 + - 3ba8d4563129 + - cd659e8cc5fa - 937aa69e715f + - 0d4acadabb04 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,15 +24,15 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 3fe632431b68 - 2477830927ec + - 3fe632431b68 - 53646aaaafef - dfd8b7f78c37 - e188dc7a68e6 @@ -49,44 +49,44 @@ tools: owner: devteam revisions: - 37b497aa133f - - e7f19d6a9af8 - 60afcc2c1d05 - - 3e1ea2facca6 - 2ff111fac1d7 + - e7f19d6a9af8 + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 09b53c1d4ab1 + - 8c6cd2650d1f - 53c0b7a1a0c3 - - 037c6e54df11 - b3eab4b67562 - - f54f5baedfdd - c0c2d0941de8 + - 6b1e195506a3 + - f54f5baedfdd - 5cc34c3f440d - 3f4d6399997b - - 8c6cd2650d1f - - 11a0d50a54e6 + - 037c6e54df11 - be1d967337e4 - - 6b1e195506a3 + - 11a0d50a54e6 - 77b2770508f6 - - 09b53c1d4ab1 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 9ee34ba73ebf - - 79b885ce78d7 - - b8f5f6e87f5c - - 00fbfac99d39 + - e403d27e8f24 - 1cd2511a396e + - 13022c3d3076 - ec9cbd6b9a49 - - e403d27e8f24 + - 9ee34ba73ebf + - 42ce70172b72 + - b8f5f6e87f5c - 178bdbdb6d24 - - 13022c3d3076 + - 00fbfac99d39 - 5ef7ec16b04f - - 42ce70172b72 + - 79b885ce78d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index a1d3deed5..449c15011 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -92,6 +92,7 @@ tools: - name: matchms_convert owner: recetox revisions: + - c990df6afc24 - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -99,17 +100,20 @@ tools: owner: recetox revisions: - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - 84af792d3a78 + - d7b517f2c5fe tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: + - 9e3c83d2afc3 - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,12 +121,14 @@ tools: owner: recetox revisions: - f04610d25411 + - b576ed720711 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - 03bc9b7f40f6 + - 1d443ed476a1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -135,6 +141,7 @@ tools: owner: recetox revisions: - 8147d93d372d + - 1d74ae228df3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -158,6 +165,7 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: + - 7627b40601f6 - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -165,6 +173,7 @@ tools: owner: recetox revisions: - 0cf68b536cd1 + - 500f473df7e4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -183,6 +192,7 @@ tools: owner: recetox revisions: - 90745ecc5e9f + - b5467dead5b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -230,18 +240,21 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: + - f2c1d0bbb074 - 5f2b58dadb39 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: + - da7722f665f4 - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: + - 79ad928a0dae - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -249,29 +262,34 @@ tools: owner: recetox revisions: - 149b9cc7499b + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - 481d769e2f7a + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - 02c772a49998 + - 9064aecc78a7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - e7305ba0dd38 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - 17a48d0a80f4 - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -279,12 +297,14 @@ tools: owner: recetox revisions: - 99d118321d5f + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - d90187b0f247 + - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -296,6 +316,7 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: + - 6b5dec818827 - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -315,6 +336,7 @@ tools: owner: recetox revisions: - 0b28816c1c2c + - 5a6bb93ec656 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 6c4602284..052026ad5 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,8 +8,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -40,10 +40,10 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 76d3d2b10738 - 65db807336bc - - 5b5a7af9fbb4 - 7c2100246a2f - - 76d3d2b10738 + - 5b5a7af9fbb4 - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,10 +51,10 @@ tools: owner: iuc revisions: - 1c35dadbe76f - - 00f5005840fa - 84fd33a60b35 - - 96336c6a2bb7 - 18a502a9d287 + - 96336c6a2bb7 + - 00f5005840fa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim @@ -62,111 +62,111 @@ tools: revisions: - f732237754fc - a9f4a217dcd6 - - addaf9d22850 - e8fba04706d3 - 34e55239e68b + - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 8c202e741d68 - 0776d824d896 - - 5fe3edf19b9c - 04c15826a0b8 + - 5fe3edf19b9c + - 8c202e741d68 - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - 8470de786d47 - - 43c99742158b - 75c8945b0da2 + - 1c9b3bcd4261 - e96bbb9e24ea + - 43c99742158b + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 306a40d4bb8f + - 1d75bd0595e2 - 5c865a382933 - - 84743da21318 - 35176674168c - - 1d75bd0595e2 - - 306a40d4bb8f + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - 32c9ea835770 + - 555ccac8a4c5 - 8daf4564ccda - - ac72310b038a - 78faebd0879c - - 555ccac8a4c5 + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - f947b4bb5107 - 7b8cb2b02978 - cae017b76acb - a58e4a43f49c + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 1bc3657cd694 - 073608a50ac3 - 04144473e59e - - 7f3b59dee073 + - 1bc3657cd694 - 7136e9ab70db + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - a7817705348e - - 9058d8943303 - 0a1224c4b781 + - a7817705348e - d943081510da - 19299bb1c6af + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: + - dbf1798c0dcc + - a68b985913ab - c4db8c4de66f - f8f56dd6449f - 65d52c693b8e - - a68b985913ab - - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 213df31ba341 - 15dbb444df71 + - 213df31ba341 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - 6d364c65c946 - 654548ae1357 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -186,9 +186,9 @@ tools: - name: humann2_renorm_table owner: iuc revisions: + - b084117133af - c6676a890f50 - d77397f09da1 - - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -232,29 +232,29 @@ tools: - name: humann_regroup_table owner: iuc revisions: + - c409a495841f - 79706f10d680 - e88b731dad59 - 31c6d107e7a5 - - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - d24841f5c3d2 - - 094ad9c068af + - 172920f67a84 - 71ea608ddfa3 + - 094ad9c068af + - d24841f5c3d2 - 714d5a28cc5c - - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 12fb63b5f63f - - a4d7148ccee4 - 4137b492233e + - 12fb63b5f63f - a293a742194f + - a4d7148ccee4 - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,12 +267,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - e2c71b852aba - - 97f7bb0851e7 + - 6fcb8ac37a3e + - cf87759761eb - 75bedfb2078b - 64bc7acc22a9 - - cf87759761eb + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -291,10 +291,10 @@ tools: owner: iuc revisions: - 080ea153677c - - c82508e76ad1 - - 2d35528d2141 - 5e5a999ffaa9 - 4033827c76b8 + - 2d35528d2141 + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann @@ -302,8 +302,8 @@ tools: revisions: - fc6c328c292f - 2cd76b089570 - - 95bf7479d53c - 6b7622dda516 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -370,10 +370,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe - 4a9da2b6c2e3 - - cdee7158adf3 + - 20e2f64aa1fe - 328c607150ff + - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -406,8 +406,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - bfae8da6082c - 27d65c78863c + - bfae8da6082c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -438,8 +438,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 4960abe31b4d - 073c867c5244 + - 4960abe31b4d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -451,8 +451,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -488,22 +488,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 327d9f4cc95f - - 2cff76cf35c6 - - 4fd3b5d8706b - - 05ad7d35ce92 - - 27250f92a01a - - e073891b2afc - 0270541aaf46 - 7f5d7b0e9884 + - e073891b2afc + - 27250f92a01a + - 05ad7d35ce92 + - 2cff76cf35c6 + - 327d9f4cc95f + - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - 76bc4efa1aeb - eb50e7eca3dc - 708abf08a626 - - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -569,29 +569,29 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - a92a632c4d9b - - 6dee4abadccb - 289b3807e80c - - fd69c607b43f + - ff8f55893e7d + - a92a632c4d9b - 1a6cdf55390f + - a16313517e55 - b89b0765695d + - 6dee4abadccb - 2131d7dca455 - - a16313517e55 - - ff8f55893e7d + - fd69c607b43f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -610,11 +610,13 @@ tools: owner: iuc revisions: - 6034c3f3ecf0 + - 2f47a294ef49 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: + - 3b133b8d578a - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -622,23 +624,27 @@ tools: owner: iuc revisions: - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: + - f53beb324696 - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: + - d6bb2e3febda - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: + - 73b56418e7f4 - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -646,6 +652,7 @@ tools: owner: iuc revisions: - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -719,13 +726,13 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - aeaa20b96ef2 + - 2fd4d4c9c5c2 - 4d83eccf5f81 + - 3b22de20bd4b - be818ae858e4 - - 4b9a8031ab74 - 141afacabcfa - - 3b22de20bd4b + - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -755,8 +762,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - 9495df9dd6ef + - 576963db5f1b - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 8869ba2d6..d28bbc559 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 7238968f58f7 - ab12df91b47f + - 7238968f58f7 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index ff785ff25..52f8f72f2 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - cd07731e4434 - - bdfbaf0c10aa - - 48c13389050d - - 2263989660f5 - - 9baa871cb1d1 - - 6ae5a7b5a0a2 - 9422c5a87ee2 + - 8b67dd48fec1 - 9eeb13a92d79 + - 94b8c6013083 + - bdfbaf0c10aa + - 098506c54016 + - 6ae5a7b5a0a2 - a74dbfee5a86 - - 8b67dd48fec1 + - 9baa871cb1d1 + - 48c13389050d + - cd07731e4434 - 80f03df2e2ce - - 098506c54016 - - 94b8c6013083 + - 2263989660f5 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c18157c68134 - - 3ff17bad4006 + - d7ce0ec78e51 + - fc2e49f91e52 + - 5abf2c2249aa + - f0af8936ed41 - '764845535798' - - 2e093badc689 + - 3ff17bad4006 + - 4a60927aaca5 + - c44f824c051a - be78f13134e2 + - aaa0d6a8b808 + - f14193ec1f50 + - 2e093badc689 - bc3831dd65c1 - - c44f824c051a - - 4a60927aaca5 + - c18157c68134 - d390fe1567dc - - fc2e49f91e52 - - f0af8936ed41 - - d7ce0ec78e51 - - f14193ec1f50 - - aaa0d6a8b808 - - 5abf2c2249aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,8 +46,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -66,21 +66,21 @@ tools: - name: mafft owner: rnateam revisions: - - f1a5908ea2cb - - c5908940967d - - f0d493f8f84f - - 15974dd17515 - a65296ffb4a0 + - f1a5908ea2cb - bf28a8cff401 + - 15974dd17515 - 6f28e90db932 + - c5908940967d + - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - b3acbb3a6af0 - - e8fdceffea4c - fbca557a4847 + - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -95,31 +95,31 @@ tools: owner: iuc revisions: - 57f042937ba7 - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: + - ebe3b0f84de9 - 4fc0cb2ac8ae - fb43e8887350 - - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - e18267f90096 - 636b049e6141 + - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - cf3c9489c088 - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index 67bb4dd70..8f3537f6a 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -3,8 +3,8 @@ tools: owner: galaxy-australia revisions: - 18a8d140ec6f - - 28928576e1ea - 7c47b3c9e493 + - 28928576e1ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado @@ -23,12 +23,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - - 72b5e9dda577 - a7228a7ea146 - - cb34f00cc10f - - 0e9e7fcdd543 - 79e9a869f40e + - 0e9e7fcdd543 + - fc8804320156 + - cb34f00cc10f + - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -49,22 +49,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - ec699520444c - - 0f5f4a208660 - - 43815fa60f3a - - cc36773a3681 - 19f3b583a9b3 - eb746fa6f514 - - 222669c4afb6 + - cc36773a3681 + - 43815fa60f3a - 2bf63b38ee9b + - edf6d4003fad + - 222669c4afb6 + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -76,43 +76,43 @@ tools: - name: nanoplot owner: iuc revisions: + - 7b379e98b9a9 + - a3c4fe6f49ab - a02b8b3f5a0c - - 0f1c34698076 - - edbb6c5028f5 - 645159bcee2d - - a3c4fe6f49ab - - 7b379e98b9a9 + - edbb6c5028f5 + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - - 3b6f94fc7e1d - 85a394edc247 + - 3b6f94fc7e1d + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - be95355fef8d - - a8d4be409446 - 90a922f32523 + - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - - 4857d5bcce52 - 449e9aeded2d + - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - bec636361cfd + - a3afc5f0a96c - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -127,8 +127,8 @@ tools: - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -140,8 +140,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -153,8 +153,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 338d15b8d6fb + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -166,8 +166,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -204,8 +204,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 977bb12c3..957b92917 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -28,8 +28,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 58341ad4fb42 - 96d2000977ab + - 58341ad4fb42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -59,18 +59,18 @@ tools: - name: data_manager_bakta owner: iuc revisions: + - 97b1b5ad1cda - d74850cf4e42 - - baceff842902 - - 3e73c97f025d - adfd6bf710bd - - 97b1b5ad1cda + - 3e73c97f025d + - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 9dd107db92c2 - 83da94c0e4a6 + - 9dd107db92c2 - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -83,18 +83,18 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - e4b4837f06f5 - - 1e34d2e3d285 - ed1518ce2237 - edacc4bcd3cb + - 2f27f3b86827 + - 1e34d2e3d285 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -113,16 +113,16 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 48a42ca61006 - 5711fc06a63e - 38ccd4589990 - - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -135,8 +135,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -155,23 +155,23 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - - 5bcf0e24f42c - b4b2b284230a + - 27a6a256cd23 - 172815da3d41 + - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - 2814c058a087 + - 6ab422fba1a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder @@ -190,9 +190,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - fea85c467896 - 19bbd19b74b3 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -205,8 +205,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -224,11 +224,11 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 9c43baa60906 + - 4ba60cb14cb0 - d8dc037e3c13 - 5fe20c915fa6 - - 4ba60cb14cb0 - 0cb27ea69dc1 - - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -241,18 +241,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 9d09724f2bf1 - aec831b54a5b - 0db22932bc39 - - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - 6e24e79d3d69 - - ed7a967cb11b - 29c738066906 + - ed7a967cb11b + - 6e24e79d3d69 + - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -265,15 +265,15 @@ tools: owner: devteam revisions: - ad90c2da4f38 - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -286,16 +286,16 @@ tools: owner: iuc revisions: - d63c1442407f - - c520a52b5174 - 64deddb6a8ec + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 625fd9476402 - 9946bc39c834 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1045,8 +1045,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbcavity @@ -1059,9 +1059,9 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - c362398df83b - - a22969b08177 - e4b7d1507a75 + - a22969b08177 + - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1075,9 +1075,9 @@ tools: revisions: - ba7b0f11e470 - 58a870ef434c - - 9a22227bb6d0 - - ab5b7f6b7198 - f77f7a7f3b83 + - ab5b7f6b7198 + - 9a22227bb6d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 9b8652fe4..189814c0b 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,22 +39,22 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - cce7b18495e4 - - 3f59ebfbfe3d - - 8834daeb9892 - - 3b8b5bde0bd9 - - b89cac5156ec - - d033ffc1c161 - - 107d3ba7024a - a6619171428e - - 5a7c56a5cc08 + - 3f59ebfbfe3d - 81e66674859e - - f04a1264e2a2 - - c78f3d7dd1db - f73435dc282b - 26de3a7b1cb9 + - 5a7c56a5cc08 + - c78f3d7dd1db + - b89cac5156ec + - cce7b18495e4 - 6a457678efcb - '841557158611' + - 8834daeb9892 + - 3b8b5bde0bd9 + - d033ffc1c161 + - 107d3ba7024a + - f04a1264e2a2 - d7c7ef3353fe tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,41 +62,41 @@ tools: owner: iuc revisions: - aa8cc71438cf - - 5fcd1ece3a6e - - e75442c7f4da + - 6a726db04d4b + - df47d4845b62 - 4755f52427c4 - - 02b8758214b0 + - 5fcd1ece3a6e + - 659517798cc4 - 5b777002c2de - - 6223845127ea + - b0af57c1a968 - 88c4aa435ded + - 6223845127ea + - e75442c7f4da + - 02b8758214b0 + - 7a2092844346 - 6283babe736e - 3b96e92e8ec3 - a185b079b095 - - 659517798cc4 - - 6a726db04d4b - - df47d4845b62 - - 7a2092844346 - - b0af57c1a968 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 524d31add34a - - f97743d52b87 - - b8476e82ac20 - d1c340a5664b - - 111bd54f6bc4 - - 24d024316465 - 70acec670c30 + - f97743d52b87 + - 524d31add34a + - 24d024316465 + - 111bd54f6bc4 + - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - feb40665d7cd - - 4f6349228462 - 9e10ba792be2 + - 4f6349228462 - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,26 +109,26 @@ tools: - name: pangolin owner: iuc revisions: - - 5f8727ff21e7 - - 83a69484cb87 - - 03ed9524dcd1 - - 9d61d3fa046c + - 81804a978fc0 + - 14ae456b8cc5 + - 2f1019071464 + - 8ad84c5753ea - 42a174224817 - b6abccb1f25b - - 437e28791761 - - abf6dbe8c9d7 - - 8ad84c5753ea + - 83a69484cb87 + - 03ed9524dcd1 + - ca337cce3888 - ca0d8cf80567 - - a2099fb98cdb - 7bb8726be37c - - 14ae456b8cc5 - - 2fa9d4f1b48f - - 2f1019071464 - - ca337cce3888 - - 81804a978fc0 + - 9d61d3fa046c + - abf6dbe8c9d7 - 3a43c3982401 - 36912871ccdc + - 2fa9d4f1b48f + - 5f8727ff21e7 + - 437e28791761 - b7e297c2ede6 + - a2099fb98cdb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -147,22 +147,23 @@ tools: - name: raxml owner: iuc revisions: - - b1e68bbe4cef - - 73a469f7dc96 - ea30d3089354 + - 73a469f7dc96 - 29ff6a849eac - a4b71be30c3c + - b1e68bbe4cef - ba29b5e2a4be tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 - - f1ccc8a6eb05 - dbe2b2204555 - - 15ac71df11a0 - e88a7de55d6e + - 91887494eb97 + - f1ccc8a6eb05 - 809e42326fc2 + - 9b2b122d0415 + - 15ac71df11a0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 9ee7b956c..d90a172b3 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -3,13 +3,13 @@ tools: owner: devteam revisions: - 7d34178f2812 - - a1f0b3f4b781 - f6ced08779c4 - - b502c227b5e6 + - 3f254c5ced1d + - a1f0b3f4b781 - fc288950c3b7 - f9242e01365a - - 3f254c5ced1d - 1aac2a13842a - 881d7645d1bf + - b502c227b5e6 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 86fd0b27c..713851440 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - ca90d17ff51b - - 6ab1a261520a + - e4a053d67e24 + - 5b85006245f3 - d00e15139065 + - eb085b3dbaf8 + - ca90d17ff51b - 2f7702fd0a4c - - a58f7eb0df2c - c0e71cb2bd1b - - 3bd420ec162d - - eb085b3dbaf8 - - e4a053d67e24 - - 5b85006245f3 - 7fbec959cf2b + - 3bd420ec162d + - 6ab1a261520a + - a58f7eb0df2c tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index 35872adbe..c1b6f7922 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,33 +2,33 @@ tools: - name: cardinal_classification owner: galaxyp revisions: + - 4c177985028a - b574b84afc4d - - 0a18ac48ac53 - - b18329a8ac14 - 277dc652246e - - f28ad96b76dc - - 4c177985028a + - b18329a8ac14 - ece627528a78 + - f28ad96b76dc + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - e988563cc6e5 + - b41107d8fe89 - bf06d196e23d - a9a28e46d54a - - e215f71d7983 - - b41107d8fe89 - 525f201b86c1 - - e988563cc6e5 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - bb6397b94018 + - 4fbffddde8cd - 8da3511c9467 - 56da27be956a - - 4fbffddde8cd - - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering @@ -37,59 +37,59 @@ tools: - f23d67e28cc8 - b8c79e70516d - 528fb09022be - - 890845926d4b - a8157342d9a3 + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 80600735685d - - a69865da6f80 + - 59e85306eae5 - a95a82eb4d50 - 25b83cbd596a - - 59e85306eae5 + - a69865da6f80 - ae304a72db7b + - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d - - e0669b1854b1 - - f1897eb07081 - 83aac7741200 - 611d80c0e29d + - f1897eb07081 + - e0669b1854b1 + - 798da6bdff3d - ed9ed1e6cca2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf + - d426a9107a6c - 5a35e3a8d013 - 74b61bf5bc4b - - d426a9107a6c + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - df2187f9013b - cc430977c8ff - 82f6c2f4332d - 91f0f5922011 - - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 10566783d718 + - d2483487e077 + - c5aa9fca18c6 - 1693b2126f30 - ba92b59cd529 + - 10566783d718 - 043f9c91f686 - - d2483487e077 - - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -108,9 +108,9 @@ tools: owner: galaxyp revisions: - bf0728e000cd - - ae4dc0c041f9 - - 9fa3dbf06f17 - ff8c9e0e8a7b + - 9fa3dbf06f17 + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,23 +129,23 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - 0fa397f4f40b - 1c5cbf8f79ce + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -157,16 +157,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - - e66f552a3c47 - d286ff4600dd + - e66f552a3c47 + - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -181,68 +181,68 @@ tools: revisions: - 97a7f34fcb6a - 1f39c833f65f - - f522c08e900c - 37d669de2828 - - 7f432d87c82c - - 4d17fcdeb8ff - - e42225f8a659 - 837224ad1694 - - 2133b0be850a - 9c52362ae7bb + - e42225f8a659 + - 4d17fcdeb8ff + - 7f432d87c82c + - f522c08e900c + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - - e63db1aa82ee - - 0ed07016d668 - 85b8866f06d7 + - 0ed07016d668 + - e63db1aa82ee + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 - 990b4560ead7 - 352b37c66d97 - 767c1d761aaf + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 4f359549383c - 35cc7ca0bdc7 - deaf035bbe9f - - 4f359549383c - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: + - c7745841de24 - c1343e3389ca - 06f6826d380c - e79958768a2c - - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - da986f83631b - - b9d453dca8d3 - d2eac53666f0 + - b9d453dca8d3 - d46d64e7964d + - da986f83631b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - - 1199751329b0 - 8bd7734309f6 - 9bf325045235 + - 1199751329b0 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -261,26 +261,26 @@ tools: - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - 28434abe6c5c - de7593c29499 - 8212e342e482 + - 593839e1f2c3 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - - 4e77b8f12cd3 - - 8960fb791701 - f4be248c3d47 + - 8960fb791701 + - 4e77b8f12cd3 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -293,18 +293,18 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - c9eff69a7c62 - f7fef900f5b2 - - 9cdf15d3cfc8 - 6ccbf9a2072c + - c9eff69a7c62 - 518b1730cf2a + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 9876bda3ec53 - 5e948629bc73 + - 9876bda3ec53 - ca88bd28f116 - dff6c756eee5 tool_panel_section_label: Proteomics @@ -312,9 +312,9 @@ tools: - name: openms_fidoadapter owner: galaxyp revisions: - - 658494a2cb00 - 890025d6e426 - 1595601708ec + - 658494a2cb00 - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -322,27 +322,27 @@ tools: owner: galaxyp revisions: - 6634cad7d797 - - 9b7977080f6d - 2a93a25f0599 - 5ad0b5bf1deb + - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - d6878d27f051 - fe4e4587d265 - 05d5e1ddc985 - 0bb5056cb775 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: + - 5ad830edc021 + - 4af67edd5aef - 52ba9695e752 - febd569ad26f - - 4af67edd5aef - - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger @@ -357,28 +357,28 @@ tools: - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - 0efbc235f314 - 9e26f5c770f8 - d3546bb9fd8e - d413dc49d650 - - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - - c28f13cab67a - 3720e349ba2a - ca1740533b59 + - c28f13cab67a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe + - a5d785af0ad8 - ca799a7246e7 + - c427a8628cbe - 382cde407f81 - - a5d785af0ad8 - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -386,27 +386,27 @@ tools: owner: galaxyp revisions: - adca857b4884 + - b5d0905419da - 8ddb7bab1138 - 39caaa778d2e - - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 1c5f31b8d632 + - 18f93351f8b6 - 34e7afee141d - - f817513840a9 - 8d4db262964c - - 18f93351f8b6 + - 1c5f31b8d632 + - f817513840a9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - 986e03d3201e - 111c3a00136d + - c69f69d7867a - 5d9f175dff81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -414,25 +414,25 @@ tools: owner: galaxyp revisions: - 0e52c85f3b15 + - 4204882495f2 - 476b5e296979 - be74a8cd7d66 - - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - 9866e1170611 - e133b5c8878f + - 9866e1170611 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - c18d8efa4474 - - f5ec766d80cf - a407b6790342 + - f5ec766d80cf + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -446,8 +446,8 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - 8098330f6d91 - 2735db4dd8d9 + - 8098330f6d91 - bf32e0bcf554 - ee860980edc6 tool_panel_section_label: Proteomics @@ -455,33 +455,33 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - - 0ced5bc9f4dd - 08488066d588 + - 0ced5bc9f4dd + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: + - 2a9ff56cb279 - de7a553552a6 - 8c01da82292c - - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - 1bf940c18d93 - - c1809c05ae8c - e8f64a7dc470 + - c1809c05ae8c + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - f861ec9fbe59 - 9f505cd4428f - 496cf619e311 - - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -495,24 +495,24 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 4bb198c0bd3e - 89254095cbf6 + - 4bb198c0bd3e - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - - 05ec9fb05ed1 - f9ed7e074900 + - 05ec9fb05ed1 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - d31426ef20f6 + - 18826fb8e5db - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -520,50 +520,50 @@ tools: owner: galaxyp revisions: - 4a7b96835140 - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: + - decc397c3b7e - 6b01678ec2fc - - 5ae104d0da6e - 3d8d4ada5405 - - decc397c3b7e + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - d6aca689dd48 - dd173849c3d8 + - e039cc5c7aed - 5182338d5e7c - 539a3a4dcc9e - - d6aca689dd48 - - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - 16026cdb1330 - - d426affe977c - 8a45fd5a608a + - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - dd71e020e2aa - 9c70a651a53e + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - d063e2fe4ba4 - - 1b03536aa3c9 - 9020199dba0a + - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -577,16 +577,16 @@ tools: owner: galaxyp revisions: - 7f6a1f27553e + - 5c2a97a234d6 - fb52e95a370c - c8b225c69a7f - - 5c2a97a234d6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -599,14 +599,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 07ff622ec007 + - 943a34df6047 - 7fdd9119cc4f + - 07ff622ec007 - 3634c90301af + - 1beff3ddce58 + - da885ca16cb2 - 3ec27b4cee7c - a72c48001f7c - - da885ca16cb2 - - 943a34df6047 - - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -660,10 +660,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - - 265c35540faa - 1a5690a5eedc - 12692567c7f9 + - 265c35540faa + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/staging.gvl.org.au/qiime_2.yml +++ b/staging.gvl.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index c99ffacb9..2ab52242b 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 42201b90e3f4 - 110a346daf36 - - e345aadf914f - - 289b7d6b69a4 - - cd5f98911089 - 2f1d464ebfd2 - - 42201b90e3f4 + - cd5f98911089 + - 289b7d6b69a4 + - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - fcce77c09289 - - c207119ba5f6 - 8501601a118d - 42d9087b4789 + - c207119ba5f6 - 0345dbaaa79b - 0cd2df8af811 + - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - ad5ab22ffe24 - - 405a212b32ab - - 04db7fd6b238 + - 89eb29319bf4 - 421c33b8bf17 - 33486216eec0 - - 89eb29319bf4 + - 405a212b32ab + - 04db7fd6b238 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 + - 7370bb65bad4 + - fa51dc5e8386 - f6e91108b7b1 + - eb784fa07f80 - 1d839ead7ad3 - 7b72fde3d27e - - fa51dc5e8386 - - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - a3e86cd9cac7 - d30e36c48c93 - - c9b77ced9a78 - 3d70c2996730 - - 1544278c272e + - c9b77ced9a78 - 8a55d29c8fcf + - a3e86cd9cac7 + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -88,11 +88,11 @@ tools: owner: iuc revisions: - b242deb58952 - - e2db212d64ad - 564c33e5c3e3 - 7b881f5f5ad5 - a5969aa9347e - 887cf585cafc + - e2db212d64ad tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - - 8cff84759bf6 - b4bab607eb05 - - bd5ff77e2036 - 9a171f9a450b + - bd5ff77e2036 + - 8cff84759bf6 + - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - adc7a7610d4f - - 6dafad990086 + - 887e0991eb24 - 33f0793edf93 - 4f65e343ecdf + - 6dafad990086 + - adc7a7610d4f - 5e10f396979e - - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: + - c5d7050e4ad7 + - 43e3eeb2e0ec - 97575d01f06b - - 4e280b27a831 - - c287418eb288 - 17d39bf0a63a - - 43e3eeb2e0ec - - c5d7050e4ad7 + - c287418eb288 + - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - 09b8edb56d80 - - 9586f08634c0 - d9bf483266a1 - - a819ec3b362d + - 09b8edb56d80 - cd034465d4a4 + - a819ec3b362d - 0b8c84a7fdb5 + - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - bf0e43ab0416 - 69842dd5aa48 + - 2645575d1bf2 - 95351dd0fd3f - - a9c34a289493 - a4b4bd84f69e - - 2645575d1bf2 - - bf0e43ab0416 + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - - cfb504394ae1 - - 912f904a6e1e + - d1fda11e602f - bb0475c884ff - 8a35a3bc6752 - - d1fda11e602f + - 912f904a6e1e + - cfb504394ae1 + - d033e1ccb386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - - d504d945a655 - 95286af4139b + - d504d945a655 + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 1d67d8e8e..763b1d654 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -3,16 +3,16 @@ tools: owner: iuc revisions: - 2d4e3aff9dc7 - - 31f8063eedea - cf01dd6c6b1f + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - - 32e542c2a773 - 125d20cb23d7 + - 32e542c2a773 + - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -68,8 +68,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -82,9 +82,9 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 6a6717a5f421 - 86285ddd4512 + - 6a6717a5f421 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -96,8 +96,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -121,10 +121,10 @@ tools: - name: describe_samples owner: iuc revisions: + - 0693ccd171c4 + - 3b36efd62b3e - e3b16fd7dd08 - 8f0181aacb7a - - 3b36efd62b3e - - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -136,13 +136,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 9a882d108833 + - 0696db066a5b - 6a3a025714d3 - - 24a09ca67621 + - 9a882d108833 - cd9874cb9019 - - 8fe98f7094de - - 0696db066a5b - d027d1f4984e + - 8fe98f7094de + - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -154,10 +154,10 @@ tools: - name: dexseq owner: iuc revisions: - - 62adf13b86ea - - b47c006d90c5 - 9a7c5b6d8f1e - 2872c633f07e + - 62adf13b86ea + - b47c006d90c5 - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -170,17 +170,17 @@ tools: - name: edger owner: iuc revisions: + - 3d89af8a44f0 + - 555659de7321 - f2843df56434 + - 9bdff28ae1b1 - 070900306913 - df0c8d0a5992 - - 5bf899c13979 - - 9bdff28ae1b1 + - a8305cf0c951 + - 6e53e565fc6a - 0cb907a2a810 + - 5bf899c13979 - 334ce9b1bac5 - - 6e53e565fc6a - - a8305cf0c951 - - 555659de7321 - - 3d89af8a44f0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -211,17 +211,17 @@ tools: - name: featurecounts owner: iuc revisions: - - f3a5f075498f - - a56fbe2d6ba7 + - f9d49f5cb597 + - 38b6d12edc68 - ea04b737afa0 - - 90d16db017d7 + - a56fbe2d6ba7 + - f3a5f075498f + - 6f66ae7c5f7a - a37612abf7f9 - - 38b6d12edc68 - e6a2a912677a - - 6f66ae7c5f7a - - 7db9d3ea71c9 - af814359d244 - - f9d49f5cb597 + - 90d16db017d7 + - 7db9d3ea71c9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -251,9 +251,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - f99dd58de04f - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -272,12 +272,12 @@ tools: owner: iuc revisions: - a86e80d3c09c - - 6c19daec423d - - 6ab42baa56e9 - 3fb01a8c902d - - d4b55e2beb12 - f4af63aaf57a - 26371a1df031 + - 6c19daec423d + - d4b55e2beb12 + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -295,8 +295,8 @@ tools: - name: htseq_count owner: lparsons revisions: - - 4418229c501e - 67b0b160903a + - 4418229c501e - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -315,11 +315,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - ce5d418183c5 - - 1c75aa5de15e - 5ae5c312d718 - - 87c11c05d238 + - 1c75aa5de15e - 01247aaf0a10 + - 87c11c05d238 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -331,9 +331,9 @@ tools: - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - - 10c98fab6c5a - 4f9c4e6566e5 + - 10c98fab6c5a + - c971db6f0fe5 - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -346,14 +346,14 @@ tools: - name: limma_voom owner: iuc revisions: - - e827f9aae031 - 32511f586472 - - 0921444c832d - - 119b069fc845 - 58c35179ebf0 + - d6f5fa4ee473 - 97e06a4c7c75 + - e827f9aae031 + - 0921444c832d - 708348a17fa1 - - d6f5fa4ee473 + - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -371,8 +371,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -402,8 +402,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -421,18 +421,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - b0f2be869d6d - - 4df95e2d7f61 - - 3ea5a2a63fa2 - - 7ed2edc1337f - - 4074fc1940e2 + - 980d2a2e1180 + - 5ec75f5dae3c - e132e7d02a3e - - c772497b2c32 - 0a563fd2f22e - - 5ec75f5dae3c - - 980d2a2e1180 - 99b17b74a8cd + - 3ea5a2a63fa2 + - 4074fc1940e2 + - b0f2be869d6d + - c772497b2c32 - b9e04854e2bb + - 4df95e2d7f61 + - 7ed2edc1337f - 79de45b5069b - c7c55b694974 tool_panel_section_label: RNA-seq @@ -459,12 +459,12 @@ tools: owner: bgruening revisions: - ebab418107f5 - - e3d32471da11 - - 2c0ca397d302 - - f4d5237a84f6 + - 53e9709776a0 - cc05793bb896 - 15cd64d7c58b - - 53e9709776a0 + - e3d32471da11 + - f4d5237a84f6 + - 2c0ca397d302 - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -477,22 +477,22 @@ tools: - name: seurat owner: iuc revisions: - - c0fd285eb553 - - 56242ff81c84 - fab6ff46e019 - 8c28affc7c48 + - 56242ff81c84 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 1ebd14235b92 + - 258d696dbd7e - 76d290331481 + - 1ebd14235b92 - cef79931dda5 - - 258d696dbd7e - - cbf488da3b2c - 914cfcba0ec8 - dd4df992d93d + - cbf488da3b2c - ae618321f34a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -529,10 +529,10 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 + - c6334cb383ff - 0db979fead3a + - d0d4cef4f967 - ffd1300599a1 - - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -544,10 +544,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - - d6a479fd4281 - ba3720d7e68b - 74217fbfba4d + - bcc5f03f1900 + - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -559,10 +559,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e - - 2fb4ee002432 - 478f36effca1 + - c2b82a94493e - 56162e446004 + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -574,9 +574,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - 3f4094b6a565 - - 9ff3765e7172 - fab23c3b5258 + - 9ff3765e7172 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -588,8 +588,8 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - 34a018cbee9c + - 4687ecf0eb2d - 870ac06dff8e - be3f26533209 tool_panel_section_label: RNA-seq @@ -603,11 +603,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 33406f5a445c - 65e7dea767ea + - 33406f5a445c + - c5fbddcac63a - 05ab8d5e04a2 - 5192f657f305 - - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -619,8 +619,8 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - a35cba31d904 - 6f0fb35b799c + - a35cba31d904 - e406ac71165d - 1fdb25a8384d tool_panel_section_label: RNA-seq @@ -634,10 +634,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: + - 37a1129c89d2 - 964b7efe2639 - 7c7fbf13aadd - c2c039e421af - - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -649,10 +649,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - - 047c22569787 - 24e94d84adc9 + - 1d689e4e1caf - eafea3083352 + - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -664,10 +664,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 04bb8bb7c198 - - 3a4ac03d1266 - 9871104ea630 + - 3a4ac03d1266 + - 04bb8bb7c198 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -691,15 +691,15 @@ tools: - name: trinity owner: iuc revisions: - - 32b86cd8eb50 - - 48636f857c4b - db1f362cca3e + - 48636f857c4b + - 32b86cd8eb50 - 8f1c3df4dd49 - - c9cfec002f71 - - d2bc35f3d1c5 - - d84caa5a98ad - cee61b3fcf78 + - d2bc35f3d1c5 + - c9cfec002f71 - 9fa24d5aac68 + - d84caa5a98ad tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index b2c45c52e..ba833d62f 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: + - 473382134e56 - 1a052c827e88 - 080fd5739bb4 - - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index c63626457..15a41d3e7 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - a53efedba9e7 - - 88eedb4abea0 - 10184eaa85fc + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,9 +16,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 993b19f20c76 - - 1dfd95ee241e - 108db6635177 + - 1dfd95ee241e + - 993b19f20c76 - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -44,8 +44,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e9b9c489aacc - e30af4e78cd3 + - e9b9c489aacc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - 9c1c0b947e46 - ef11139d4545 + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - - 30a201c9c310 - 19ece8afbaab + - 30a201c9c310 - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -163,9 +163,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - 6856f8a01905 - 9149ad20699a + - 12749212f61b - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: + - 06dc50b7b711 - 92ec40abcdcf - 33208952b99d - c89806670ab9 - - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,10 +205,10 @@ tools: - name: samtools_fastx owner: iuc revisions: - - b3d99709fe1a - 66e23b11feae - - a8d69aee190e - 720217c23995 + - a8d69aee190e + - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -226,10 +226,10 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - db17d5321bad + - cc61ade70eb8 - fe34990e5ce7 + - db17d5321bad - 22970df7a40e - - cc61ade70eb8 - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -243,10 +243,10 @@ tools: owner: devteam revisions: - 88b8c2916784 - - 7a6034296ae9 - fa5d3e61e429 - 7def34e6cf4d - 811fc2d75ad4 + - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -264,8 +264,8 @@ tools: - name: samtools_merge owner: iuc revisions: - - 65a38e8c8e2a - 740ce0a18f0d + - 65a38e8c8e2a - b40e2d865d52 - 36677f429310 tool_panel_section_label: SAM/BAM @@ -273,11 +273,11 @@ tools: - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - 9da0311ab1dd - - b61f5d6a7f25 - 583abf29fc8e + - 329deb17a9f7 - fa7ad9b89f4a + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -289,8 +289,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -302,10 +302,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - - d7b4851d1971 - db000c6007a0 + - bb8cfc6f6e0c - 30388d878f81 + - d7b4851d1971 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -323,9 +323,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - b5c88b7b153e - a4a10c7924d1 - 344fc91e1bfd + - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -337,9 +337,9 @@ tools: - name: samtools_sort owner: devteam revisions: + - cab3f8d35989 - e613c1ad4c4c - a577ea614bed - - cab3f8d35989 - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -352,11 +352,11 @@ tools: - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - b7f7826ef1cd - - 5d9ae78f34d3 - bd850490c7f1 + - 5d9ae78f34d3 - bcedabb53ddf + - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -368,10 +368,10 @@ tools: - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f - fed4aa48ba09 - 1cc79f49b8d5 - 24c5d43cb545 + - 3a0efe14891f - 5a08c09b9311 - 145f6d74ff5e tool_panel_section_label: SAM/BAM @@ -385,14 +385,14 @@ tools: - name: samtools_view owner: iuc revisions: - - bf328cec6a42 - - 6be888be75f9 - - c370440f901e - - b72793637686 - 0dbf49c414ae + - 6be888be75f9 + - bf328cec6a42 - 350bbc5c2ffd - - b01db2684fa5 - 5826298f6a73 + - b72793637686 + - b01db2684fa5 + - c370440f901e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index ce3e17338..6700f4143 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d - - ea5e944f447d - - d147d6455873 + - 5cb6146337d8 - 4aab5ae907b6 - 6f6537780379 - 59bb6d34fca6 - - 5cb6146337d8 + - ea5e944f447d + - a62c4a11a67d + - d147d6455873 - 480d9e9d156b tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 587175e60..618f61af7 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -10,27 +10,27 @@ tools: revisions: - c9944a2600f1 - f2000bc73102 - - e4c01dcece8b - ecb9ea6269ee + - e4c01dcece8b - e32b215b7c04 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - e1c3c2f2a834 - c0b037b12765 + - e1c3c2f2a834 - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 32e547223c9e - - fb9e030ffae4 - - 93dd15e13e6a - cfc3f5a57dc6 - 00712416fdaa + - fb9e030ffae4 + - 93dd15e13e6a + - 32e547223c9e - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -43,12 +43,12 @@ tools: - name: anndata_inspect owner: iuc revisions: - - b9fac48532eb - - 688357ad5e61 - 39e945f0b2c1 + - 688357ad5e61 - 038e32885fec - - ee98d611afc6 - 6f0d0c784f09 + - b9fac48532eb + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -60,12 +60,12 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 3d748954434b + - d4af736e7b83 - b85871dd69f9 - 9bd945a03d7b - 43cb7b5a6fe7 - - d4af736e7b83 - ed4996a16f7f + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -78,34 +78,34 @@ tools: owner: ebi-gxa revisions: - a4774b7b2e85 - - fe75d2414dc0 - 2e8022f1923c + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 4fff5a293013 + - 769d815e4b0d - 0e70b2dfe4be - 02b1fe7aed76 - - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - aa4a6f0916b4 - 344c2af50552 + - c29e7bb492bf - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - b13d3e4c48e1 - 050cf43887d3 - c32347702e12 - - b13d3e4c48e1 - 5b7c81b35b89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -151,11 +151,11 @@ tools: - name: dropletutils owner: iuc revisions: - - cdf4443d5625 - 8855361fcfc5 - - a9caad671439 + - cdf4443d5625 - 2c1200fba922 - cfe1e6c28d95 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -212,15 +212,15 @@ tools: - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - f47ac4a0b337 - 013e53ccc7ac + - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - b892fa1fcaec - a63e9713c39d + - b892fa1fcaec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -268,15 +268,15 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 3a6a5381db36 - 4401ed529d2c + - 3a6a5381db36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat @@ -303,15 +303,15 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - 0410b6aada45 + - ffc33339cd3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 77d8e0fd162a - 5dfba24d7bdd + - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites @@ -324,15 +324,15 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - 7f7c6ead2d0d + - 409396ea5cf0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - 51e40e9b6c3c - e4f8fceab96a + - 51e40e9b6c3c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -352,8 +352,8 @@ tools: - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize @@ -366,8 +366,8 @@ tools: - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - ea5d67ec94ab - dd9988943f53 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -394,8 +394,8 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -420,25 +420,25 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - f36828ebdc54 - 27fe5cd1729c + - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - 11a3385e03b5 + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - 4b0adaa31c95 - - eeab712b0b99 - - 59be31ac9dc3 - 7784821452ac - e98619de2776 + - eeab712b0b99 + - 59be31ac9dc3 + - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -451,8 +451,8 @@ tools: owner: bgruening revisions: - 7ffaa0968da3 - - 2cfd0db49bbc - 282819d09a4f + - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -484,11 +484,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - c4f39bf4a068 - - f911a64454fb - 0bff0ee0683a - - 7e014059a88d + - f911a64454fb + - c4f39bf4a068 - a4b734cd253b + - 7e014059a88d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -500,10 +500,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - 43c146e25a43 - - 7608d5faee41 - - d45f092caf24 - b83fbc90161e + - d45f092caf24 + - 7608d5faee41 + - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -515,9 +515,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 2b0d3e2f402a - - f3eb2291da05 - 37a47c4fd84d + - f3eb2291da05 + - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -530,8 +530,8 @@ tools: owner: iuc revisions: - df8e4e54d367 - - 69018f285aa3 - a6821f856a1e + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -543,10 +543,10 @@ tools: - name: raceid_trajectory owner: iuc revisions: + - 2af7c5086a96 + - 44b935f2271b - c92d0f9338c5 - 72979cac22b2 - - 44b935f2271b - - 2af7c5086a96 - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -572,12 +572,13 @@ tools: owner: iuc revisions: - aaa5da8e73a9 - - 6f83f8fd381f + - 64ff3ef24fae + - 6acb08931836 - b2df381a6004 + - 6f83f8fd381f + - 77b91b9bdf52 - edec35114f72 - 4d8f983cd751 - - 6acb08931836 - - 77b91b9bdf52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -589,31 +590,32 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 3c86f71498bc + - b409c2486353 - d636ce5cde16 - - 277313130da5 - a03ff8633507 - - b409c2486353 + - 277313130da5 + - 3c86f71498bc - a97abb8cd15b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - d636ce5cde16 + - aa0059118fb9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - c5d3684f7c4c - - 3081ff5c84a3 - - cc0deb593fc8 - - 6bd82ed14acd - - 6c145a6868cc - - f54f0f0598ad + - ca086f24422f - 5e9171dc8244 + - cc0deb593fc8 - 5c3ebe2adc77 + - f54f0f0598ad + - c5d3684f7c4c + - 6c145a6868cc + - 6bd82ed14acd + - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -626,13 +628,13 @@ tools: owner: iuc revisions: - d844935c906c - - 94c19fb1281c - - 3bcd5445cd7a - - f3ad813a58a3 - - c9cb76cf8d6c - ab55fe8030b6 - a407e7f8bdc1 + - 3bcd5445cd7a + - c9cb76cf8d6c + - 94c19fb1281c - 7b9fafe32c86 + - f3ad813a58a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -644,32 +646,33 @@ tools: - name: scanpy_plot owner: iuc revisions: + - 95777145cb92 + - f7446fd8d5e7 - aa0c474463c2 + - 70fa84e99463 - 7647e5cd1b8b - - 6adf98e782f3 - - f7446fd8d5e7 - - 95777145cb92 - 6f5349dd5c49 - - 9b0cdb8cf6be + - 6adf98e782f3 - dbbe1ea8ecb1 + - 9b0cdb8cf6be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - f7446fd8d5e7 + - 70fa84e99463 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 458e8f43a775 + - e66884b1c1a5 - f2f6c703da06 - - c65fce500915 - 215733a383f2 - - d18e7a6e5cd4 - - e66884b1c1a5 + - 458e8f43a775 - 73ab2ac53d06 + - d18e7a6e5cd4 + - c65fce500915 - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -682,9 +685,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - - b834074a9aff - 8f333f90d8d6 + - b834074a9aff + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -696,9 +699,9 @@ tools: - name: scater_filter owner: iuc revisions: - - b7ea9f09c02f - - 7a365ec81b52 - 652923ce664f + - 7a365ec81b52 + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -716,9 +719,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - - 2e41b35b5bdd - ef4c80837bc5 + - 2e41b35b5bdd + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -736,8 +739,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - c99ba278dfa9 + - 9e5c0bb18d08 - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -979,8 +982,8 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 88192fe25375 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index dcfbad4ec..d682759a3 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 4c07ddedc198 + - 419027d822d6 - 746e8e4bf929 - 562f3c677828 + - 4c07ddedc198 - 2f3c6f2dcf39 - - 419027d822d6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: + - 6c29c7e347e8 - 7a15159140d1 - cb1c59d69557 - - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e - aef56d0e7a61 - - 4c4ec859c31a + - 7442b94d6a1e - 840f29aad145 - b1eda492f063 + - 4c4ec859c31a - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - - 375bbd555f4a - - 30d21a6041f6 - 07843f917990 + - 375bbd555f4a - 9fda0b82f419 + - 30d21a6041f6 + - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad + - 4cc980df6265 - 8b1b2b91f8d0 - 7ae443e6217d + - 2c58b83c9bad - cd02bf168d23 - - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - ad7e0b4291ee - - 1dd433d2c92c + - 4bbaf77573ef - 7dd3fb35904f - bb9fc9d46ea4 - e10e776f2109 - - 4bbaf77573ef + - 1dd433d2c92c + - ad7e0b4291ee tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index b41fcb22b..f75516d6d 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - 626658afe4cb - - 6e8d94597139 + - 13b6f0007d9e - 9cd341095afd - - be25c075ed54 - - 464b9305180e - 6595517c2dd8 + - be25c075ed54 - 02026300aa45 - - 13b6f0007d9e + - 6e8d94597139 + - 626658afe4cb + - 464b9305180e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -79,10 +79,10 @@ tools: owner: iuc revisions: - 9cc411a62277 - - 557ec8d7087d - 34d29339abab - - 90f657745fea + - 557ec8d7087d - 37cde8134c6a + - 90f657745fea tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -114,22 +114,22 @@ tools: - name: query_tabular owner: iuc revisions: - - 1ea4e668bf73 - - 83069b38aa85 - - cf34c344508d - 623f3eb7aa48 - - cf4397560712 - - 3a6b78c39dca - 2e8f945f7285 + - 1ea4e668bf73 + - cf4397560712 - 33d61c89fb8d + - cf34c344508d + - 3a6b78c39dca + - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - 399da6b5ec21 - - 503bcd6ebe4b - ae8c4b2488e7 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,9 +142,9 @@ tools: owner: iuc revisions: - bce29ec10b78 + - c4d18aa4ec4a - b722161a845a - f768f6183386 - - c4d18aa4ec4a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -157,14 +157,14 @@ tools: - name: text_processing owner: bgruening revisions: - - 9ff72e942410 + - ddf54b12c295 + - f46f0e4f75c4 + - 0a8c6b61f0f4 + - d698c222f354 + - fbf99087e067 - 12615d397df7 - a6f147a050a2 - 74a8bef53a00 - - fbf99087e067 - - d698c222f354 - - f46f0e4f75c4 - - ddf54b12c295 - - 0a8c6b61f0f4 + - 9ff72e942410 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index f607ac1fe..b9457609d 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -2,9 +2,9 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 85c57cc9b558 - 82fb5e3bb93e + - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -22,49 +22,49 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 - - 156b60c1530f - - a5937157062f - ef2c525bd8cd + - a5937157062f + - 156b60c1530f - 57def2d7c093 + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 791f73caa0c8 - - e61c9ac190ad - 435b157bed6d + - e61c9ac190ad - 09d6e4693887 + - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 03627f24605f - - 074d44697036 - - 3b4b2121842f - - 65432c3abf6c - - e1461b5c52a0 - dfadc322b065 + - e1461b5c52a0 + - 074d44697036 + - 03627f24605f - 4805fe3d8fda + - 65432c3abf6c + - 3b4b2121842f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 701d134358ad - 9cb929f21cfa - 7dfca164d2e3 - - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: + - c27549b9aa1f - f4473557ffc7 - 426d707dfc47 - 971e07ca4456 - - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -90,11 +90,11 @@ tools: - name: snippy owner: iuc revisions: + - d220115f882b + - 5bbf9eada9c2 - fa016f1eea1a - - c9a8ef2aa380 - 9bccc8404a3c - - 5bbf9eada9c2 - - d220115f882b + - c9a8ef2aa380 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -136,21 +136,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 32f14a2723ec - 3b1e7c170b10 + - 40f0591deda0 - ee4a90760848 - - 32f14a2723ec - e7aff4a85df5 - - 40f0591deda0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 42818629ec4c + - 02d81b994ef5 - 4934c0ac6197 - adc0645b945c - 9793bc5d741b - - 02d81b994ef5 + - 42818629ec4c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 4ea6ecc8e..98899d5a1 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - 265fe0f9ea64 - - 95815a0bb307 - - e075b1be5abb - 8a2e296c07ef - - ebe5fc018e72 + - e075b1be5abb + - 265fe0f9ea64 - b7ea370b8f5d + - ebe5fc018e72 - 6a88248893c4 + - 95815a0bb307 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -20,13 +20,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 1001172b5089 - - 21687e35f066 + - 22637b1a55bf + - c37b684e7f4e - 544cb432072b - - 0fba2c15b40d + - 21687e35f066 + - 1001172b5089 - b03984136ce4 - - c37b684e7f4e - - 22637b1a55bf + - 0fba2c15b40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 01d6b7d6365e - - 8627b2b383b4 + - 8ca3647c90fd + - 3a7084316a6e + - 8408bffd5616 - 0238f68ad641 + - 01d6b7d6365e - 143796b504eb - bf1f4994f104 - - 3a7084316a6e - - 8ca3647c90fd - - 8408bffd5616 + - 8627b2b383b4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,12 +59,12 @@ tools: revisions: - abd489215f73 - f430a1ec7ee4 - - 9b5abbf50d23 - - d144af39073a + - 03e0645395d2 + - 6b6c992d3a14 - 62ca6da715bf - 81426b3cf18b - - 6b6c992d3a14 - - 03e0645395d2 + - 9b5abbf50d23 + - d144af39073a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -76,13 +76,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: + - d37e313a41be + - 1171446da5db + - 2363ef414c9b - e522022137f6 - - 1829900b5dcd - 95c6f3f4c77f - - 2363ef414c9b - - 1171446da5db + - 1829900b5dcd - d3081540d175 - - d37e313a41be tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,13 +94,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - b14ff40958cb - - 348cd212dbad - - 09f37afb3621 - 92c0aff8b53e - - 1137ce8efc1e - d58d2e8c7a57 + - b14ff40958cb + - 1137ce8efc1e + - 09f37afb3621 - 9b29129fb491 + - 348cd212dbad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -112,12 +112,12 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 7291189e98b4 - - 55c0e906c14c - - 367ba501b6eb - 1f2183a23823 + - 367ba501b6eb + - 7291189e98b4 - de68c11034f6 - ecc9192912b8 + - 55c0e906c14c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 64a8f7dae3ad - - ae68ceb4cca3 + - 6c790a091c7c - 039ea3f1dea9 + - ae68ceb4cca3 - e6f4badbe6f3 - 7cbf3c66d4ad - - 6c790a091c7c + - 64a8f7dae3ad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -146,13 +146,13 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 963a3635b2e1 - - 5d6653c989cb - - 6ea7170a016d + - cdb7b4927742 - e7452697afd9 - - 33bd9301568c + - 6ea7170a016d - 277719af4dd7 - - cdb7b4927742 + - 5d6653c989cb + - 963a3635b2e1 + - 33bd9301568c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -164,13 +164,13 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 26d97cdd5410 - - a29a2f40b665 - - 501bfb078342 - - 5a321fab1fe4 - - 91c1e57d5c7f - a1213a0b7b66 + - 5a321fab1fe4 + - 501bfb078342 - b7f0f59baa7e + - 26d97cdd5410 + - 91c1e57d5c7f + - a29a2f40b665 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -182,14 +182,14 @@ tools: - name: bcftools_isec owner: iuc revisions: - - d7d1663559e9 - - 709dd8291b83 - - 768d04526638 + - 81e4014fa809 - c803c34361e0 + - 768d04526638 - 97d19c008d15 - - 81e4014fa809 - - 5f27e814a119 + - 709dd8291b83 - 15da1ddcfeff + - 5f27e814a119 + - d7d1663559e9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -201,13 +201,13 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 86296490704e - - 7ba36babba2d - 85ee7e6c4204 - b931e65638b8 + - 86296490704e + - 2215287d5cc9 - b84fda8ebef0 - b1eba148b35b - - 2215287d5cc9 + - 7ba36babba2d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 4e1d23e5c691 - - 5660b21a0dbd - - cf06b44624c7 - 56556e1267de - - 9c711df3258d - - f506df85c652 - 37757ffb4c5f - - ce9396ddcb2b + - cf06b44624c7 + - 4e1d23e5c691 + - 5660b21a0dbd - 31ea13dfe5e6 + - ce9396ddcb2b + - f506df85c652 + - 9c711df3258d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,10 +239,10 @@ tools: - name: bcftools_norm owner: iuc revisions: + - 6deb4d549bc9 - 1ca7418e46ee - - 19905c025d2a - a404f786a94c - - 6deb4d549bc9 + - 19905c025d2a - 021693fdadaa - 48291658fdf6 tool_panel_section_label: VCF/BCF @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: + - 71c78e0eea52 + - 3f6fadf8b8ff - 69d8b7567281 - - 5ad5d4243987 - - f7879f1e77f9 - c450406f722b - - 3f6fadf8b8ff + - f7879f1e77f9 + - 5ad5d4243987 - 97e8145d7e30 - - 71c78e0eea52 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 6cf13a657cf6 - - 0fe007201caf - - 52f9e4a660e3 - - 2514e684f8a3 - d31a2e310a52 - cc7f9a4e186b + - 0fe007201caf + - 6cf13a657cf6 + - 52f9e4a660e3 - 79f7a1acc2cd + - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -292,13 +292,13 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 1411bef27a75 + - 6963a6841d22 + - 230e424bde67 - 0a62420cb9cd - - 80e6e399ccd0 - 75ddd081f608 + - 80e6e399ccd0 - 026a989b7cee - - 230e424bde67 - - 6963a6841d22 + - 1411bef27a75 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - bca7ce81688f - - e493702b19eb - - ba20340426fe - - 5808f77b2bb6 - 444e6a756c35 + - 5808f77b2bb6 + - e493702b19eb + - bca7ce81688f - 450a265f92e8 - 5acfca5a76af + - ba20340426fe tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -329,12 +329,12 @@ tools: owner: iuc revisions: - 157ffcdd3fa7 - - d52b8947b269 + - c43399f161f4 - 4d236c696844 - - f2482aa4862e - - 12152af85697 - 68fec03a63b7 - - c43399f161f4 + - 12152af85697 + - d52b8947b269 + - f2482aa4862e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -346,13 +346,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 8dbce095986c - - 0e5d11004815 + - 8f2fc0ab30fb + - 6f8e223f78f3 - cbe39e530cbf - 29ba253e2e05 - - 6f8e223f78f3 - - 8f2fc0ab30fb + - 8dbce095986c - 75becf493cd3 + - 0e5d11004815 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: + - 9708e3086f32 - e0a856def0b0 - 3ff5654b4e7d - - 9708e3086f32 - - a367a15c6de5 - - a8630d4fbaf8 - f544f71adb73 + - a367a15c6de5 - 88bb477f45f7 + - a8630d4fbaf8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -384,11 +384,11 @@ tools: revisions: - 4ed46189d6c6 - 34dc0bbc7e93 + - 31c096c6b156 - 96d0145c041a - - 5c9729d54721 - - 03e30f06f15f - 6ce175385dd9 - - 31c096c6b156 + - 03e30f06f15f + - 5c9729d54721 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -400,12 +400,12 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - a1aad8b559c6 - - 46eb13bc2c73 + - 2c4941386820 - 09f5e45a8212 - - 681bdf1e22ff - 11af7fce71cf - - 2c4941386820 + - 681bdf1e22ff + - 46eb13bc2c73 + - a1aad8b559c6 - 40daf124be88 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -418,14 +418,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 882b2e649602 - - b74b8cbfc1f1 - - 0594ea1417c8 - - 6cbb9c47795c - 8cb121b6a1d2 + - 0594ea1417c8 - f272b8ba0983 - - 743cd1472aeb + - 882b2e649602 + - 6cbb9c47795c + - b74b8cbfc1f1 - 12038f59c0f4 + - 743cd1472aeb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -438,12 +438,12 @@ tools: owner: iuc revisions: - 18cf9de1cf73 - - adee7e8b746f + - a9826db86d9a - cced6715f926 - eccb508bb678 - - a9826db86d9a - - 238f78e38a8b - dba06328556a + - adee7e8b746f + - 238f78e38a8b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -455,13 +455,13 @@ tools: - name: bcftools_query owner: iuc revisions: - - fdec14f69010 - - c9935c9e8a24 + - f64e7ca2efd2 - e53501abf992 - - e0ad88dec40d - 3ce32adc55b2 + - fdec14f69010 + - e0ad88dec40d + - c9935c9e8a24 - 9f36041495a3 - - f64e7ca2efd2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -473,13 +473,13 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - 4db0695a6fc7 - b7be725976b6 - - d43eb39b989e - - fd3539749127 - 79489d5685dd - d68c43202172 - - 4db0695a6fc7 - 3b7b1fe7b937 + - d43eb39b989e + - fd3539749127 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -491,13 +491,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 5296d26b0373 - - 78cd8b69da4c - - 1ccf0e7fb4f6 - - b0d39ef600a7 - 58091e1be01b - - 6a636d58dfc2 + - b0d39ef600a7 - 1a989b4110da + - 78cd8b69da4c + - 5296d26b0373 + - 6a636d58dfc2 + - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -509,13 +509,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - baa8823f8073 - - '388983871932' - - bf8325a07ce7 - e8af591435d1 - - b17394940c7a + - '388983871932' - 4d3ce9dc1525 + - b17394940c7a - b641062a2587 + - bf8325a07ce7 + - baa8823f8073 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,12 +527,12 @@ tools: - name: bcftools_view owner: iuc revisions: - - e6b5cbbf449b - - 3ca3de4e5291 - d1f8f55f564d - - 3a233c8eb814 + - 3ca3de4e5291 - c2ab91a0d506 - 59fa8742285e + - e6b5cbbf449b + - 3a233c8eb814 - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -545,15 +545,15 @@ tools: - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - 6ea73d6151ec - afc0ba768690 + - 6ea73d6151ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -580,8 +580,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - aea8e90ad788 - 9edfe5145ba8 + - aea8e90ad788 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -594,22 +594,22 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine owner: devteam revisions: - - 1f0ba67cc85a - 53edb91ed051 + - 1f0ba67cc85a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples owner: devteam revisions: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -623,43 +623,43 @@ tools: owner: devteam revisions: - 6b935ab36d7b - - fa24bf0598f4 - eae7c08ebb6f + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - f285aa6bdcfb - b24e368ae7b1 + - f285aa6bdcfb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -686,15 +686,15 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 958b6484a7f1 - 2ba3b87f904f + - 958b6484a7f1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - dd44c3f416c3 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 05559479f..eabe718b3 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - 4efdca267d51 - - c2ef298da409 - - 78c75f134c16 - 6e9aea89e388 + - 78c75f134c16 + - c2ef298da409 + - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -33,30 +33,30 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: + - 3e1f6f6d557e + - fe3ca740a485 - 4f2967b27e67 + - 44018dd6b447 + - b5d8e5475247 - a79ee60b6926 - - 1aae04680c4b - - cd2480f35935 - f29602ae449e - - fe3ca740a485 - - 3e1f6f6d557e - 133f36c29579 - - 44018dd6b447 - - b5d8e5475247 + - 1aae04680c4b + - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -70,24 +70,24 @@ tools: - name: augustus owner: bgruening revisions: - - 28433faa6e42 - 09855551d713 - ca6d970d931c + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: + - da5f1924bb2e - 728dacaf08a9 - 92eee5f31117 - - da5f1924bb2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 8fd427007e93 - fe48aa4ccd5e + - 8fd427007e93 - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -100,24 +100,24 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat owner: bgruening revisions: + - 8e9e228c54c4 - 7ccc6234b54e - 1ac12c0cc7a0 - - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -141,45 +141,45 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 9f2455341fac - - 3bbe70fef6df + - 756376aeb1ae - 582fd74dc2a1 - - 9c15ca7e764e - b6b5cd37f2a2 - - 756376aeb1ae + - 3bbe70fef6df + - 9f2455341fac + - 9c15ca7e764e - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 73428a792541 + - 30fb23d4c31c + - 989f7c061f35 - 0ffe5be70caf + - 73428a792541 + - a230ea445788 - 1691af4a0d17 - 8e1ace8f77c6 - - 989f7c061f35 - - 30fb23d4c31c - - a230ea445788 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 57c6718cbfcc + - 5a5ae61da69c - 494f0bb4a993 - - e94187d661df + - 57c6718cbfcc - 563a19373357 - - 5a5ae61da69c - 30f08d74024f + - e94187d661df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: + - d6c7106b7b2e + - f77d7b685bb3 - 2bba2ff070d9 - 7abc5f6dd595 - - f77d7b685bb3 - - d6c7106b7b2e - f31125bb85ea - 1bc5a03faf2e tool_panel_section_label: Annotation @@ -187,13 +187,13 @@ tools: - name: funannotate_sort owner: iuc revisions: - - 52af33194019 + - 54961e026fe4 - d3af38b9c7e1 - - 520e30695ec3 + - 52af33194019 - fed64e676186 - d77fdcca400e - - 54961e026fe4 - b3cf4684e9c7 + - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -205,9 +205,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 07d7991bf205 - 79261884facd - 2aea122fbd25 + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -219,10 +219,10 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - - 43798b4caee0 - ef2ad746b589 + - 43798b4caee0 - 8b3e3657034e + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -246,16 +246,16 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: + - 98cafcbd2578 - c55643c3d813 - 74810db257cc - - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -280,18 +280,18 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - - 370c210d9541 - 3c1a01127868 + - 370c210d9541 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - e95d52d295d7 + - 033755194fe9 - b815ec682418 - 624606f7c996 - - 033755194fe9 - - e95d52d295d7 - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -328,10 +328,10 @@ tools: - name: prokka owner: crs4 revisions: - - a17498c603ec - 8a22554cdde2 - - d643e3b03500 + - a17498c603ec - bf68eb663bc3 + - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -343,8 +343,8 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler @@ -363,22 +363,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5b80f544c67f - - cfcf33df7fc0 - - 68693743661e - - 5c7b70713fb5 - 268d162b9c49 + - 5b80f544c67f + - 5a29ab10dba6 - 8f92c2b26e6d - 9473cd297a76 - - 5a29ab10dba6 + - 68693743661e + - cfcf33df7fc0 + - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - 09d6806c609e - - 2b3e65a4252f - 5fab4f81391d + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -397,24 +397,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - 037a11682176 - - 45083d070fb8 + - 4839e590cb26 - d03af1c7002c - - 200c378d85f3 + - 037a11682176 - ba6f87115e13 - - 4839e590cb26 - ac8250086ac3 - - 51dd22484644 + - 45083d070fb8 + - 37213cf56392 + - 200c378d85f3 - e1a9d6fd258d - 809dfc93d593 - - 37213cf56392 + - 51dd22484644 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index fa41475c7..0c704161f 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,26 +2,26 @@ tools: - name: abyss owner: iuc revisions: - - a929ce596a34 + - 8f1b150a2487 + - 890b794c997d - 0124fce4654a - - 841084c5fc46 - - fa5259cc561b - - 0e93176640ac + - a929ce596a34 - 553bfe8bd0b5 - 7547fcab5d19 - - 890b794c997d - - 8f1b150a2487 + - 0e93176640ac + - fa5259cc561b + - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 067592b6b312 - 21e491ad532a + - b2860df42e16 + - 067592b6b312 - ddddce450736 - - 94fe43e75ddc - b9e31c5c01c7 - - b2860df42e16 + - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -34,46 +34,46 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - 5258e18bbe23 - - 3371c5bdc17a - - a7f16f24e9a1 - 22286dab5aa1 + - a7f16f24e9a1 + - 3371c5bdc17a + - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - 8c2167481e72 + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: + - 5ecdeca79a0d - e824f5d958d0 - - cf13a1e03e5b + - 41030a6c03b7 + - ea8146ee148f + - e4bd1e99bacf + - 602fb8e63aa7 - bb935709506a + - cf13a1e03e5b - 1440ae06552f + - 0d243f458b53 - 2dd755c1c6ff - - 94170eee0ad8 - - e4bd1e99bacf - 46ae58b1d792 - - 41030a6c03b7 - - 602fb8e63aa7 - 1e62c28ba91d - - 5ecdeca79a0d - - 0d243f458b53 - 4048d82f0c88 - - ea8146ee148f + - 94170eee0ad8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - c5b7390290b1 - 86f150c8019d - 5732f959936a - - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -86,12 +86,12 @@ tools: owner: bgruening revisions: - 291923e6f276 - - e27815e82dd4 - - 1ce9b1d72ec3 - 3ee0ef312022 + - e27815e82dd4 - 276f5d8712d5 - 8d4f03b5fe9d - cb8dfd28c16f + - 1ce9b1d72ec3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope @@ -107,17 +107,17 @@ tools: owner: iuc revisions: - ba88bc5a6446 - - 06bcf65179fb - 8b330a577046 - 7348b69e5109 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3fba9c77550a - - 690c2caa367e - 5127a713de83 + - 690c2caa367e + - 3fba9c77550a - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -130,22 +130,22 @@ tools: - name: hifiasm owner: bgruening revisions: - - 41cea2aa2dce - - 045c7c3d8e59 - - 60024a528cbd - - 5bec28269d95 - - 366a11d316a7 + - da9d8bf98802 - 9ef6920c3089 - - 0ee0c3089254 - - 6505bd37670d - - df25d4fb79b7 - - ec9e21e9c71b - - 5f625c63b8bc - 284a1cb82b61 + - 5f625c63b8bc + - 045c7c3d8e59 - 3f7be05a1597 - f3c89da3af16 - - da9d8bf98802 - 71740308d412 + - 60024a528cbd + - 6505bd37670d + - 41cea2aa2dce + - ec9e21e9c71b + - 0ee0c3089254 + - df25d4fb79b7 + - 366a11d316a7 + - 5bec28269d95 - 2061fb3b81b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -170,43 +170,43 @@ tools: - name: megahit owner: iuc revisions: + - a96f3ad4e0d8 - de387b2b2803 - - 14ddfc8ffb93 - 7518ee87b53d - - a96f3ad4e0d8 + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - eb7b00ec347d - f8113c25bc6b + - d7edbc9c3a07 - 09c589057ee8 + - eb7b00ec347d - 9d79beb19ac3 - - d7edbc9c3a07 - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - - 51c2360aa807 - eadfd71dde37 + - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 606b09cc9860 - - 3ca2d2a9068c - - f338e9942b27 - - 99ecfdafc64f - - fd128c111ab0 - e731ea24e48d + - eb7a370f6588 + - f338e9942b27 - 2ecf5a570907 - f369ef5f210b - - eb7a370f6588 + - 606b09cc9860 + - 3ca2d2a9068c + - fd128c111ab0 + - 99ecfdafc64f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -219,10 +219,10 @@ tools: owner: iuc revisions: - 8b6d0d85252b - - 73a3846701e1 - - b799a615995d - 8dee0218ac7d + - b799a615995d - a7b889b90140 + - 73a3846701e1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -241,8 +241,8 @@ tools: owner: iuc revisions: - 15200570e926 - - 64a1c751d99b - 7c2f5268d01c + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -255,68 +255,68 @@ tools: owner: iuc revisions: - dfb8a4497339 - - d256a51a656b - - 79b48f02db49 + - 2b16ba799da9 - bbe19ef04a74 - - 02831bf9e95f - 8fef980d48b5 - - 2b16ba799da9 + - 02831bf9e95f + - d256a51a656b + - 79b48f02db49 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 59db8ea8c845 - 6fcbee531de6 - - 342a1d1fed7b - - 72472698a2df - 3061c8b029e5 - - 675488238c96 - - ebb0dcdb621a + - 342a1d1fed7b - 875d0f36d66f - - 59db8ea8c845 + - ebb0dcdb621a + - 675488238c96 + - 72472698a2df - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 78c533842eeb - - a199cd7ac344 + - d865b62f501c + - cd06929b224b - 39bed8de8017 + - 78c533842eeb - aa39b19ca11e - - cd06929b224b - - d865b62f501c + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - f8564b2d7f63 + - 2b2a352488fa + - 3edba9afc9bc + - 33b7d8481a76 - 5c55448d0f33 - f11b994b7eb2 - - 33b7d8481a76 - - 3edba9afc9bc - - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - e122f9101584 - - 5fc94b3a4704 - 28189050e437 - - ef69617ecb42 + - e122f9101584 - 1d06c8b38e77 - - 378e55aeeb25 - 53c2bc8c2ae3 + - ef69617ecb42 + - 5fc94b3a4704 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -328,195 +328,195 @@ tools: - name: shovill owner: iuc revisions: + - 865119fcb694 + - 196a599ec43d + - ad80238462c1 - 83ead2be47b2 - d9f6a00b6db7 - - 865119fcb694 - f698c7604b3b - - 196a599ec43d - ee17a294d3a3 - - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 015283de3004 - 24e471d13fe9 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1fc82fe7ebef - - 1bb12736175c - 7490b213baa9 - - 051fd2db8a27 - - 604782a8a53a - - c33a476f4001 - 904bf932cf78 + - 1bb12736175c + - 1fc82fe7ebef + - c33a476f4001 + - 604782a8a53a + - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - fee85957cebe - - ad8b536d1caa + - 655fa188c3cc + - 808b3a0a6716 - 9678993ca5bd - d6e617c4e338 - - 808b3a0a6716 + - ad8b536d1caa + - fee85957cebe - 34305b013402 - - 655fa188c3cc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 7e27faaad80e - 8d4b90bf9caf - - 037f9927c4ff - b8002c3f7141 - - 6b5a5842531e - - e5a3b75a271f - 21da31ed41a1 + - 037f9927c4ff + - 7e27faaad80e + - e5a3b75a271f + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 7922870efcca - - 5b26685e5d3b - 2a10645aeadd - 86f66ab58e14 + - f1532cb33c75 + - 7922870efcca + - 5b26685e5d3b - 328aa71f0f3c - 9de69775f512 - - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - e41dcb0e913b - - 1708851f8804 + - 340bc17f49cf - 8cc856b935ee + - 6aad515a5270 + - 1708851f8804 - 85fb02c43042 - - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - 249f6a28c751 + - b3490b036c5a + - d5fb354f745d + - de1260f8a300 - 6357b127161e - b65a43f70b99 - d159735a6a9f - - de1260f8a300 - - b3490b036c5a - - d5fb354f745d - - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - 7897763d14ec + - d5887ace0dd4 - d2d1df21dfb9 - - b7829778729f - - dd7ad84f3943 - - a90db5dbaaf3 - 33368fec3b70 + - a90db5dbaaf3 + - dd7ad84f3943 + - b7829778729f - 9006e5836729 - - d5887ace0dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ed2425b9fd27 - 189e837009c9 - - 8f631679571f + - ed2425b9fd27 + - 6f4c8ad6ea01 - 505a9833ab5d - ced385aa976d - - 6f4c8ad6ea01 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e + - 9ded6109434a - e59bee4565b3 - - 356afed970b4 - 19bdfd1e6fe3 + - 356afed970b4 + - d40ed4eb0c0e - f31d376ce725 - - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 80a17897564d + - b23249f81bc4 - af40e971a8cc - - ebd801e712bc - 6dd935e4984b - - b23249f81bc4 + - 80a17897564d + - ebd801e712bc - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 59bd28f6265d - b5e35a2ca4f3 - - bb11fefb23a3 - cb1e3db43020 - - b64696992ee9 - 937ea677d437 + - 59bd28f6265d + - b64696992ee9 + - bb11fefb23a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 05bd7504fdb2 - cb4768eeca3b - - 2628f6790eda - 6bfab4a4a988 - - 05bd7504fdb2 - 6015aa0303f2 + - 2628f6790eda - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - e022dff952df + - 9e3e80cc4ad4 - 6e26c9afd301 + - 0a3a602cd1e3 - 3e44ef016b45 - - 9e3e80cc4ad4 - - e022dff952df - e92675014ac9 - 8f9f06995f98 - - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 920677cd220f - 8d09f8be269e - - 08256557922f - 5da9a0e2fb2d + - 08256557922f + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 4a53b89fa703 - 82398ba86ba7 - 37d88f41c810 - - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs owner: iuc revisions: - - 39495e107274 - 425e63adcc5d + - 39495e107274 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 7115a7b03..e2f16350c 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,26 +2,26 @@ tools: - name: integron_finder owner: iuc revisions: - - bfd290fe1588 - - 1ae00120dd24 - - 4768f7f8e93f - 392f100eebcd + - 4768f7f8e93f + - 1ae00120dd24 + - bfd290fe1588 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - ded48b36f3b7 + - 1f5641a52664 - 8e8dc9a1e3e5 - 31812e7a1315 - - 1f5641a52664 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 5c8ff92e38a9 - - 24a7a95867b0 - 17fcac7ddf54 + - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index c574c5a0b..0c960a426 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - 159b04e36791 - - d1f62024a08b - - 1c427e24fb79 - - 0840ba83860c - a9c9d768b751 - 204a131e47db + - 0840ba83860c + - d1f62024a08b + - 1c427e24fb79 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 62f5c151f..0d0b7c46a 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - a68aa6c1204a - - a8eabd2838f6 + - b28e0cfa7ba1 + - 64e2edfe7a2c - 589e7e57fd6d - - 07e8b80f278c - - ce3c7f062223 - dde39ba9c031 - - 64e2edfe7a2c - - a1a923cd89e8 - - b28e0cfa7ba1 + - ce3c7f062223 - 87ee588b3d45 - e19bebe96cd2 + - a68aa6c1204a + - a1a923cd89e8 + - a8eabd2838f6 + - 07e8b80f278c - 0a5c785ac6db tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index c5da37d7f..7d998f50c 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -10,28 +10,28 @@ tools: revisions: - 54f751e413f4 - 62c9df8382c2 - - e8ac2b53f262 - f921014aba5a + - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 2889433c7ae1 - - cbf3f518b668 - - d999e774072a - 6f386c5dc4fb + - cbf3f518b668 + - 0e3cf9594bb7 - acf4e47b734c - - e25d3acf6e68 - - a52d2d93e595 - 5edc472ec434 - - 0e3cf9594bb7 + - a52d2d93e595 + - e25d3acf6e68 + - d999e774072a + - 2889433c7ae1 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 60ffe03a2..2eac81b5e 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,12 +8,12 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - da6bd1975a71 + - 6ca543ec1bf8 - 27ee142314a9 - f4230f116196 - 710301bc46fa - 095ad4d096d1 - - 6ca543ec1bf8 + - da6bd1975a71 - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,8 +105,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -125,38 +125,38 @@ tools: owner: chemteam revisions: - 0fac8e2afc13 - - 79cfd9ead848 - - bfb65cb551d8 - - 88076940fa94 - 3b8a9d5ced85 + - 88076940fa94 + - bfb65cb551d8 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - eb6564a60136 - f5d979cb4b54 + - b46d4b4d995c + - 715cd0e87781 - 55918daa5651 - - eb6564a60136 - d532b7e5f64b - - 715cd0e87781 - - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - d2f955aea23a - fdf2cc80adb5 - f26afd1b7104 - 5579659312e6 - dae135dfd519 - - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - 319a28774da9 + - bc31d02be922 - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,34 +164,34 @@ tools: owner: chemteam revisions: - 4da9ee404eab - - 2c349b027a01 - ed736e6eee39 - - cac1886249a2 - 070e3ecc3fda + - cac1886249a2 + - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 2e219a2d9327 - da8753545526 + - 525ca7c8065f - 73008ef1f487 - c0c9a5024177 - - f197e34c33a9 - 807aa4c9293d - - 525ca7c8065f + - f197e34c33a9 + - 2e219a2d9327 - d1f803b5943c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - - c4fbab8e03c5 - 7568ae18908a - 61094e01eff9 - - 27ea4e1a3f95 + - 1809414a9454 - 2c8ed1b52bf7 + - c4fbab8e03c5 + - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -204,17 +204,17 @@ tools: owner: chemteam revisions: - 79e8ab8f1e81 + - ccfbd956a2d3 - 730ef07b90ae - d7ec25187599 - ba83f0923369 - - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -263,8 +263,8 @@ tools: owner: bgruening revisions: - b59c91adeac1 - - e6011617c748 - e2c36f62e22f + - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -342,8 +342,8 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - 9b48456a96fe + - 85fad59f8168 - d4c67ced6abc - bf99565cec1f tool_panel_section_label: ChemicalToolBox diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index de7425b1d..20596043f 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,11 +2,11 @@ tools: - name: diffbind owner: bgruening revisions: - - fa56d93f7980 - c97a786e8fb5 - - 163688bb8f73 - - 2605cbdaa7d8 - f907216064f6 + - 2605cbdaa7d8 + - fa56d93f7980 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -18,18 +18,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 495a4173006f - 640d3af5d833 - - f5d67c722d67 - - 424aefbd7777 - 86e2413cf3f8 + - 424aefbd7777 + - f5d67c722d67 + - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator @@ -42,7 +42,7 @@ tools: - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 542a34811..98376fa0e 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - 90981f86000f - - 25136a2b0cfe - 33151a38533a - 830961c48e42 + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 2dae863c8f42 - - 6cbe2f30c2d7 - baabc30154cd - 0046692724f9 + - 6cbe2f30c2d7 + - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 190ad80cc..4a5c39522 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -14,32 +14,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 3b6f97e7094c + - 0b3c3ad92827 - 367b1ed91207 - - e3cbd2287f63 - - 4a6ee918c13a - ab9350a8ab4d + - 3b6f97e7094c + - 4a6ee918c13a - f3a19509108a + - e3cbd2287f63 - 5e1240a87bcb - - a3b86937ead6 - - 0b3c3ad92827 - 6ef0b5664c69 + - a3b86937ead6 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - d4d4e9febf5c - - 584008e574b2 - - e525f9ffb9ac + - 1b5fc03380d4 - bd46669113b9 - 54ccb7e1f49a - e177a8ea0bf1 - - 501c21cce614 + - 584008e574b2 - 72ed72122deb - - 1b5fc03380d4 - 33c99804a32f - 091bb5922a82 + - 501c21cce614 + - e525f9ffb9ac + - d4d4e9febf5c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -72,15 +72,15 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -92,9 +92,9 @@ tools: - name: gffread owner: devteam revisions: + - 3e436657dcd0 - 4dea02886337 - 154d00cbbf2d - - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -112,8 +112,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 705821bf30d2 + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram @@ -139,10 +139,10 @@ tools: owner: galaxyp revisions: - b9b385097f13 - - 19e45916daf9 - - 63769c4217a7 - 26c6706bfb07 + - 19e45916daf9 - 92ac8e086317 + - 63769c4217a7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 4bf4d9568..264dd364c 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,23 +2,23 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - e821645ef8fc - - de72ba3ed6f2 - - 268e91e540ee - - 29451af70c52 - - a1ca9bccc7f2 - 5f6d123679f4 + - 268e91e540ee + - de72ba3ed6f2 - c929a006727f + - a1ca9bccc7f2 + - e821645ef8fc + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - 7a7fd0f5f15d - - bb1e4f63e0e6 - - 2d2cf5c1ea8a - 12af64f93288 + - bb1e4f63e0e6 - 5d11599b8a7d + - 2d2cf5c1ea8a - 0e143b4c3987 - 0e49b109abc2 tool_panel_section_label: DeepTools @@ -26,71 +26,71 @@ tools: - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 7c1beb6d6eca - - 81b1e3e1fc6c - - 195e98217334 - dc059492a995 - 1d848bc4585f + - 81b1e3e1fc6c + - 7c1beb6d6eca + - 195e98217334 - c06951d10364 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 - 71aa86af6762 - - a67ac707496a - - bfff7454b59a - - 3d211717a775 - 93eb012d9eed + - a67ac707496a + - 07418a30ed01 - 26e7304d6737 + - 3d211717a775 + - bfff7454b59a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - dd0b7398bb96 - - 5be24eba848d + - 56d5b797ce84 - b8858746dc1f - - 26983857c91a - 2bc10a9ca58b - 29fcfd36e90a - - 56d5b797ce84 + - dd0b7398bb96 + - 26983857c91a + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - 9384cd033f30 - - c3e012dfe21f - - ee3a1b0f45f1 - 72bfafe3330b - 7ef978dc1b8a - 7e6bcd2e5128 - e6d0bff01239 + - c3e012dfe21f + - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - a60c359ec43c - - b73e213add0c - - fb9cf9c97ec4 - - 167788df3b46 - 514fa53b5efb + - 167788df3b46 + - 9470f29702f8 - fd1275e01605 - d9a637e83828 - - 9470f29702f8 + - a60c359ec43c + - b73e213add0c + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - c34d11ea4ba6 - - 86febdcc4283 - - e479c7ca5570 - a02cfa31e9cb - 2c37ce318bc3 + - e479c7ca5570 + - 86febdcc4283 + - c34d11ea4ba6 - 5bffaa8354a1 - ca0616bb2cdf tool_panel_section_label: DeepTools @@ -98,25 +98,25 @@ tools: - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 004aea905d4d - - 01fb6a7654e6 - - 69a8621ca2f0 - - 192ef85c0b0b - - 1fcb7adc39b8 - 78f405266706 + - 69a8621ca2f0 - 2d466b530754 + - 01fb6a7654e6 + - 1fcb7adc39b8 + - 192ef85c0b0b + - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - 137c4beed34b - - db940c262830 - - d9ce4897dbb2 - - 459cfa861f0b + - 3c9f0c486cca - 9ecba5e225a6 - d580d6acd1df - - 3c9f0c486cca + - db940c262830 + - 459cfa861f0b + - d9ce4897dbb2 - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -124,83 +124,83 @@ tools: owner: bgruening revisions: - 2c66e43f1c86 - - f264afa9fa6f - - fd408d755394 - - fbe773640707 - - bad3ca889618 - 32e451def88c - bd7db9e2f2cb + - bad3ca889618 + - fd408d755394 + - f264afa9fa6f + - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 56bce3c82278 - - 7e361d147872 + - 231994413f89 + - 3b9d990a0a0e - 9368fbc49c8b + - 7e361d147872 - 7fda5607e777 - 4e12ea27f788 - - 3b9d990a0a0e - - 231994413f89 + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 - - ce4ce3316f74 - 4431f39ede55 - - c03c3384cd81 - e65d16fb2724 + - c03c3384cd81 + - ce4ce3316f74 - b1779366c8e9 - 94ca68515826 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 23f7c5f1fdaf + - b88ebb3672a1 + - d57251071381 - f8fc4e5aff9d - 793665fff0f8 - - b88ebb3672a1 - 4ed32329e0ed - - 23f7c5f1fdaf - 2da482e408b8 - - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - c60570fa602f - 512155688d98 - - a7849312d328 + - ba6efa77fb79 - e4c7985d4585 - a4dfb122e52b - - 25d830337d31 - - ba6efa77fb79 - - c60570fa602f + - a7849312d328 - 010e58e9d822 + - 25d830337d31 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 443d9a9d6d11 - aa200e4f3939 - - 4d678170d29b - - 38e3f226248b - - 69264da0ce77 - 00d869ea03a1 + - 4d678170d29b - c899e0ccff8c + - 69264da0ce77 + - 443d9a9d6d11 + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - c361b12d207a + - aac8444d6681 - d806504e96d9 - 10301d137111 - - aac8444d6681 - - 6662b1a8d326 - - c361b12d207a - a2d70c4fd406 + - 6662b1a8d326 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 67eec516c..5f8621846 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,15 +23,15 @@ tools: - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 2a6d2feda..1d754b2ab 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -4,7 +4,7 @@ tools: revisions: - 63dd26468588 - ce385837c160 - - 832c20329690 - dba489bfcd62 + - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index d0be2b0fe..0c21caf67 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 62f5fab76dfb - 29bdbc353f20 - cf1322aeb137 - - 6da3972210ee + - 62f5fab76dfb - d82648ad25a3 + - 6da3972210ee tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index c2c958c46..fc263b6d5 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,25 +8,25 @@ tools: - name: cutadapt owner: lparsons revisions: - - 660cffd8d92a - - 64172f1c1202 - - b1c926deaa2d - - c4b82dce8335 - - e4691e1589d3 - - 8c0175e03cee - - 49370cb85f0f - - de6cebe3c043 - - fe74900d6dc7 - c5e2e5902201 - - 135b80fb1ac2 - - 44e2cc14f75b - 48f587c13075 + - e4691e1589d3 + - c4b82dce8335 + - 5915ea1ec9b1 - 093678460093 + - 288f97432497 + - 135b80fb1ac2 - c053d4cad713 - - 8665bcc8b847 - - 5915ea1ec9b1 + - 660cffd8d92a + - 64172f1c1202 - 5eb7e84243f2 - - 288f97432497 + - 49370cb85f0f + - 8c0175e03cee + - 8665bcc8b847 + - b1c926deaa2d + - de6cebe3c043 + - 44e2cc14f75b + - fe74900d6dc7 - 4e5056fefd88 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,8 +34,8 @@ tools: owner: devteam revisions: - 8889eb864cef - - 9db07fd39f85 - f666895cbebd + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -60,9 +60,9 @@ tools: - name: fasta_formatter owner: devteam revisions: + - 859422bcb689 - 516b97a23d7e - 9457a20156db - - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -75,48 +75,49 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - - f773e98b26cf - f81d4362b6c1 + - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: + - cd0874854f51 - 56022eb50bbd - 0dbb995c7d35 - 9c620a950d3a - - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: + - 65b93b623c77 - 1d8fe9bc4cb0 - - c59d48774d03 - dbf9c561ef29 - - 65b93b623c77 + - c59d48774d03 + - d60c3f704da0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -136,8 +137,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -157,31 +158,31 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: + - 249c8393f2d4 - e39cc71d3ed6 - 35e38452bb3f - - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: + - 045f0e1043f7 - 74db4cffab1f - 54053ea6c77e - - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f0e7deab6518 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -202,17 +203,17 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 4bedca26c133 + - 8abdedf55101 - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 - - 90858c306551 - bdf1ce174e39 + - 90858c306551 + - cb1e251cac37 - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,35 +221,35 @@ tools: owner: devteam revisions: - 421f0af4ee95 - - 07497255281e - 7ce1891db6f5 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: + - f984bb114520 - 02f8a17a4ebd - 3599f5451ee2 - b29d37ca9e41 - - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 0c2907307ba4 - 177f0621c266 - 6027ef51ef91 - e246088b6e34 + - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 377ac2829eac - 547e8d00f11c - - 61b4cedc8934 - 73194cdd4f57 - - 377ac2829eac + - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -262,13 +263,14 @@ tools: revisions: - 2f804526f5fd - b4c6f054210a + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort @@ -295,8 +297,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -309,10 +311,10 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 8250ea3a1501 + - 24013bf85a6f - a535cf1e5da4 + - 8250ea3a1501 - e654095ab143 - - 24013bf85a6f - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -325,11 +327,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 27ac32a22ad2 - f3759eec3018 - 6a675c3aa610 - - 7accf7407811 - 828dba98cdb4 + - 7accf7407811 + - 27ac32a22ad2 - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index ac99c3dce..09e0b1c2e 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - 7b4468117008 - - e41385662e5e - ce9cd02d5b88 + - 64e9a6afdd0c + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,36 +18,36 @@ tools: - name: fastqc owner: devteam revisions: - - f2e8552cf1d0 - - 3d0c7bdf12f5 - 2c64fded1286 - - 9da02be9c6cc - - ff9530579d1f - 2b0c9d9fc6ca - 5ec9f6bceaee + - f2e8552cf1d0 + - 9da02be9c6cc + - 3d0c7bdf12f5 + - ff9530579d1f - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: + - b6b54ba71bd8 - ad116ae3f4d9 - 18a51655db17 - - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - 59003d0543cd + - cc0fd298cc17 - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,22 +62,22 @@ tools: - name: multiqc owner: iuc revisions: - - 75c93c70d094 - - 9a913cdee30e + - b2f1f75d49c4 + - c1a4b5f3b432 - 5e33b465d8d5 - abfd8a6544d7 - - b2f1f75d49c4 + - 75c93c70d094 - 1c2db0054039 + - 9a913cdee30e - bf675f34b056 - 3d93dd18d9f8 - - c1a4b5f3b432 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - cd7e644cae1d - 949f01671246 - 084bbd8ba7b8 - - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index c3759224d..7093955ea 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -16,9 +16,9 @@ tools: - name: gemini_annotate owner: iuc revisions: + - 8f53b238a360 - 0c8f7322f8fc - f2f3bc622a16 - - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -45,22 +45,22 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -87,8 +87,8 @@ tools: owner: iuc revisions: - 45296e47d565 - - cf61daf064fe - b2c25142267e + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -115,16 +115,16 @@ tools: - name: gemini_qc owner: iuc revisions: - - 86e46972e183 - 9e83673fa6d2 + - 86e46972e183 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - 666f60a9331a - 840fb4850be3 - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -144,15 +144,15 @@ tools: - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index f729cfa4c..0fe27413f 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,22 +9,22 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 4bb888286..28ecd046a 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,9 +2,9 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - b39347891609 - - e9df53a75f3c - c1b437242fee + - e9df53a75f3c + - b39347891609 - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,50 +18,50 @@ tools: owner: iuc revisions: - 28587613264f - - e063168e0a81 - 1c58de56d587 + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 7068f48d0ef9 + - 83c7d564b128 + - 1790dcf3c32d + - 6ea73833cf67 - 4df8de2d0e48 - - f8054ea1c365 - - 734abc7ac21d + - e407b9da183a + - ba931a59dd59 - c441583adae5 - - 9a776b080193 - 1ec814014652 - - 4317d3cb6cba - - 6591f049cf7e - - e08a7ad4378b - - e407b9da183a - - 5e6237d58b0c + - 9a776b080193 + - 653e89d73fc4 + - f5ea3ce9b9b0 - 516a54ddf218 - 69ebb7f46e45 - - 6ea73833cf67 + - 4317d3cb6cba - aad3885b3216 - - 1790dcf3c32d - - 83c7d564b128 - - 653e89d73fc4 - - f5ea3ce9b9b0 - - ba931a59dd59 + - 7068f48d0ef9 + - e08a7ad4378b + - 734abc7ac21d + - f8054ea1c365 + - 6591f049cf7e + - 5e6237d58b0c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 34758ab8aaa4 - - 21a560af5913 - 9aaa46d45472 - 75b3b3d0adbf + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 468c71dac78a - bfdc6a7ffd3a + - 468c71dac78a - af5eccf83605 - 054483e27a35 tool_panel_section_label: Get Data diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index a3c2c8860..09b80db23 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 740057a5126d + - ae9994cf526f - df7356989ac1 - - 7f13dc906cb9 - c4bde687c846 + - 740057a5126d + - 290a11559985 - a64dc31ab7f2 - 4b519282a05b - fd59d783248a - - ae9994cf526f - - 290a11559985 + - 7f13dc906cb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -29,8 +29,8 @@ tools: owner: devteam revisions: - 7cf5b1d072b5 - - f95284aa2946 - 867ab348287d + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,21 +42,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - '566197475670' - 3b37b1b1c3a7 - ca7cb0eaad62 - - '566197475670' - - 374e9062d874 - 53460afd5115 + - 374e9062d874 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - d3a9e32672ec - - 3d059e9c2fba + - 10515715c940 - da4c086cff5b + - 3d059e9c2fba + - d3a9e32672ec - 391a4cc45fea - - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -74,12 +74,12 @@ tools: - name: ggplot2_point owner: iuc revisions: + - e3a675da7fd0 + - 299307abd804 + - 5fe1dc76176e - 1acf88921176 - d0fc8b746d57 - - 5fe1dc76176e - - e3a675da7fd0 - 3b12bf9b4b87 - - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -97,8 +97,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 97e3b735ed22 - 5d6f8f0bef7c + - 97e3b735ed22 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -123,17 +123,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 - - 112eb40ba6cf - - 4542035c1075 - - 2bb2e07a7a21 - - 836d1aa3e89a - a6e57ff585c0 - - 667e17248bfe - ca2def38369c - 1cfc579079a6 + - 2bb2e07a7a21 - 17359b808b01 + - 836d1aa3e89a + - 667e17248bfe - fd5dbf0f732e + - 112eb40ba6cf + - 6cd09d7b5f37 + - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -166,15 +166,16 @@ tools: owner: bgruening revisions: - 1c5dcef5ce0f - - 62e3a4e8c54c + - f234e2e59d76 - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -187,8 +188,8 @@ tools: owner: iuc revisions: - 6c571966cfb9 - - 7c9417381ad5 - 44c66e8d21e6 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -200,23 +201,23 @@ tools: - name: pygenometracks owner: iuc revisions: + - 7dd841a32245 - 2824d77cd8f8 - - a1abfa420d9d - - 326a3db8d9d1 - - 4ac4e7083b7e - - 360df4999907 - 14e7c35f3d00 - - 7dd841a32245 + - 360df4999907 - 36b848d5f3ec + - a1abfa420d9d + - 4ac4e7083b7e + - 326a3db8d9d1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd - - 44608d0193ed - 83c573f2e73c + - 44608d0193ed - 2f557f6abbfb + - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index cae7545a7..2e0d45587 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,15 +21,15 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 7779b9dcf040 - 22bd5861706d + - 7779b9dcf040 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -42,15 +42,15 @@ tools: - name: scanpy_filter_genes owner: ebi-gxa revisions: - - cc64914b0cf4 - 23d838d1569d + - cc64914b0cf4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - fc4b3b46dc9d - 36735850e461 + - fc4b3b46dc9d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers @@ -70,8 +70,8 @@ tools: - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - 9d76c3d6dff6 - c9da9192eee5 + - 9d76c3d6dff6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat @@ -84,30 +84,30 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - 94697510d55f - - ff6decc0f432 - 9a2f72d7dbd2 + - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 70cb0596ffef - 53ce0e336840 + - 70cb0596ffef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -127,8 +127,8 @@ tools: - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -141,22 +141,22 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - d18ed15697bb + - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -169,8 +169,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - ea91cfd0444e - 767a675b5254 - 0f98603d0116 + - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index b6c826ac4..0d60b7ab2 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,31 +2,31 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - ed2cca6b5de4 + - 29f66c353bcb - 9edf8894a22d + - ed2cca6b5de4 - 921a2da49a0c - - 29f66c353bcb - a4c13ddcc8ee tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - - ec4b948dc6f0 - 5746d61f0a91 + - ec4b948dc6f0 - 755df866ad0c + - d404277cc87a - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - - 9e357a8b2ec3 + - 03dd3c16ae4e - 11fa44ee0603 - 4d511437b1e5 - - 03dd3c16ae4e + - 9e357a8b2ec3 + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca @@ -42,11 +42,11 @@ tools: - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 12d51d7be66f - 7babd8a46fe0 - - b63363075c2e - - 9939786dd9c9 - 5308ca68ef3d + - 12d51d7be66f + - 9939786dd9c9 + - b63363075c2e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 9c25d094f..e54229371 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -4,42 +4,42 @@ tools: revisions: - 0c777d708acc - 8bccb36e055a - - 81f0cbca04a7 - - 7db4fc31dbee - 3df9f0a4bf34 + - 7db4fc31dbee + - 81f0cbca04a7 - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - 2436a8807ad1 - - 5791a7f65275 - 5bc8cdc17fd0 + - 5791a7f65275 + - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: + - 6ad1d3cfdea1 - 9d47aabda459 - e576b73a2e2f - - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 70316d792fc9 - b1c2c210813c + - 70316d792fc9 - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - f70b215d155c + - dba87c4b32d3 - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,9 +53,9 @@ tools: owner: imgteam revisions: - b07f4839ca77 + - fcadded98e61 - 85edbb7a436b - 10eed33aa9b2 - - fcadded98e61 - f3360fbeda64 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,9 +77,9 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - eb6c08714244 - e917a2424690 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -100,9 +100,9 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - cdf8e3c57dae - ef4aed1d34c4 + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image @@ -116,33 +116,33 @@ tools: - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - 11f177b1a59e - f2ed92b011a9 - bace5a93a97c - - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - d0178bdcd00e - - f24c370e5ea4 - f8fa0f6718a3 + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - ad271f78a87a - 31d195bedf6d - 3245681b2f6d - - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 87d4d92d7487 - - 993faa34333b - b6eec6087271 + - 993faa34333b + - 87d4d92d7487 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -156,49 +156,49 @@ tools: - name: cp_mask_image owner: bgruening revisions: + - 3a05117669cf - b178453ea8d1 - 667a513e67e4 - - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - ac5bea85a391 - - 2564f461de62 - a1a961c46d4b + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - a32c3f810ade - 91e03287f285 + - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - 5499dc6f8ac1 - 8536b1ae0254 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 980aed9e8fd5 - e52c75a28c4b - 407925835dd9 + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape @@ -212,9 +212,9 @@ tools: - name: cp_measure_texture owner: bgruening revisions: - - b76841ee5560 - 035a58c7f54a - 80b200ae516b + - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -227,17 +227,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - 27edbb90ab2b - 33f4fa1413fb + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -249,8 +249,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -263,8 +263,8 @@ tools: owner: imgteam revisions: - 7b6d9412c7f8 - - 236ec78b2e53 - f8b4eada923c + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 1c6ae3c74..13a27deff 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -3,13 +3,13 @@ tools: owner: iuc revisions: - 78bbd17d0703 - - 40737febe339 + - f362150bef41 - 3a72fede57ce - - e319b5b65879 - a38934e303b9 - - f362150bef41 - - d6e72da3ec35 + - 40737febe339 - 3e4f434a69c6 + - d6e72da3ec35 + - e319b5b65879 - 1069f6db0a0e - e4ee04da1c19 tool_panel_section_label: iVar @@ -17,78 +17,78 @@ tools: - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e - - f91cfb73d369 - 0135f1d487a0 + - c88553ec696e - fcbeda41d0ac - - 7fe36019c073 + - 8f8df367470d + - f91cfb73d369 - 2b95d5c04908 - 72ddd32392cd - - 618297d23022 - 9537184d421f - - 8f8df367470d + - 618297d23022 + - 7fe36019c073 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - ad0dc9f4c9e2 - - fafb3d685fa9 - - d7e79eb3bcb3 - 2cf4a1cafc16 + - d7e79eb3bcb3 + - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - a1c2aecd7a0d - - 9eaadf03e0df - - 7f1cfa4c0e32 - - bd2a7d1316b9 - - 28a6f1908fcc - - 5dc33613c288 - - 8c05afb547fa - 8d36959b000d - - ee2beb764a7b - - 3d18f8c3c0f6 + - 28a6f1908fcc + - bd2a7d1316b9 - 94df24c6bc00 - - 6a1515bb0687 - 43aac8d29685 - ee29337f905c + - 6a1515bb0687 + - 5dc33613c288 + - a1c2aecd7a0d + - ee2beb764a7b + - 7f1cfa4c0e32 + - 9eaadf03e0df + - 3d18f8c3c0f6 + - 8c05afb547fa tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - a250929be21b - - c092052ed673 - e3bb03cf207a + - c092052ed673 + - 5671e1d3d5ee - 364f4ffec275 - - 5d6ed46cc101 - 8858fa037a15 - - 5671e1d3d5ee - - 86a20ae274fc - - bcaa0d571ce2 - 9f978da6528a + - a250929be21b + - 86a20ae274fc + - 5d6ed46cc101 - cb903c9dc33d - - db536ad45f28 - d37ede8589b2 + - db536ad45f28 + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - c5c9f02b6167 - - e1a015876aa9 - - 584beffa972b - - abbc8041e8ec - - ed28dd32141c - - 3b6a16d82c1b - - 194e3ceee923 - - f95f403841ad - 12d66d0d05ac + - 230b05597996 + - abbc8041e8ec - 38b91a3190cd - 49236b03e4fd - - 230b05597996 + - f95f403841ad + - e1a015876aa9 + - c5c9f02b6167 + - 194e3ceee923 + - ed28dd32141c + - 584beffa972b + - 3b6a16d82c1b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index fe942883b..3fbf82ce0 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - 0f1724dd59d2 + - 17e3b698dd52 - f198773344e4 - b8a457820315 - - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a + - 22c2a1ac7ae3 - ac092723240d - - ba0c40780ecf - a513e3fbb4c5 - - 22c2a1ac7ae3 + - 374cb875d38a + - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 1b4e918fd..cab7cda80 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,36 +2,36 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - - 66d7efc06000 - 522137aaa9c4 + - 66d7efc06000 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - 8a794e6d3388 - - 4d81e3e2fb63 - f22a9297440f + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - f1b9a42d6809 - 818f9b69d8a0 - - e1317b5502fa - b6ef6d0cb6b7 + - e1317b5502fa + - f1b9a42d6809 - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 1588f9076e32 - 947c2eacccb8 - - c80db5d6fd8c - 05143043ca13 + - 1588f9076e32 + - c80db5d6fd8c - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,53 +39,53 @@ tools: owner: bgruening revisions: - 25b46af53232 - - 83228baae3c5 - 29e4122c90de - - 9991c4ddde14 - 1552b8cb4a94 + - 83228baae3c5 + - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 - - 060ca94ac049 - a07ab242b0b5 - f3dfa4bdf87e + - 841a6cc5fc58 - 1a53edc4b438 + - 060ca94ac049 - 53616c8b0865 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 40f4447733b2 - - 2fc89dcd41c8 - 91c4e3331208 - - 927586a18553 + - 40f4447733b2 - dc4b5fd604a6 + - 927586a18553 - d4808d5b83da + - 2fc89dcd41c8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - - 25ab6b4e376e - 7626ea9c2e1b - - e5a5ad882f1f - 36e8d6d5d01b - 301e07345c93 + - 25ab6b4e376e + - e5a5ad882f1f + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb - - 02d2be90dedb - - f9639b488779 - b7c3e9a3b954 - 0630258dcf35 + - 02d2be90dedb + - 4ed102b922cb + - f9639b488779 - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -94,7 +94,7 @@ tools: revisions: - ec69cbe34b73 - caeb57858702 - - 14180f9c831e - 61634a87efc7 + - 14180f9c831e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 00d49be8e..ec2ad9e83 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - d5ceb9f3c25b - - cd659e8cc5fa - - 937aa69e715f - f6877ad76b00 - a6d65b0c67af - - 17062a0decb7 - - 3ba8d4563129 - - 017aba02828d - 749c918495f7 - - 0d4acadabb04 + - 3ba8d4563129 - 03e9b2fbc005 + - 17062a0decb7 + - d5ceb9f3c25b + - cd659e8cc5fa + - 0d4acadabb04 + - 017aba02828d + - 937aa69e715f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: + - 2477830927ec - 53646aaaafef + - 64f11cf59c6e - e188dc7a68e6 - dfd8b7f78c37 - 3fe632431b68 - - 64f11cf59c6e - - 2477830927ec tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -49,44 +49,44 @@ tools: owner: devteam revisions: - 60afcc2c1d05 + - e7f19d6a9af8 - 3e1ea2facca6 - 37b497aa133f - - e7f19d6a9af8 - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - f54f5baedfdd - - b3eab4b67562 + - 8c6cd2650d1f - 5cc34c3f440d - - 11a0d50a54e6 - - 09b53c1d4ab1 - - 037c6e54df11 - - c0c2d0941de8 - 77b2770508f6 - - 8c6cd2650d1f - - 3f4d6399997b - 53c0b7a1a0c3 - 6b1e195506a3 + - b3eab4b67562 + - 3f4d6399997b + - 11a0d50a54e6 + - 09b53c1d4ab1 + - 037c6e54df11 - be1d967337e4 + - f54f5baedfdd + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 178bdbdb6d24 - - ec9cbd6b9a49 - - 9ee34ba73ebf - - b8f5f6e87f5c - 42ce70172b72 - - e403d27e8f24 - 79b885ce78d7 - - 13022c3d3076 - - 00fbfac99d39 + - e403d27e8f24 - 5ef7ec16b04f + - ec9cbd6b9a49 - 1cd2511a396e + - 00fbfac99d39 + - 178bdbdb6d24 + - 13022c3d3076 + - b8f5f6e87f5c + - 9ee34ba73ebf tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index cb7b79553..b56f9bfc1 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -75,11 +75,13 @@ tools: owner: recetox revisions: - b9cc12600553 + - c990df6afc24 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: + - 00e66c401366 - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,11 +89,13 @@ tools: owner: recetox revisions: - 84af792d3a78 + - d7b517f2c5fe tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: + - 9e3c83d2afc3 - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -99,11 +103,13 @@ tools: owner: recetox revisions: - f04610d25411 + - b576ed720711 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: + - 1d443ed476a1 - 03bc9b7f40f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,6 +123,7 @@ tools: owner: recetox revisions: - 8147d93d372d + - 1d74ae228df3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -141,12 +148,14 @@ tools: owner: recetox revisions: - 9ff95a1a2705 + - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - 0cf68b536cd1 + - 500f473df7e4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -158,6 +167,7 @@ tools: - name: msmetaenhancer owner: recetox revisions: + - b5467dead5b1 - 90745ecc5e9f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -206,6 +216,7 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: + - f2c1d0bbb074 - 5f2b58dadb39 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -213,41 +224,48 @@ tools: owner: recetox revisions: - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - 7b42ee54d757 + - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - 149b9cc7499b + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - 481d769e2f7a + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: + - 9064aecc78a7 - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: + - b3413f335327 - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - 17a48d0a80f4 - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -255,11 +273,13 @@ tools: owner: recetox revisions: - 99d118321d5f + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: + - ffbabefbd2e2 - d90187b0f247 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -273,6 +293,7 @@ tools: owner: recetox revisions: - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -290,6 +311,7 @@ tools: - name: rmassbank owner: recetox revisions: + - 5a6bb93ec656 - 0b28816c1c2c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 0fe028df3..f7263c35d 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -9,15 +9,15 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: combine_metaphlan2_humann2 @@ -29,101 +29,101 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 + - 65db807336bc - 7c2100246a2f - - 5b5a7af9fbb4 + - 76d3d2b10738 - 63f86089423e - - 65db807336bc + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 00f5005840fa - - 84fd33a60b35 - - 96336c6a2bb7 - 1c35dadbe76f + - 84fd33a60b35 - 18a502a9d287 + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - a9f4a217dcd6 - - addaf9d22850 + - 34e55239e68b - f732237754fc - e8fba04706d3 - - 34e55239e68b + - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 8c202e741d68 - - 0776d824d896 - 04c15826a0b8 + - 0776d824d896 - 75403243703a + - 8c202e741d68 - 5fe3edf19b9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - e96bbb9e24ea + - 43c99742158b - 75c8945b0da2 + - 1c9b3bcd4261 - 8470de786d47 - - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f - - 35176674168c + - 84743da21318 - 5c865a382933 + - 35176674168c - 1d75bd0595e2 - - 84743da21318 + - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 78faebd0879c - - 555ccac8a4c5 - 32c9ea835770 - - ac72310b038a - 8daf4564ccda + - ac72310b038a + - 78faebd0879c + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - cae017b76acb + - a58e4a43f49c - d60df8727f59 - 7b8cb2b02978 - - a58e4a43f49c - f947b4bb5107 - - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7f3b59dee073 - - 073608a50ac3 - 7136e9ab70db - 1bc3657cd694 - 04144473e59e + - 073608a50ac3 + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 9058d8943303 - - 19299bb1c6af - a7817705348e - d943081510da + - 9058d8943303 - 0a1224c4b781 + - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -136,11 +136,11 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 65d52c693b8e - - a68b985913ab - - c4db8c4de66f - dbf1798c0dcc + - a68b985913ab - f8f56dd6449f + - c4db8c4de66f + - 65d52c693b8e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -153,8 +153,8 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -168,24 +168,24 @@ tools: owner: iuc revisions: - 6aad8ca3918b - - bd7a9c6efb10 - e66ab198ec15 + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - d77397f09da1 - - c6676a890f50 - b084117133af + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - 7f208f1eb64f - - cad93abecac9 - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -223,25 +223,25 @@ tools: revisions: - c409a495841f - 79706f10d680 - - e88b731dad59 - 31c6d107e7a5 + - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c - - 172920f67a84 + - 71ea608ddfa3 - d24841f5c3d2 + - 172920f67a84 + - 714d5a28cc5c - 094ad9c068af - - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - 4137b492233e + - a293a742194f - a4d7148ccee4 - d7e9a3c41657 - 12fb63b5f63f @@ -256,11 +256,11 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 64bc7acc22a9 - - 97f7bb0851e7 - 6fcb8ac37a3e - - cf87759761eb - e2c71b852aba + - 64bc7acc22a9 + - cf87759761eb + - 97f7bb0851e7 - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -281,17 +281,17 @@ tools: revisions: - 5e5a999ffaa9 - 2d35528d2141 - - c82508e76ad1 - - 4033827c76b8 - 080ea153677c + - 4033827c76b8 + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - - 95bf7479d53c - 6b7622dda516 + - 95bf7479d53c + - 2cd76b089570 - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -353,17 +353,17 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe - - cdee7158adf3 - 328c607150ff - 4a9da2b6c2e3 + - 20e2f64aa1fe + - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -421,8 +421,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 4960abe31b4d + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -434,8 +434,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -471,22 +471,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b - - 27250f92a01a - - 05ad7d35ce92 - - 2cff76cf35c6 - - e073891b2afc - - 327d9f4cc95f - 7f5d7b0e9884 + - e073891b2afc - 0270541aaf46 + - 05ad7d35ce92 + - 327d9f4cc95f + - 2cff76cf35c6 + - 27250f92a01a + - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 76bc4efa1aeb - - 708abf08a626 - eb50e7eca3dc + - 708abf08a626 + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -552,18 +552,18 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - 1a6cdf55390f - - fd69c607b43f - a16313517e55 - - b89b0765695d - 289b3807e80c + - fd69c607b43f + - b89b0765695d - a92a632c4d9b - ff8f55893e7d - 6dee4abadccb @@ -599,11 +599,13 @@ tools: owner: iuc revisions: - 6034c3f3ecf0 + - 2f47a294ef49 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: + - 3b133b8d578a - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -611,23 +613,27 @@ tools: owner: iuc revisions: - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: + - 73b56418e7f4 - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -635,6 +641,7 @@ tools: owner: iuc revisions: - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -646,8 +653,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 8e2ac1b8f70a - 0ba7dfaa941d + - 8e2ac1b8f70a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -696,13 +703,13 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - 3b22de20bd4b - 4d83eccf5f81 - 141afacabcfa - - 4b9a8031ab74 + - 2fd4d4c9c5c2 + - 3b22de20bd4b - be818ae858e4 - aeaa20b96ef2 + - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 76bc50eb9..2f857a822 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 938523e33..531ad4753 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - bdfbaf0c10aa - - 9baa871cb1d1 - - 8b67dd48fec1 - - 94b8c6013083 - - 098506c54016 + - a74dbfee5a86 - cd07731e4434 + - 94b8c6013083 - 9422c5a87ee2 - - 2263989660f5 - - 48c13389050d - - a74dbfee5a86 + - 8b67dd48fec1 + - bdfbaf0c10aa - 80f03df2e2ce + - 098506c54016 - 9eeb13a92d79 + - 9baa871cb1d1 + - 48c13389050d - 6ae5a7b5a0a2 + - 2263989660f5 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - d7ce0ec78e51 - aaa0d6a8b808 - - bc3831dd65c1 - be78f13134e2 - - d390fe1567dc - - f0af8936ed41 + - bc3831dd65c1 - fc2e49f91e52 - - 2e093badc689 - - c18157c68134 - c44f824c051a + - 3ff17bad4006 + - 2e093badc689 + - f0af8936ed41 + - d7ce0ec78e51 + - '764845535798' + - d390fe1567dc - 4a60927aaca5 + - c18157c68134 - f14193ec1f50 - - '764845535798' - 5abf2c2249aa - - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,8 +53,8 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -66,20 +66,20 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - - 15974dd17515 - - a65296ffb4a0 - f1a5908ea2cb - - bf28a8cff401 - c5908940967d + - a65296ffb4a0 - 6f28e90db932 + - 15974dd17515 + - f0d493f8f84f + - bf28a8cff401 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,23 +87,23 @@ tools: owner: iuc revisions: - 60698466facd - - c9685bc0407c - 5561a1193611 + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 57f042937ba7 - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b + - 57f042937ba7 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - fb43e8887350 - 4fc0cb2ac8ae + - fb43e8887350 - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -118,8 +118,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 - cf3c9489c088 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 9507c0e97..341913ad0 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,9 +2,9 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 7c47b3c9e493 - 18a8d140ec6f - 28928576e1ea + - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado @@ -17,21 +17,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - - 72b5e9dda577 - 79e9a869f40e + - 72b5e9dda577 + - cb34f00cc10f - fc8804320156 - - a7228a7ea146 - 0e9e7fcdd543 + - a7228a7ea146 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - fa11aa8103b2 - db25ec99c3ea - - d6cddc06aeae - 18505fe2bdb1 - - fa11aa8103b2 + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -43,22 +43,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - 222669c4afb6 - - eb746fa6f514 - - edf6d4003fad - - 2bf63b38ee9b - 19f3b583a9b3 - ec699520444c - cc36773a3681 - - 0f5f4a208660 - 43815fa60f3a + - eb746fa6f514 + - 2bf63b38ee9b + - 222669c4afb6 + - edf6d4003fad + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -71,58 +71,58 @@ tools: owner: iuc revisions: - 0f1c34698076 - - edbb6c5028f5 - - 7b379e98b9a9 - - a3c4fe6f49ab - - 645159bcee2d - a02b8b3f5a0c + - 645159bcee2d + - a3c4fe6f49ab + - 7b379e98b9a9 + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - 3b6f94fc7e1d + - d219b6d8158a - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - 90a922f32523 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - - d376944466bf - 449e9aeded2d + - d376944466bf + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - 93d623d9979c - 5f76b20953e5 + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -134,8 +134,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -147,8 +147,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 338d15b8d6fb - 336791b5665f + - 338d15b8d6fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -160,15 +160,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 4fe6b96aff72 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 618adc957..b721f9055 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -27,19 +27,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - d74850cf4e42 - adfd6bf710bd - - 97b1b5ad1cda - 3e73c97f025d + - 97b1b5ad1cda - baceff842902 + - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - - 9dd107db92c2 - 83da94c0e4a6 + - 9dd107db92c2 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,19 +51,19 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 13851aefa67a - - ed1518ce2237 - 19b6a2f0dbe2 - - e4b4837f06f5 + - ed1518ce2237 - 2f27f3b86827 - 1e34d2e3d285 + - e4b4837f06f5 + - 13851aefa67a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -82,16 +82,16 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - 48a42ca61006 + - 5711fc06a63e - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -104,15 +104,15 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -124,23 +124,23 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - - 172815da3d41 - b4b2b284230a - 52b6a4d98009 + - 27a6a256cd23 + - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - 2814c058a087 + - 629464b96c2e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder @@ -159,8 +159,8 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - 19bbd19b74b3 + - 87febc68b45b - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -193,18 +193,18 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - a88f077f1994 - 9c43baa60906 + - 4ba60cb14cb0 - 0cb27ea69dc1 + - d8dc037e3c13 - 5fe20c915fa6 - - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite @@ -218,10 +218,10 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: - - 29c738066906 - - df30a2f1db55 - 6e24e79d3d69 - ed7a967cb11b + - df30a2f1db55 + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -254,17 +254,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - c520a52b5174 - 64deddb6a8ec - d63c1442407f - - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - 9946bc39c834 - 94a50db37d1a + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -318,8 +318,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -775,8 +775,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -788,11 +788,11 @@ tools: - name: salsa owner: iuc revisions: + - ab5b7f6b7198 + - f77f7a7f3b83 - ba7b0f11e470 - - 9a22227bb6d0 - 58a870ef434c - - f77f7a7f3b83 - - ab5b7f6b7198 + - 9a22227bb6d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 8d359a697..de81c79f0 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,64 +33,64 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 26de3a7b1cb9 - - 5a7c56a5cc08 + - b89cac5156ec + - '841557158611' + - cce7b18495e4 + - 3f59ebfbfe3d + - d033ffc1c161 - d7c7ef3353fe - - 8834daeb9892 - - 81e66674859e + - 5a7c56a5cc08 - 6a457678efcb - - c78f3d7dd1db - - 3b8b5bde0bd9 - - cce7b18495e4 + - 81e66674859e - f73435dc282b - - a6619171428e - - '841557158611' - 107d3ba7024a - - d033ffc1c161 - f04a1264e2a2 - - b89cac5156ec - - 3f59ebfbfe3d + - 3b8b5bde0bd9 + - a6619171428e + - 26de3a7b1cb9 + - c78f3d7dd1db + - 8834daeb9892 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - 7a2092844346 + - 6223845127ea + - 3b96e92e8ec3 + - 6a726db04d4b + - df47d4845b62 - b0af57c1a968 - - e75442c7f4da - 4755f52427c4 + - 5b777002c2de - 88c4aa435ded - 5fcd1ece3a6e - - 6223845127ea + - a185b079b095 - 02b8758214b0 - - df47d4845b62 - - 659517798cc4 - - 5b777002c2de - - 6a726db04d4b - - aa8cc71438cf + - e75442c7f4da - 6283babe736e - - 7a2092844346 - - a185b079b095 - - 3b96e92e8ec3 + - aa8cc71438cf + - 659517798cc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 24d024316465 + - b8476e82ac20 + - 111bd54f6bc4 - d1c340a5664b - f97743d52b87 + - 24d024316465 - 70acec670c30 - - 111bd54f6bc4 - c1d53e95327f - - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 4f6349228462 - daddf188c13f - feb40665d7cd + - 4f6349228462 - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -103,33 +103,33 @@ tools: - name: pangolin owner: iuc revisions: - - a2099fb98cdb + - 36912871ccdc + - ca337cce3888 + - 83a69484cb87 + - b6abccb1f25b + - 42a174224817 - 437e28791761 - - 2fa9d4f1b48f - - 5f8727ff21e7 - - 7bb8726be37c - - 14ae456b8cc5 - - abf6dbe8c9d7 - 3a43c3982401 - - ca0d8cf80567 - 81804a978fc0 - - 2f1019071464 - - 9d61d3fa046c + - 14ae456b8cc5 + - a2099fb98cdb + - 5f8727ff21e7 + - ca0d8cf80567 + - b7e297c2ede6 + - 2fa9d4f1b48f + - abf6dbe8c9d7 + - 7bb8726be37c - 03ed9524dcd1 - - ca337cce3888 - - b6abccb1f25b - - 42a174224817 + - 9d61d3fa046c - 8ad84c5753ea - - b7e297c2ede6 - - 36912871ccdc - - 83a69484cb87 + - 2f1019071464 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -141,22 +141,23 @@ tools: - name: raxml owner: iuc revisions: - - b1e68bbe4cef - - ea30d3089354 - ba29b5e2a4be - - 73a469f7dc96 - a4b71be30c3c + - ea30d3089354 + - 73a469f7dc96 + - b1e68bbe4cef - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - e88a7de55d6e - dbe2b2204555 - - 91887494eb97 + - f1ccc8a6eb05 - 809e42326fc2 + - 9b2b122d0415 + - e88a7de55d6e - 15ac71df11a0 - - f1ccc8a6eb05 + - 91887494eb97 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index b94c0ef5e..15c17fac3 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - b502c227b5e6 + - 7d34178f2812 - 881d7645d1bf - - f6ced08779c4 - f9242e01365a - - 7d34178f2812 - - fc288950c3b7 - - a1f0b3f4b781 + - f6ced08779c4 - 1aac2a13842a + - b502c227b5e6 - 3f254c5ced1d + - fc288950c3b7 + - a1f0b3f4b781 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 36521f9a8..b1c0ce8e6 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - a58f7eb0df2c - - 6ab1a261520a - c0e71cb2bd1b - 2f7702fd0a4c - - eb085b3dbaf8 - - d00e15139065 - ca90d17ff51b - - 3bd420ec162d - 5b85006245f3 - - 7fbec959cf2b - e4a053d67e24 + - d00e15139065 + - 6ab1a261520a + - a58f7eb0df2c + - eb085b3dbaf8 + - 3bd420ec162d + - 7fbec959cf2b tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index 2283661bb..f022b0e24 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,11 +2,11 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 277dc652246e + - 4c177985028a - b574b84afc4d - - 0a18ac48ac53 - ece627528a78 - - 4c177985028a + - 277dc652246e + - 0a18ac48ac53 - f28ad96b76dc - b18329a8ac14 tool_panel_section_label: Proteomics @@ -14,81 +14,81 @@ tools: - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - - a9a28e46d54a + - bf06d196e23d - e215f71d7983 - - b41107d8fe89 + - 525f201b86c1 - e988563cc6e5 - - bf06d196e23d + - b41107d8fe89 + - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 + - bb6397b94018 - 56da27be956a - 4fbffddde8cd - - bb6397b94018 + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - f23d67e28cc8 - - 528fb09022be - - b8c79e70516d - - a8157342d9a3 - 890845926d4b + - a8157342d9a3 + - b8c79e70516d + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - ae304a72db7b - - 80600735685d - - 59e85306eae5 - 25b83cbd596a - - a69865da6f80 - a95a82eb4d50 + - 80600735685d + - a69865da6f80 + - ae304a72db7b + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - f1897eb07081 + - 83aac7741200 + - 798da6bdff3d + - ed9ed1e6cca2 - 611d80c0e29d + - f1897eb07081 - e0669b1854b1 - - ed9ed1e6cca2 - - 798da6bdff3d - - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - - 74b61bf5bc4b - - a7fb9b395ddf - d426a9107a6c + - a7fb9b395ddf + - 74b61bf5bc4b + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - 82f6c2f4332d - cc430977c8ff - df2187f9013b - 91f0f5922011 - - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - 10566783d718 - - ba92b59cd529 - - c5aa9fca18c6 - 1693b2126f30 + - c5aa9fca18c6 - 043f9c91f686 + - ba92b59cd529 - d2483487e077 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,8 +109,8 @@ tools: revisions: - ae4dc0c041f9 - bf0728e000cd - - ff8c9e0e8a7b - 9fa3dbf06f17 + - ff8c9e0e8a7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,23 +129,23 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - - 1c5cbf8f79ce - 0fa397f4f40b + - 1c5cbf8f79ce + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - fb192dd6658a - 36880dfd9fa7 + - fb192dd6658a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -157,55 +157,55 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - d286ff4600dd + - 160538a890a6 - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 7f432d87c82c - - 4d17fcdeb8ff - - 1f39c833f65f - - 2133b0be850a + - 37d669de2828 - 837224ad1694 + - 2133b0be850a - e42225f8a659 - - 9c52362ae7bb - f522c08e900c - - 37d669de2828 + - 7f432d87c82c + - 1f39c833f65f - 97a7f34fcb6a + - 4d17fcdeb8ff + - 9c52362ae7bb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: + - 85b8866f06d7 + - e63db1aa82ee - 0ed07016d668 - a72ac2c7cc5b - - e63db1aa82ee - - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 1974224d63c2 - - 352b37c66d97 - 990b4560ead7 + - 352b37c66d97 - 767c1d761aaf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -214,8 +214,8 @@ tools: revisions: - 4f359549383c - 99450519d727 - - 35cc7ca0bdc7 - deaf035bbe9f + - 35cc7ca0bdc7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample @@ -230,18 +230,18 @@ tools: - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 + - da986f83631b - d2eac53666f0 - d46d64e7964d - - da986f83631b + - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - - 9bf325045235 - 8bd7734309f6 + - 9bf325045235 + - 944b43462104 - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -261,26 +261,26 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - - 593839e1f2c3 - - 8212e342e482 - de7593c29499 + - 8212e342e482 + - 593839e1f2c3 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - 4e77b8f12cd3 - - 01dbaf6a57e0 - - f4be248c3d47 - 8960fb791701 + - f4be248c3d47 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -293,20 +293,20 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 + - 518b1730cf2a - f7fef900f5b2 - - 6ccbf9a2072c + - 9cdf15d3cfc8 - c9eff69a7c62 - - 518b1730cf2a + - 6ccbf9a2072c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: + - 5e948629bc73 - dff6c756eee5 - ca88bd28f116 - 9876bda3ec53 - - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter @@ -314,118 +314,118 @@ tools: revisions: - 41859bbdc16e - 658494a2cb00 - - 890025d6e426 - 1595601708ec + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 6634cad7d797 + - 5ad0b5bf1deb - 9b7977080f6d - 2a93a25f0599 - - 5ad0b5bf1deb - - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - fe4e4587d265 - - d6878d27f051 - 05d5e1ddc985 + - d6878d27f051 - 0bb5056cb775 + - fe4e4587d265 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - 4af67edd5aef - febd569ad26f + - 5ad830edc021 - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc + - 27cba4c5fc42 - 92352a475eed + - b2fc8da99bcc - 39e8fde08881 - - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 9e26f5c770f8 - d413dc49d650 - 0efbc235f314 - d3546bb9fd8e + - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - c28f13cab67a - 8a04ed1c1d1b - - ca1740533b59 - 3720e349ba2a - - c28f13cab67a + - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - a5d785af0ad8 - - c55dddc5844a - ca799a7246e7 - - 382cde407f81 + - a5d785af0ad8 - c427a8628cbe + - 382cde407f81 + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - adca857b4884 - - 8ddb7bab1138 - - 39caaa778d2e - b5d0905419da + - 39caaa778d2e + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 18f93351f8b6 - - f817513840a9 + - 34e7afee141d - 8d4db262964c - 1c5f31b8d632 - - 34e7afee141d + - f817513840a9 + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - 986e03d3201e - - c69f69d7867a + - 5d9f175dff81 - 111c3a00136d + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - be74a8cd7d66 - - 476b5e296979 - 0e52c85f3b15 - 4204882495f2 + - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: + - f5ec766d80cf - c18d8efa4474 - - 2b2a7551a857 - a407b6790342 - - f5ec766d80cf + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -439,10 +439,10 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - 2735db4dd8d9 - - bf32e0bcf554 - 8098330f6d91 + - 2735db4dd8d9 - ee860980edc6 + - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -457,56 +457,56 @@ tools: owner: galaxyp revisions: - de7a553552a6 - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - 1bf940c18d93 - e8f64a7dc470 - c1809c05ae8c + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - 496cf619e311 - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: + - d4396637b9f5 - c99d5004b74f - 0bddef8d144e - - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 89254095cbf6 - - 8b814eafce2c - 4bb198c0bd3e + - 8b814eafce2c + - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - - d31426ef20f6 - 6e8cc5ed2a9b + - d31426ef20f6 + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -520,20 +520,20 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - 6b01678ec2fc - - 3d8d4ada5405 - 5ae104d0da6e + - decc397c3b7e + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - dd173849c3d8 - - d6aca689dd48 - 539a3a4dcc9e + - d6aca689dd48 - e039cc5c7aed - 5182338d5e7c + - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -571,8 +571,8 @@ tools: revisions: - c8b225c69a7f - fb52e95a370c - - 7f6a1f27553e - 5c2a97a234d6 + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -585,21 +585,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 3ec27b4cee7c - - 07ff622ec007 - - 943a34df6047 - 7fdd9119cc4f - - 1beff3ddce58 - - da885ca16cb2 + - 07ff622ec007 - a72c48001f7c - 3634c90301af + - da885ca16cb2 + - 3ec27b4cee7c + - 943a34df6047 + - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -653,10 +653,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - - 12692567c7f9 - - 1a5690a5eedc - 265c35540faa + - 1a5690a5eedc + - 12692567c7f9 + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index bf015d3f9..52697721b 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 6e07990fb..1bfb45ce4 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,23 +2,23 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 2f1d464ebfd2 - - 110a346daf36 - - cd5f98911089 - 289b7d6b69a4 + - cd5f98911089 - 42201b90e3f4 + - 110a346daf36 - e345aadf914f + - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - - 0cd2df8af811 - - 42d9087b4789 - c207119ba5f6 - - fcce77c09289 - 8501601a118d + - fcce77c09289 + - 0cd2df8af811 + - 42d9087b4789 + - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -26,64 +26,64 @@ tools: revisions: - ad5ab22ffe24 - 04db7fd6b238 - - 405a212b32ab + - 33486216eec0 - 421c33b8bf17 - 89eb29319bf4 - - 33486216eec0 + - 405a212b32ab tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 - 7b72fde3d27e + - f6e91108b7b1 + - eb784fa07f80 - fa51dc5e8386 - - 7370bb65bad4 - 1d839ead7ad3 - - f6e91108b7b1 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - d30e36c48c93 - - 1544278c272e - - 3d70c2996730 - 8a55d29c8fcf - a3e86cd9cac7 + - 3d70c2996730 + - 1544278c272e - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: + - 7b881f5f5ad5 + - e2db212d64ad - a5969aa9347e - 564c33e5c3e3 - - e2db212d64ad - - 887cf585cafc - b242deb58952 - - 7b881f5f5ad5 + - 887cf585cafc tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - 9a171f9a450b - - e897c74a48bb + - b4bab607eb05 - bd5ff77e2036 - 8cff84759bf6 - - b4bab607eb05 + - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 + - 5e10f396979e - 4f65e343ecdf - adc7a7610d4f - - 6dafad990086 - 33f0793edf93 - - 5e10f396979e + - 6dafad990086 + - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -92,42 +92,42 @@ tools: - c287418eb288 - 4e280b27a831 - 17d39bf0a63a - - c5d7050e4ad7 - - 43e3eeb2e0ec - 97575d01f06b + - 43e3eeb2e0ec + - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - d9bf483266a1 - a819ec3b362d + - 09b8edb56d80 + - 0b8c84a7fdb5 - 9586f08634c0 - cd034465d4a4 - - 0b8c84a7fdb5 - - d9bf483266a1 - - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 95351dd0fd3f + - 2645575d1bf2 - a9c34a289493 - 69842dd5aa48 + - 95351dd0fd3f - bf0e43ab0416 - a4b4bd84f69e - - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - 912f904a6e1e - - d033e1ccb386 - - cfb504394ae1 - d1fda11e602f - - 8a35a3bc6752 - bb0475c884ff + - 8a35a3bc6752 + - cfb504394ae1 + - d033e1ccb386 + - 912f904a6e1e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - d504d945a655 - d1fad35bdb4a - 95286af4139b - - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index fbc6e4c1e..6e8e9d4b3 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,8 +2,8 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - 31f8063eedea + - cf01dd6c6b1f - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -11,8 +11,8 @@ tools: owner: iuc revisions: - 125d20cb23d7 - - 703a2cb3fb38 - 32e542c2a773 + - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: chira_collapse @@ -95,15 +95,15 @@ tools: owner: devteam revisions: - cf747d1bd79a - - 6a6717a5f421 - 86285ddd4512 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -127,48 +127,48 @@ tools: - name: describe_samples owner: iuc revisions: + - e3b16fd7dd08 - 3b36efd62b3e - - 0693ccd171c4 - 8f0181aacb7a - - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 9a882d108833 - - 6a3a025714d3 - 0696db066a5b - - 8fe98f7094de + - 6a3a025714d3 - d027d1f4984e - - cd9874cb9019 - 24a09ca67621 + - cd9874cb9019 + - 9a882d108833 + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: + - b47c006d90c5 + - df929f257179 - 2872c633f07e - 9a7c5b6d8f1e - - df929f257179 - 62adf13b86ea - - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - a8305cf0c951 - - 070900306913 - - 5bf899c13979 - - 0cb907a2a810 - 6e53e565fc6a - - 3d89af8a44f0 - - f2843df56434 - df0c8d0a5992 + - 5bf899c13979 + - 9bdff28ae1b1 + - f2843df56434 + - 070900306913 + - 3d89af8a44f0 + - 0cb907a2a810 - 334ce9b1bac5 - 555659de7321 - - 9bdff28ae1b1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -187,17 +187,17 @@ tools: - name: featurecounts owner: iuc revisions: - - 7db9d3ea71c9 - - 38b6d12edc68 - - f9d49f5cb597 + - ea04b737afa0 - a37612abf7f9 + - 90d16db017d7 + - f3a5f075498f - a56fbe2d6ba7 + - 38b6d12edc68 + - 6f66ae7c5f7a - af814359d244 - - f3a5f075498f - e6a2a912677a - - 90d16db017d7 - - ea04b737afa0 - - 6f66ae7c5f7a + - f9d49f5cb597 + - 7db9d3ea71c9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -221,8 +221,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 + - 0f710191a66d - f99dd58de04f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -235,21 +235,21 @@ tools: - name: hisat2 owner: iuc revisions: + - 6ab42baa56e9 - f4af63aaf57a - - 26371a1df031 - - 3fb01a8c902d - d4b55e2beb12 - a86e80d3c09c + - 26371a1df031 - 6c19daec423d - - 6ab42baa56e9 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - 4418229c501e - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -262,32 +262,32 @@ tools: owner: iuc revisions: - 01247aaf0a10 + - 5ae5c312d718 - 87c11c05d238 - - ce5d418183c5 - 1c75aa5de15e - - 5ae5c312d718 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - 10c98fab6c5a - c971db6f0fe5 + - 40985510cd98 - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - e827f9aae031 - - d6f5fa4ee473 - - 0921444c832d - - 119b069fc845 - - 58c35179ebf0 - 97e06a4c7c75 - - 708348a17fa1 + - 119b069fc845 + - 0921444c832d - 32511f586472 + - d6f5fa4ee473 + - e827f9aae031 + - 708348a17fa1 + - 58c35179ebf0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -299,8 +299,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -324,8 +324,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -343,20 +343,20 @@ tools: - name: rgrnastar owner: iuc revisions: - - b9e04854e2bb - - c772497b2c32 + - 99b17b74a8cd - 79de45b5069b + - c772497b2c32 + - 5ec75f5dae3c - e132e7d02a3e - - 0a563fd2f22e - - 980d2a2e1180 + - 7ed2edc1337f + - b9e04854e2bb - 4df95e2d7f61 - - b0f2be869d6d - - 3ea5a2a63fa2 - c7c55b694974 - - 7ed2edc1337f - - 99b17b74a8cd + - 980d2a2e1180 - 4074fc1940e2 - - 5ec75f5dae3c + - b0f2be869d6d + - 3ea5a2a63fa2 + - 0a563fd2f22e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -368,13 +368,13 @@ tools: - name: salmon owner: bgruening revisions: - - 53e9709776a0 - - cc05793bb896 - - 15cd64d7c58b - - e3d32471da11 - - f4d5237a84f6 - ebab418107f5 + - f4d5237a84f6 - 2c0ca397d302 + - e3d32471da11 + - 15cd64d7c58b + - 53e9709776a0 + - cc05793bb896 - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -383,21 +383,21 @@ tools: revisions: - 56242ff81c84 - fab6ff46e019 - - 8c28affc7c48 - c0fd285eb553 + - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - dd4df992d93d - cbf488da3b2c - - 258d696dbd7e - cef79931dda5 - 914cfcba0ec8 - - ae618321f34a - 76d290331481 - 1ebd14235b92 - - dd4df992d93d + - 258d696dbd7e + - ae618321f34a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -427,10 +427,10 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - ffd1300599a1 - - d0d4cef4f967 + - c6334cb383ff - 0db979fead3a + - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -438,62 +438,62 @@ tools: revisions: - 74217fbfba4d - ba3720d7e68b - - bcc5f03f1900 - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - c2b82a94493e - - 478f36effca1 - 2fb4ee002432 - 56162e446004 + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - 9ff3765e7172 - fab23c3b5258 - 3f4094b6a565 + - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c - - 870ac06dff8e - be3f26533209 - 4687ecf0eb2d + - 34a018cbee9c + - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 65e7dea767ea - 33406f5a445c - - c5fbddcac63a - - 5192f657f305 + - 65e7dea767ea - 05ab8d5e04a2 + - 5192f657f305 + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - a35cba31d904 - e406ac71165d - - 6f0fb35b799c - 1fdb25a8384d - - a35cba31d904 + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - 37a1129c89d2 + - 7c7fbf13aadd - c2c039e421af - 964b7efe2639 - - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -508,9 +508,9 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - - 9871104ea630 - 1812dbc5bb7b + - 9871104ea630 + - 04bb8bb7c198 - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -529,14 +529,14 @@ tools: - name: trinity owner: iuc revisions: - - 9fa24d5aac68 - - cee61b3fcf78 + - d84caa5a98ad + - 8f1c3df4dd49 + - 48636f857c4b - d2bc35f3d1c5 + - cee61b3fcf78 - db1f362cca3e - - 48636f857c4b - 32b86cd8eb50 - - 8f1c3df4dd49 - - d84caa5a98ad + - 9fa24d5aac68 - c9cfec002f71 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index ee91e8906..b41c54fe8 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: + - 080fd5739bb4 - 1a052c827e88 - 473382134e56 - - 080fd5739bb4 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index fa60dc6e3..ac8f004f1 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,18 +2,18 @@ tools: - name: bam_to_sam owner: devteam revisions: + - a53efedba9e7 - 88eedb4abea0 - 10184eaa85fc - - a53efedba9e7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: + - 108db6635177 + - cb20f99fd45b - 993b19f20c76 - 1dfd95ee241e - - cb20f99fd45b - - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -25,8 +25,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -77,15 +77,15 @@ tools: revisions: - 19ece8afbaab - e7fd6754d093 - - 5f8e69cc4c6e - 30a201c9c310 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -110,8 +110,8 @@ tools: - name: sam_to_bam owner: devteam revisions: - - 9bd1568619cd - cf1ffd88f895 + - 9bd1568619cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -123,26 +123,26 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 46c6639921f1 - 6856f8a01905 + - 12749212f61b - 9149ad20699a + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - c89806670ab9 + - 92ec40abcdcf - 06dc50b7b711 + - c89806670ab9 - 33208952b99d - - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,10 +160,10 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 720217c23995 - - 66e23b11feae - - a8d69aee190e - b3d99709fe1a + - a8d69aee190e + - 66e23b11feae + - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate @@ -175,21 +175,21 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - 22970df7a40e - cc61ade70eb8 - - fefd89ab563c - - fe34990e5ce7 - db17d5321bad + - 22970df7a40e + - fe34990e5ce7 + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - - 7a6034296ae9 - fa5d3e61e429 - - 88b8c2916784 - 7def34e6cf4d + - 7a6034296ae9 + - 88b8c2916784 + - 811fc2d75ad4 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -201,35 +201,35 @@ tools: - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 - - 65a38e8c8e2a - 740ce0a18f0d - 36677f429310 + - 65a38e8c8e2a + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - - b61f5d6a7f25 - - 9da0311ab1dd - 8da515fbc1bf + - 9da0311ab1dd + - 329deb17a9f7 - 583abf29fc8e + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: + - d7b4851d1971 - 30388d878f81 - db000c6007a0 - - d7b4851d1971 - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -242,8 +242,8 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - a4a10c7924d1 + - 344fc91e1bfd - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -251,29 +251,29 @@ tools: owner: devteam revisions: - 6c2c1836728b - - a577ea614bed - - e613c1ad4c4c - cab3f8d35989 + - e613c1ad4c4c + - a577ea614bed tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - - b7f7826ef1cd - bcedabb53ddf - 5d9ae78f34d3 + - 135c85f4cfaf - bd850490c7f1 + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f + - 145f6d74ff5e + - 24c5d43cb545 - 5a08c09b9311 - fed4aa48ba09 - - 24c5d43cb545 - - 145f6d74ff5e + - 3a0efe14891f - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -281,12 +281,12 @@ tools: owner: iuc revisions: - 6be888be75f9 - - b01db2684fa5 - - bf328cec6a42 - 0dbf49c414ae - - c370440f901e - - b72793637686 - - 350bbc5c2ffd - 5826298f6a73 + - 350bbc5c2ffd + - bf328cec6a42 + - b01db2684fa5 + - b72793637686 + - c370440f901e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index 331baad1a..119903537 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d - - 480d9e9d156b - - 4aab5ae907b6 - - 5cb6146337d8 - 59bb6d34fca6 + - 4aab5ae907b6 + - a62c4a11a67d - d147d6455873 - - ea5e944f447d + - 5cb6146337d8 + - 480d9e9d156b - 6f6537780379 + - ea5e944f447d tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index d70829f6d..e0cff9a9e 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,77 +8,77 @@ tools: - name: alevin owner: bgruening revisions: - - c9944a2600f1 - - f2000bc73102 - ecb9ea6269ee - - e4c01dcece8b - e32b215b7c04 + - f2000bc73102 + - c9944a2600f1 + - e4c01dcece8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: + - c0b037b12765 - 707023fa62fe - e1c3c2f2a834 - - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - 32e547223c9e - fb9e030ffae4 - cfc3f5a57dc6 - - 93dd15e13e6a - - 32e547223c9e - 00712416fdaa + - 93dd15e13e6a - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 038e32885fec - - 6f0d0c784f09 - b9fac48532eb + - 6f0d0c784f09 - ee98d611afc6 - - 39e945f0b2c1 + - 038e32885fec - 688357ad5e61 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - d4af736e7b83 + - 9bd945a03d7b - 43cb7b5a6fe7 - b85871dd69f9 - - d4af736e7b83 - ed4996a16f7f - 3d748954434b - - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - fe75d2414dc0 - - a4774b7b2e85 - 2e8022f1923c + - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: + - 0e70b2dfe4be - 4fff5a293013 - - 02b1fe7aed76 - 769d815e4b0d - - 0e70b2dfe4be + - 02b1fe7aed76 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - - aa4a6f0916b4 - 344c2af50552 + - aa4a6f0916b4 + - c29e7bb492bf - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,17 +87,17 @@ tools: revisions: - c32347702e12 - 050cf43887d3 - - 5b7c81b35b89 - b13d3e4c48e1 + - 5b7c81b35b89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 1d77986f9ddc - 239193b96d72 - - ae969fdb8442 + - 1d77986f9ddc - 02fc39c8610d + - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -133,11 +133,11 @@ tools: - name: dropletutils owner: iuc revisions: + - 2c1200fba922 + - cdf4443d5625 - 8855361fcfc5 - - a9caad671439 - cfe1e6c28d95 - - cdf4443d5625 - - 2c1200fba922 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -167,22 +167,22 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 9d42a6133690 - 57aeaf6b237d + - 9d42a6133690 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 163fd744e235 - 23b8d6b8960c + - 163fd744e235 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint @@ -195,8 +195,8 @@ tools: - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - b892fa1fcaec - a63e9713c39d + - b892fa1fcaec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -216,15 +216,15 @@ tools: - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - f881c94fb3b3 - 40fee49bc6c3 + - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - 2dccb6bb0add - e06265d204f6 + - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts @@ -237,15 +237,15 @@ tools: - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - c72fa6cb8817 - 8a11d70b6cd8 + - c72fa6cb8817 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization @@ -258,8 +258,8 @@ tools: - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - 2ba6cee8e4db - c0737631eea1 + - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix @@ -293,15 +293,15 @@ tools: - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - 972dcccb5bbc + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 7f7c6ead2d0d - 409396ea5cf0 + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo @@ -342,8 +342,8 @@ tools: - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - dd9988943f53 - ea5d67ec94ab + - dd9988943f53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -356,29 +356,29 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - 337705015ee8 - b4e780e93c91 + - 337705015ee8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - 58de3c7c8e89 - 8d203e74869b + - 58de3c7c8e89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - 36dfa2825a59 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -396,8 +396,8 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - f36828ebdc54 + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations @@ -410,11 +410,11 @@ tools: - name: modify_loom owner: iuc revisions: - - e98619de2776 + - 7784821452ac - 59be31ac9dc3 - 4b0adaa31c95 + - e98619de2776 - eeab712b0b99 - - 7784821452ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -427,8 +427,8 @@ tools: owner: bgruening revisions: - 282819d09a4f - - 7ffaa0968da3 - 2cfd0db49bbc + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -460,18 +460,18 @@ tools: - name: raceid_clustering owner: iuc revisions: - - 0bff0ee0683a + - a4b734cd253b + - f911a64454fb - 7e014059a88d - c4f39bf4a068 - - f911a64454fb - - a4b734cd253b + - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - 7608d5faee41 - 43c146e25a43 + - 7608d5faee41 - b83fbc90161e - d45f092caf24 tool_panel_section_label: Single-cell @@ -487,19 +487,19 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - a6821f856a1e + - df8e4e54d367 - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 + - 2af7c5086a96 - 44b935f2271b + - c92d0f9338c5 - e93b008c637a - 72979cac22b2 - - 2af7c5086a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -517,89 +517,92 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 6f83f8fd381f + - 64ff3ef24fae - 4d8f983cd751 + - 77b91b9bdf52 - 6acb08931836 - - b2df381a6004 - aaa5da8e73a9 - - 77b91b9bdf52 + - b2df381a6004 + - 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owner: iuc revisions: - - dbbe1ea8ecb1 - - aa0c474463c2 + - 6f5349dd5c49 - f7446fd8d5e7 - 9b0cdb8cf6be + - 70fa84e99463 - 95777145cb92 - 6adf98e782f3 - 7647e5cd1b8b - - 6f5349dd5c49 + - aa0c474463c2 + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - bf2017df9837 - - 73ab2ac53d06 - - 215733a383f2 - - c65fce500915 - - 458e8f43a775 - e66884b1c1a5 + - 73ab2ac53d06 - d18e7a6e5cd4 + - 458e8f43a775 + - 215733a383f2 - f2f6c703da06 + - c65fce500915 + - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - b834074a9aff + - fd808de478b1 - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - b7ea9f09c02f - 652923ce664f + - b7ea9f09c02f - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -612,8 +615,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - 81e5bdff4853 + - 2e41b35b5bdd - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -862,8 +865,8 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - afb90d3485df + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif @@ -883,8 +886,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index f5e1bd01c..42cdf5e63 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -33,9 +33,9 @@ tools: owner: iuc revisions: - 746e8e4bf929 - - 4c07ddedc198 - - 419027d822d6 - 2f3c6f2dcf39 + - 419027d822d6 + - 4c07ddedc198 - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,8 +49,8 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -70,8 +70,8 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - 6c29c7e347e8 + - 7a15159140d1 - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 4c4ec859c31a - 9c3e1d3235c8 - - 7442b94d6a1e - - 840f29aad145 - aef56d0e7a61 - b1eda492f063 - - 4c4ec859c31a + - 7442b94d6a1e + - 840f29aad145 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - 07843f917990 - - 30d21a6041f6 + - 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tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view owner: iuc revisions: - - d1f8f55f564d - c2ab91a0d506 - 3a233c8eb814 - - e6b5cbbf449b - 3ca3de4e5291 - 38d75661c235 - 59fa8742285e + - d1f8f55f564d + - e6b5cbbf449b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo @@ -391,8 +391,8 @@ tools: - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -405,8 +405,8 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -419,8 +419,8 @@ tools: - name: vcfcombine owner: devteam revisions: - - 1f0ba67cc85a - 53edb91ed051 + - 1f0ba67cc85a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples @@ -440,44 +440,44 @@ tools: - name: vcffilter owner: devteam revisions: - - fa24bf0598f4 - 6b935ab36d7b - eae7c08ebb6f + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - b24e368ae7b1 - f285aa6bdcfb + - b24e368ae7b1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -511,8 +511,8 @@ tools: - name: vcfsort owner: devteam revisions: - - dd44c3f416c3 - 5b7120c66efc + - dd44c3f416c3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_isec @@ -524,7 +524,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/viral_tools.yml b/usegalaxy.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/usegalaxy.org.au/viral_tools.yml +++ b/usegalaxy.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu