From 367885110e5fee6ecbffbae84947b5a189d9a1f6 Mon Sep 17 00:00:00 2001 From: admin Date: Tue, 15 Oct 2024 03:11:29 +0000 Subject: [PATCH] Jenkins install build 1675. --- automated_tool_installation_log.tsv | 1 + requests/gprofiler_gost@latest.yml | 5 - staging.gvl.org.au/annotation.yml | 134 ++++---- staging.gvl.org.au/assembly.yml | 264 ++++++++-------- staging.gvl.org.au/bacterial_typing.yml | 8 +- staging.gvl.org.au/bb_tools.yml | 8 +- staging.gvl.org.au/bed.yml | 16 +- staging.gvl.org.au/blast.yml | 10 +- staging.gvl.org.au/chemicaltoolbox.yml | 56 ++-- staging.gvl.org.au/chip_seq.yml | 12 +- staging.gvl.org.au/collection_operations.yml | 6 +- staging.gvl.org.au/convert_formats.yml | 52 +-- staging.gvl.org.au/deeptools.yml | 132 ++++---- staging.gvl.org.au/dna_metabarcoding.yml | 6 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 6 +- staging.gvl.org.au/fastafastq.yml | 126 ++++---- staging.gvl.org.au/fastq_quality_control.yml | 34 +- staging.gvl.org.au/filter_and_sort.yml | 4 +- staging.gvl.org.au/gemini_tools.yml | 28 +- staging.gvl.org.au/genome_editing.yml | 2 +- staging.gvl.org.au/get_data.yml | 38 +-- staging.gvl.org.au/graphdisplay_data.yml | 78 ++--- staging.gvl.org.au/hca_single_cell.yml | 28 +- staging.gvl.org.au/hicexplorer.yml | 24 +- staging.gvl.org.au/imaging.yml | 58 ++-- staging.gvl.org.au/ivar.yml | 70 ++--- .../join_subtract_and_group.yml | 8 +- staging.gvl.org.au/machine_learning.yml | 46 +-- staging.gvl.org.au/mapping.yml | 50 +-- staging.gvl.org.au/metabolomics.yml | 32 +- staging.gvl.org.au/metagenomic_analysis.yml | 176 +++++------ staging.gvl.org.au/mothur.yml | 6 +- staging.gvl.org.au/multiple_alignments.yml | 58 ++-- staging.gvl.org.au/nanopore.yml | 54 ++-- staging.gvl.org.au/none.yml | 60 ++-- staging.gvl.org.au/phylogenetics.yml | 98 +++--- staging.gvl.org.au/picard.yml | 12 +- staging.gvl.org.au/proteomic_ai.yml | 16 +- staging.gvl.org.au/proteomics.yml | 198 ++++++------ staging.gvl.org.au/rad_seq.yml | 78 ++--- staging.gvl.org.au/rna_seq.yml | 180 +++++------ staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 76 ++--- staging.gvl.org.au/send_data.yml | 10 +- staging.gvl.org.au/single_cell.yml | 198 ++++++------ staging.gvl.org.au/statistics.yml | 26 +- staging.gvl.org.au/text_manipulation.yml | 42 +-- staging.gvl.org.au/variant_calling.yml | 42 +-- staging.gvl.org.au/vcfbcf.yml | 270 ++++++++-------- staging.gvl.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 112 +++---- usegalaxy.org.au/assembly.yml | 262 ++++++++-------- usegalaxy.org.au/bacterial_typing.yml | 10 +- usegalaxy.org.au/bb_tools.yml | 8 +- usegalaxy.org.au/bed.yml | 16 +- usegalaxy.org.au/blast.yml | 14 +- usegalaxy.org.au/chemicaltoolbox.yml | 56 ++-- usegalaxy.org.au/chip_seq.yml | 10 +- usegalaxy.org.au/collection_operations.yml | 12 +- usegalaxy.org.au/convert_formats.yml | 36 +-- usegalaxy.org.au/deeptools.yml | 122 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 8 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 6 +- usegalaxy.org.au/fastafastq.yml | 120 +++---- usegalaxy.org.au/fastq_quality_control.yml | 34 +- usegalaxy.org.au/filter_and_sort.yml | 4 +- usegalaxy.org.au/gemini_tools.yml | 16 +- usegalaxy.org.au/genome_editing.yml | 6 +- usegalaxy.org.au/get_data.yml | 42 +-- usegalaxy.org.au/graphdisplay_data.yml | 64 ++-- usegalaxy.org.au/hca_single_cell.yml | 22 +- usegalaxy.org.au/hicexplorer.yml | 26 +- usegalaxy.org.au/imaging.yml | 74 ++--- usegalaxy.org.au/ivar.yml | 66 ++-- usegalaxy.org.au/join_subtract_and_group.yml | 4 +- usegalaxy.org.au/machine_learning.yml | 50 +-- usegalaxy.org.au/mapping.yml | 56 ++-- usegalaxy.org.au/metabolomics.yml | 38 +-- usegalaxy.org.au/metagenomic_analysis.yml | 164 +++++----- usegalaxy.org.au/mothur.yml | 2 +- usegalaxy.org.au/multiple_alignments.yml | 60 ++-- usegalaxy.org.au/nanopore.yml | 50 +-- usegalaxy.org.au/none.yml | 54 ++-- usegalaxy.org.au/phylogenetics.yml | 94 +++--- usegalaxy.org.au/picard.yml | 12 +- usegalaxy.org.au/proteomic_ai.yml | 12 +- usegalaxy.org.au/proteomics.yml | 188 +++++------ usegalaxy.org.au/rad_seq.yml | 68 ++-- usegalaxy.org.au/rna_seq.yml | 178 +++++------ usegalaxy.org.au/rseqc.yml | 4 +- usegalaxy.org.au/sambam.yml | 82 ++--- usegalaxy.org.au/send_data.yml | 10 +- usegalaxy.org.au/single_cell.yml | 198 ++++++------ usegalaxy.org.au/statistics.yml | 32 +- usegalaxy.org.au/text_manipulation.yml | 42 +-- usegalaxy.org.au/variant_calling.yml | 32 +- usegalaxy.org.au/vcfbcf.yml | 296 +++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 100 files changed, 2918 insertions(+), 2910 deletions(-) delete mode 100644 requests/gprofiler_gost@latest.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 98a9aa2a7..a9340252f 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7943,3 +7943,4 @@ Update 213 09/10/24 20:29:28 umi_tools_group False Installed iuc 428735be9764 42 Update 213 09/10/24 20:35:18 umi_tools_whitelist False Installed iuc e4e12f0b3af1 e4e12f0b3af1 4/4 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_213/install_log.txt Install 1671 15/10/24 02:20:57 plot_ragtag_paf True Shed-tools error galaxy-australia latest Staging Installation Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1671/install_log.txt Install 1673 15/10/24 02:33:30 plot_ragtag_paf True Tests failed galaxy-australia 94e0834ae4ed latest Staging Testing 0/3 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1673/install_log.txt +Install 1675 15/10/24 03:11:07 gprofiler_gost True Tests failed iuc bf39cdd007f5 latest Staging Testing 0/2 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1675/install_log.txt diff --git a/requests/gprofiler_gost@latest.yml b/requests/gprofiler_gost@latest.yml deleted file mode 100644 index a0a49dbd5..000000000 --- a/requests/gprofiler_gost@latest.yml +++ /dev/null @@ -1,5 +0,0 @@ -tools: -- name: gprofiler_gost - owner: iuc - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index d84236479..eb15ad45b 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - - 3f3e247c053d + - 4efdca267d51 - c2ef298da409 - 78c75f134c16 - - 4efdca267d51 + - 6e9aea89e388 + - 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 @@ -33,23 +33,23 @@ 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 - b5d8e5475247 - - 133f36c29579 - - cd2480f35935 - 44018dd6b447 - 1aae04680c4b - - fe3ca740a485 + - cd2480f35935 - a79ee60b6926 - - 4f2967b27e67 - f29602ae449e + - 3e1f6f6d557e + - 133f36c29579 + - fe3ca740a485 + - 4f2967b27e67 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,19 +62,19 @@ tools: - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 + - 6519ebe25019 - f1e653756174 - 7be22100e5e1 - - 6519ebe25019 + - dc027fa56d55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 28433faa6e42 - ca6d970d931c - - bd0e53f3a891 - 09855551d713 + - bd0e53f3a891 + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -82,16 +82,16 @@ tools: revisions: - 92eee5f31117 - da5f1924bb2e - - 728dacaf08a9 - d77802fe76f7 + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - fe48aa4ccd5e - 7355bbf5e05f - 8fd427007e93 - - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -124,9 +124,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 63662ae295d6 - - d9c3016f7283 - 9d1fbff733cf + - d9c3016f7283 + - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -150,61 +150,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 14f588312c56 - - b6b5cd37f2a2 - - 9c15ca7e764e - - 582fd74dc2a1 - 756376aeb1ae - 3bbe70fef6df + - 582fd74dc2a1 + - b6b5cd37f2a2 + - 9c15ca7e764e - 9f2455341fac + - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - a230ea445788 - - 8e1ace8f77c6 - 30fb23d4c31c - 989f7c061f35 + - 73428a792541 + - 8e1ace8f77c6 - 0ffe5be70caf - 1691af4a0d17 - - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: + - 57c6718cbfcc - e94187d661df + - 0418d28136de - 563a19373357 + - 5a5ae61da69c - 494f0bb4a993 - - 0418d28136de - 30f08d74024f - - 5a5ae61da69c - - 57c6718cbfcc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - - f31125bb85ea + - d6c7106b7b2e + - 2bba2ff070d9 - 1bc5a03faf2e + - f31125bb85ea + - 7abc5f6dd595 - f77d7b685bb3 - - 2bba2ff070d9 - - d6c7106b7b2e - 4b96ced19f75 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d77fdcca400e - - 520e30695ec3 - - d3af38b9c7e1 - - b3cf4684e9c7 - 54961e026fe4 - - 52af33194019 + - b3cf4684e9c7 + - d3af38b9c7e1 + - 520e30695ec3 + - d77fdcca400e - fed64e676186 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -217,8 +217,8 @@ tools: owner: iuc revisions: - 79261884facd - - 07d7991bf205 - 2aea122fbd25 + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -230,10 +230,10 @@ tools: - name: goseq owner: iuc revisions: - - 8b3e3657034e - - ef2ad746b589 - - 43798b4caee0 - 602de62d995b + - 43798b4caee0 + - ef2ad746b589 + - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -242,6 +242,12 @@ tools: - de3e053bd6a5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: gprofiler_gost + owner: iuc + revisions: + - bf39cdd007f5 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: helixer owner: genouest revisions: @@ -257,16 +263,16 @@ 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: - - c55643c3d813 - - 98cafcbd2578 - 74810db257cc + - 98cafcbd2578 + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -291,18 +297,18 @@ tools: - name: maker owner: iuc revisions: - - 370c210d9541 - 3c1a01127868 - d46d803ca6cc + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 - - c8ac28e8ac44 + - 624606f7c996 - b815ec682418 + - c8ac28e8ac44 - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -345,11 +351,11 @@ tools: - name: prokka owner: crs4 revisions: + - eaee459f3d69 - 8a22554cdde2 - d643e3b03500 - - bf68eb663bc3 - - eaee459f3d69 - a17498c603ec + - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -361,15 +367,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -394,20 +400,20 @@ tools: owner: iuc revisions: - 5a29ab10dba6 - - cfcf33df7fc0 - - 268d162b9c49 + - 6322be79bd8e + - 8f92c2b26e6d - 5b80f544c67f - 5c7b70713fb5 + - 268d162b9c49 + - cfcf33df7fc0 - 68693743661e - - 6322be79bd8e - - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - 2b3e65a4252f + - 09d6806c609e - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -420,8 +426,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -433,24 +439,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - ac8250086ac3 - - 37213cf56392 - - ba6f87115e13 - - 4839e590cb26 - - 809dfc93d593 - 45083d070fb8 - 037a11682176 - - e1a9d6fd258d - - d03af1c7002c + - ac8250086ac3 + - 809dfc93d593 + - ba6f87115e13 - 200c378d85f3 - 51dd22484644 + - e1a9d6fd258d + - 37213cf56392 + - 4839e590cb26 + - d03af1c7002c 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/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index c72df8020..15ea9dce6 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,27 +2,27 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - 0e93176640ac + - fa5259cc561b + - 8f1b150a2487 + - 841084c5fc46 + - 0124fce4654a - 553bfe8bd0b5 - - a929ce596a34 + - 7547fcab5d19 - 890b794c997d - d6d5ccc2c581 - - 0124fce4654a - - 841084c5fc46 - - fa5259cc561b - - 8f1b150a2487 + - 0e93176640ac + - a929ce596a34 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - 067592b6b312 - - b9e31c5c01c7 - - ddddce450736 - 94fe43e75ddc - - 21e491ad532a + - ddddce450736 - b2860df42e16 + - b9e31c5c01c7 + - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,48 +35,48 @@ tools: - name: bionano_scaffold owner: bgruening revisions: + - 3371c5bdc17a - 22286dab5aa1 + - a7f16f24e9a1 - faee8629b460 - 5258e18bbe23 - - a7f16f24e9a1 - - 3371c5bdc17a 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: - - bb935709506a - - cf13a1e03e5b - - 1440ae06552f - - 46ae58b1d792 - 41030a6c03b7 - - ea8146ee148f + - e824f5d958d0 - 2dd755c1c6ff + - 1440ae06552f + - ea8146ee148f + - e4bd1e99bacf + - 602fb8e63aa7 - 4048d82f0c88 + - 46ae58b1d792 + - cf13a1e03e5b - 5ecdeca79a0d - - 94170eee0ad8 - 2babe6d5c561 - - e4bd1e99bacf - - 0d243f458b53 - f18f0b887c31 + - 94170eee0ad8 + - bb935709506a - 1e62c28ba91d - - e824f5d958d0 - - 602fb8e63aa7 + - 0d243f458b53 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - - c5b7390290b1 - 86f150c8019d + - c5b7390290b1 + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -88,42 +88,42 @@ tools: - name: flye owner: bgruening revisions: - - 291923e6f276 - - 1ce9b1d72ec3 - - cb8dfd28c16f - - 276f5d8712d5 - - e27815e82dd4 - - 3ee0ef312022 - 3e4f8642c77e + - 3ee0ef312022 - 1f0769f0b56b + - 276f5d8712d5 + - cb8dfd28c16f + - 1ce9b1d72ec3 + - 291923e6f276 + - e27815e82dd4 - 8d4f03b5fe9d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 460fad600dce - - b2f674562a18 - 3169a38c2656 + - b2f674562a18 - 01210c4e9144 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - ba88bc5a6446 - - 8b330a577046 + - 06bcf65179fb - 7348b69e5109 + - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - 3ef480892a9f - - 5127a713de83 - - 690c2caa367e - 3fba9c77550a + - 690c2caa367e + - 5127a713de83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -135,23 +135,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 41cea2aa2dce - - da9d8bf98802 - - 5f625c63b8bc - - 045c7c3d8e59 + - f3c89da3af16 + - ec9e21e9c71b + - 0ee0c3089254 + - df25d4fb79b7 - 9ef6920c3089 - - 284a1cb82b61 + - 2061fb3b81b4 + - 3f7be05a1597 - 5bec28269d95 - - 0ee0c3089254 - - f3c89da3af16 - - 71740308d412 - 60024a528cbd - - 2061fb3b81b4 - - 366a11d316a7 - - ec9e21e9c71b + - 284a1cb82b61 + - 5f625c63b8bc - 6505bd37670d - - 3f7be05a1597 - - df25d4fb79b7 + - 71740308d412 + - da9d8bf98802 + - 41cea2aa2dce + - 045c7c3d8e59 + - 366a11d316a7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -169,43 +169,43 @@ tools: - name: megahit owner: iuc revisions: - - de387b2b2803 - a96f3ad4e0d8 - 7518ee87b53d - 14ddfc8ffb93 + - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - - 09c589057ee8 - f8113c25bc6b + - 9d79beb19ac3 - d7edbc9c3a07 + - 39edec572bae + - 09c589057ee8 - eb7b00ec347d - - 9d79beb19ac3 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: - - 3ca2d2a9068c - - f338e9942b27 - - 2ecf5a570907 - e731ea24e48d - - fd128c111ab0 - 99ecfdafc64f - - eb7a370f6588 - - 606b09cc9860 - f369ef5f210b + - fd128c111ab0 + - 2ecf5a570907 + - 606b09cc9860 + - 3ca2d2a9068c + - f338e9942b27 + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -218,10 +218,10 @@ tools: owner: iuc revisions: - b799a615995d - - 8dee0218ac7d - a7b889b90140 - - 8b6d0d85252b + - 8dee0218ac7d - 73a3846701e1 + - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -239,9 +239,9 @@ tools: - name: novoplasty owner: iuc revisions: + - 7c2f5268d01c - 15200570e926 - 64a1c751d99b - - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -253,13 +253,13 @@ tools: - name: pretext_map owner: iuc revisions: - - dfb8a4497339 - - 2b16ba799da9 - - 02831bf9e95f - d256a51a656b - - bbe19ef04a74 - - 79b48f02db49 - 8fef980d48b5 + - 79b48f02db49 + - 02831bf9e95f + - bbe19ef04a74 + - 2b16ba799da9 + - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -274,25 +274,25 @@ tools: owner: iuc revisions: - 6fcbee531de6 + - 342a1d1fed7b + - 72472698a2df - 59db8ea8c845 - - 875d0f36d66f - 3061c8b029e5 - 7594365c546b - - 72472698a2df - 675488238c96 - - 342a1d1fed7b - ebb0dcdb621a + - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - d865b62f501c - a199cd7ac344 + - aa39b19ca11e - 39bed8de8017 - 78c533842eeb - - aa39b19ca11e + - cd06929b224b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -311,10 +311,10 @@ tools: owner: iuc revisions: - 2b2a352488fa - - f11b994b7eb2 - 5c55448d0f33 - - 33b7d8481a76 - f8564b2d7f63 + - f11b994b7eb2 + - 33b7d8481a76 - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -329,12 +329,12 @@ tools: owner: iuc revisions: - 378e55aeeb25 - - 53c2bc8c2ae3 - - e122f9101584 - 1d06c8b38e77 - - ef69617ecb42 + - e122f9101584 + - 53c2bc8c2ae3 - 28189050e437 - 5fc94b3a4704 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,13 +346,13 @@ tools: - name: shovill owner: iuc revisions: + - 865119fcb694 + - d9f6a00b6db7 - ee17a294d3a3 - ad80238462c1 + - 83ead2be47b2 - f698c7604b3b - - 865119fcb694 - 196a599ec43d - - 83ead2be47b2 - - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot @@ -366,171 +366,171 @@ tools: - name: spades_biosyntheticspades owner: iuc revisions: + - 051fd2db8a27 + - c33a476f4001 + - 7490b213baa9 - 604782a8a53a - - 1fc82fe7ebef - 1bb12736175c - 904bf932cf78 - - c33a476f4001 - - 051fd2db8a27 - - 7490b213baa9 + - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 808b3a0a6716 - - 655fa188c3cc - 34305b013402 - - fee85957cebe - d6e617c4e338 - - ad8b536d1caa - 9678993ca5bd + - 655fa188c3cc + - 808b3a0a6716 + - fee85957cebe + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 037f9927c4ff - 8d4b90bf9caf - - b8002c3f7141 - 7e27faaad80e + - e5a3b75a271f - 6b5a5842531e + - 037f9927c4ff + - b8002c3f7141 - 21da31ed41a1 - - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 328aa71f0f3c + - 5b26685e5d3b - 86f66ab58e14 - 2a10645aeadd - - 9de69775f512 - f1532cb33c75 + - 328aa71f0f3c + - 9de69775f512 - 7922870efcca - - 5b26685e5d3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: + - e41dcb0e913b + - 8cc856b935ee + - 85fb02c43042 - 340bc17f49cf - 6aad515a5270 - - 85fb02c43042 - 1708851f8804 - - e41dcb0e913b - - 8cc856b935ee tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d159735a6a9f + - 6357b127161e - b3490b036c5a + - d159735a6a9f + - 249f6a28c751 - d5fb354f745d - b65a43f70b99 - - 6357b127161e - de1260f8a300 - - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d5887ace0dd4 + - 33368fec3b70 + - 9006e5836729 - 7897763d14ec - - b7829778729f - - a90db5dbaaf3 + - d5887ace0dd4 - d2d1df21dfb9 - - 9006e5836729 - - 33368fec3b70 - dd7ad84f3943 + - b7829778729f + - a90db5dbaaf3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - 6f4c8ad6ea01 - - 8f631679571f - 189e837009c9 + - ced385aa976d - ed2425b9fd27 + - 8f631679571f - 505a9833ab5d - - ced385aa976d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 356afed970b4 - - 19bdfd1e6fe3 - - e59bee4565b3 - d40ed4eb0c0e - - f31d376ce725 - 9ded6109434a + - 19bdfd1e6fe3 + - f31d376ce725 + - e59bee4565b3 + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - af40e971a8cc - - ebd801e712bc - - b23249f81bc4 - 4688ae3b49b5 + - b23249f81bc4 + - af40e971a8cc - 80a17897564d - 6dd935e4984b + - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - 937ea677d437 + - cb1e3db43020 - b5e35a2ca4f3 - b64696992ee9 - - 937ea677d437 - - bb11fefb23a3 - 59bd28f6265d - - cb1e3db43020 + - bb11fefb23a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 + - cb4768eeca3b - 6bfab4a4a988 - - 05bd7504fdb2 + - 6015aa0303f2 - 2628f6790eda - 383bb5ad32e2 - - cb4768eeca3b + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - 9e3e80cc4ad4 - - 8f9f06995f98 - - 3e44ef016b45 - - e022dff952df - 6e26c9afd301 - - e92675014ac9 - 0a3a602cd1e3 + - e92675014ac9 + - e022dff952df + - 3e44ef016b45 + - 8f9f06995f98 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 08256557922f + - 920677cd220f - 8d09f8be269e - 5da9a0e2fb2d - - 920677cd220f - - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 82398ba86ba7 + - 0e2b4e3f9ca1 - d81360ea69d8 - - 37d88f41c810 - 4a53b89fa703 - - 0e2b4e3f9ca1 - - 82398ba86ba7 + - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 7fcacf91d..7cf4e390b 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,8 +2,8 @@ tools: - name: integron_finder owner: iuc revisions: - - bfd290fe1588 - 1ae00120dd24 + - bfd290fe1588 - 392f100eebcd - 4768f7f8e93f tool_panel_section_label: Bacterial Typing @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 31812e7a1315 - - 8e8dc9a1e3e5 - ded48b36f3b7 + - 8e8dc9a1e3e5 + - 31812e7a1315 - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 24a7a95867b0 - 5c8ff92e38a9 - 17fcac7ddf54 + - 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 422ac123e..569544ee9 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - - 0840ba83860c - - 204a131e47db - - a9c9d768b751 - 1c427e24fb79 + - a9c9d768b751 + - 0840ba83860c - d1f62024a08b + - 204a131e47db - 7beb76ffbc0f + - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 9951f6fca..594eb9d6e 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 - - a8eabd2838f6 - - e19bebe96cd2 - - 07e8b80f278c - a68aa6c1204a - - b28e0cfa7ba1 - - 589e7e57fd6d - 87ee588b3d45 - - ce3c7f062223 - dde39ba9c031 - - a1a923cd89e8 + - b28e0cfa7ba1 + - a8eabd2838f6 + - 07e8b80f278c - 0a5c785ac6db + - a1a923cd89e8 + - e19bebe96cd2 + - 589e7e57fd6d + - 64e2edfe7a2c + - ce3c7f062223 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 c5a9e9ab7..e1a887906 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - 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: - - 0e3cf9594bb7 - - 2889433c7ae1 + - d999e774072a - 5edc472ec434 - acf4e47b734c - e25d3acf6e68 - - d999e774072a + - 0e3cf9594bb7 - 6f386c5dc4fb - - a52d2d93e595 - cbf3f518b668 + - 2889433c7ae1 + - a52d2d93e595 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 3040b7e5a..e1a4a2471 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: - - c8cdde00b105 - - 710301bc46fa - - f4230f116196 - - 27ee142314a9 - - da6bd1975a71 - 095ad4d096d1 + - 27ee142314a9 + - f4230f116196 + - c8cdde00b105 - 6ca543ec1bf8 + - da6bd1975a71 + - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -111,8 +111,8 @@ 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 @@ -130,73 +130,73 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 0fac8e2afc13 + - 88076940fa94 - 3b8a9d5ced85 - bfb65cb551d8 - - 88076940fa94 - 79cfd9ead848 + - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 715cd0e87781 + - f5d979cb4b54 - d532b7e5f64b - - b46d4b4d995c + - 715cd0e87781 - 55918daa5651 - eb6564a60136 - - f5d979cb4b54 + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - f26afd1b7104 - - 5579659312e6 - fdf2cc80adb5 - - d2f955aea23a + - 5579659312e6 - 97872d87ba80 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - d1d0efda35c0 + - bc31d02be922 - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 2c349b027a01 - - cac1886249a2 - - 070e3ecc3fda - ed736e6eee39 + - 070e3ecc3fda + - 2c349b027a01 - 4da9ee404eab + - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - 73008ef1f487 + - c0c9a5024177 - 807aa4c9293d - f197e34c33a9 - - c0c9a5024177 - d1f803b5943c + - da8753545526 - 525ca7c8065f - 2e219a2d9327 - - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 + - 27ea4e1a3f95 - 2c8ed1b52bf7 - 1809414a9454 - - 27ea4e1a3f95 - 7568ae18908a + - c4fbab8e03c5 - 61094e01eff9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -209,18 +209,18 @@ tools: - name: md_converter owner: chemteam revisions: + - 730ef07b90ae - ccfbd956a2d3 + - d7ec25187599 - 79e8ab8f1e81 - - 730ef07b90ae - ba83f0923369 - - d7ec25187599 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 @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e6011617c748 - - 1400d1977e7b - b59c91adeac1 - 4242b4d68e9c + - e6011617c748 + - 1400d1977e7b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -338,10 +338,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 + - bf99565cec1f - 9b48456a96fe - d4c67ced6abc - - bf99565cec1f - - 85fad59f8168 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 0b3fe15e6..328651e97 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: - - fa56d93f7980 - - c97a786e8fb5 - f907216064f6 + - fa56d93f7980 - 163688bb8f73 + - c97a786e8fb5 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: - - 424aefbd7777 - - 640d3af5d833 - - 495a4173006f - f5d67c722d67 + - 495a4173006f - 86e2413cf3f8 + - 640d3af5d833 + - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - 5c2cc3b58c7d - - 4a14714649b4 - 74c9214cc8e6 + - 4a14714649b4 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 a014b943d..245bdf800 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -9,10 +9,10 @@ tools: - name: collapse_collections owner: nml revisions: + - 33151a38533a - 90981f86000f - - 25136a2b0cfe - 830961c48e42 - - 33151a38533a + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -32,8 +32,8 @@ tools: owner: bgruening revisions: - baabc30154cd - - 6cbe2f30c2d7 - 0046692724f9 + - 6cbe2f30c2d7 - 2dae863c8f42 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 a10945ec4..3e9a3fe3c 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -15,39 +15,39 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 3b6f97e7094c - - 6ef0b5664c69 - - 0b3c3ad92827 - - a3b86937ead6 + - ab9350a8ab4d + - 4a6ee918c13a - 367b1ed91207 + - 0b3c3ad92827 + - 5e1240a87bcb - f3a19509108a + - 6ef0b5664c69 + - 3b6f97e7094c + - a3b86937ead6 - e3cbd2287f63 - - 4a6ee918c13a - - 5e1240a87bcb - - ab9350a8ab4d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e177a8ea0bf1 - 501c21cce614 - - 33c99804a32f - 72ed72122deb + - e525f9ffb9ac - 1b5fc03380d4 - d4d4e9febf5c - - 091bb5922a82 - - e525f9ffb9ac - - 584008e574b2 + - 33c99804a32f - bd46669113b9 + - 584008e574b2 + - 091bb5922a82 + - e177a8ea0bf1 - 54ccb7e1f49a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - a0d092f27fdf - 11c3eb512633 + - a0d092f27fdf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -59,24 +59,24 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 8979c288aefb - - 77b41c89d856 - 186b8d913e6c + - 77b41c89d856 + - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - - 4b347702c4aa - 43807a65369f + - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -88,8 +88,8 @@ tools: - 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 @@ -101,9 +101,9 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 3e436657dcd0 - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -135,25 +135,25 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0a7799698fe5 - 0b4e36026794 + - 0a7799698fe5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - 68f57cc8fad0 - - 2dcfbbf9071a - 78fb18899c99 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 26c6706bfb07 - - 19e45916daf9 - 63769c4217a7 + - 26c6706bfb07 - b9b385097f13 + - 19e45916daf9 - 92ac8e086317 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -166,15 +166,15 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - 3c6f9e8a4c17 + - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - a2f83a375bf2 - 98704d357ede + - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 1502214ab..5771902e2 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,182 +2,182 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - c929a006727f + - a1ca9bccc7f2 + - e821645ef8fc + - 29451af70c52 - 5f6d123679f4 - de72ba3ed6f2 - - 29451af70c52 - - e821645ef8fc - 268e91e540ee - - a1ca9bccc7f2 - - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - - 7a7fd0f5f15d - 0e49b109abc2 - - 5d11599b8a7d - - 12af64f93288 - 0e143b4c3987 + - bb1e4f63e0e6 + - 12af64f93288 + - 5d11599b8a7d - 2d2cf5c1ea8a + - 7a7fd0f5f15d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 7c1beb6d6eca + - 81b1e3e1fc6c + - 1d848bc4585f - dc059492a995 - 195e98217334 - c06951d10364 - - 81b1e3e1fc6c - - 1d848bc4585f - - 7c1beb6d6eca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 71aa86af6762 - - 26e7304d6737 - - bfff7454b59a - - 07418a30ed01 - a67ac707496a - - 3d211717a775 - 93eb012d9eed + - 3d211717a775 + - bfff7454b59a + - 71aa86af6762 + - 07418a30ed01 + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 2bc10a9ca58b - dd0b7398bb96 - - 26983857c91a - - 56d5b797ce84 - 5be24eba848d - - b8858746dc1f - 29fcfd36e90a + - 26983857c91a + - b8858746dc1f + - 2bc10a9ca58b + - 56d5b797ce84 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 9384cd033f30 - - ee3a1b0f45f1 - 72bfafe3330b + - 9384cd033f30 - c3e012dfe21f - e6d0bff01239 - - 7e6bcd2e5128 - 7ef978dc1b8a + - 7e6bcd2e5128 + - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 - - b73e213add0c - fb9cf9c97ec4 - - 9470f29702f8 - - 167788df3b46 - - a60c359ec43c - - fd1275e01605 - 514fa53b5efb + - d9a637e83828 + - fd1275e01605 + - a60c359ec43c + - 167788df3b46 + - 9470f29702f8 + - b73e213add0c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - c34d11ea4ba6 - 2c37ce318bc3 - - 86febdcc4283 - - ca0616bb2cdf + - e479c7ca5570 - 5bffaa8354a1 + - 86febdcc4283 - a02cfa31e9cb - - e479c7ca5570 - - c34d11ea4ba6 + - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 2d466b530754 - - 69a8621ca2f0 - - 01fb6a7654e6 - 004aea905d4d + - 69a8621ca2f0 + - 2d466b530754 - 1fcb7adc39b8 - - 192ef85c0b0b + - 01fb6a7654e6 - 78f405266706 + - 192ef85c0b0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 + - db940c262830 - 137c4beed34b + - 2f9e4843f480 + - 9ecba5e225a6 - 459cfa861f0b - - db940c262830 - - 3c9f0c486cca - d580d6acd1df - - 2f9e4843f480 - d9ce4897dbb2 + - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fd408d755394 - - fbe773640707 - - bd7db9e2f2cb - - f264afa9fa6f - - bad3ca889618 - 2c66e43f1c86 + - f264afa9fa6f + - bd7db9e2f2cb + - fbe773640707 + - fd408d755394 - 32e451def88c + - bad3ca889618 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 - - 231994413f89 - 9368fbc49c8b - - 7e361d147872 - 56bce3c82278 - - 3b9d990a0a0e - 7fda5607e777 + - 7e361d147872 + - 231994413f89 + - 3b9d990a0a0e + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - e65d16fb2724 - - ce4ce3316f74 - - b1779366c8e9 + - d9114ef1c8a5 - 4431f39ede55 - - 94ca68515826 + - b1779366c8e9 - c03c3384cd81 - - d9114ef1c8a5 + - 94ca68515826 + - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - 793665fff0f8 - - 4ed32329e0ed + - d57251071381 + - b88ebb3672a1 - f8fc4e5aff9d - 23f7c5f1fdaf - - d57251071381 + - 4ed32329e0ed - 2da482e408b8 - - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - c60570fa602f - - a7849312d328 - 010e58e9d822 - e4c7985d4585 - a4dfb122e52b - - 25d830337d31 + - a7849312d328 + - c60570fa602f - ba6efa77fb79 + - 25d830337d31 - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -185,22 +185,22 @@ tools: owner: bgruening revisions: - 00d869ea03a1 - - 4d678170d29b - 443d9a9d6d11 + - c899e0ccff8c + - 4d678170d29b + - 38e3f226248b - aa200e4f3939 - 69264da0ce77 - - 38e3f226248b - - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - - a2d70c4fd406 - - c361b12d207a - 6662b1a8d326 - 10301d137111 + - a2d70c4fd406 - d806504e96d9 + - aac8444d6681 + - 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 2143ba96b..20cae0f1d 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -37,8 +37,8 @@ tools: - 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 @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 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/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 83e65c370..c87ebd957 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: - - 832c20329690 + - 63dd26468588 - dba489bfcd62 + - 832c20329690 - ce385837c160 - - 63dd26468588 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 4a62cc5d8..bc5ddf712 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 29bdbc353f20 - - d82648ad25a3 - - cf1322aeb137 - 62f5fab76dfb + - d82648ad25a3 - 6da3972210ee + - 29bdbc353f20 + - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 092fd5b88..0b9e25709 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 - - 48f587c13075 - - 135b80fb1ac2 - - 44e2cc14f75b - - b1c926deaa2d - - 5eb7e84243f2 - - 64172f1c1202 - 660cffd8d92a - - c053d4cad713 - 49370cb85f0f - - c4b82dce8335 - - fe74900d6dc7 - - e4691e1589d3 - - c5e2e5902201 + - c053d4cad713 + - 8c0175e03cee + - 5eb7e84243f2 - 288f97432497 - - de6cebe3c043 - - 5915ea1ec9b1 - 8665bcc8b847 - 4e5056fefd88 + - b1c926deaa2d - 093678460093 + - e4691e1589d3 + - 44e2cc14f75b + - 48f587c13075 + - 5915ea1ec9b1 + - 64172f1c1202 + - c5e2e5902201 + - c4b82dce8335 + - fe74900d6dc7 + - 135b80fb1ac2 + - de6cebe3c043 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -40,8 +40,8 @@ tools: owner: devteam revisions: - 8889eb864cef - - f666895cbebd - 9db07fd39f85 + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -81,8 +81,8 @@ tools: owner: devteam revisions: - 516b97a23d7e - - 9457a20156db - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -101,9 +101,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: + - ec0b5076173a - f81d4362b6c1 - f773e98b26cf - - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -115,8 +115,8 @@ tools: - name: fasta_stats owner: iuc revisions: - - 0dbb995c7d35 - cd0874854f51 + - 0dbb995c7d35 - 56022eb50bbd - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ @@ -130,11 +130,11 @@ tools: - name: fastp owner: iuc revisions: - - 1d8fe9bc4cb0 - - 65b93b623c77 - - dbf9c561ef29 - c59d48774d03 + - dbf9c561ef29 + - 65b93b623c77 - d60c3f704da0 + - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -160,9 +160,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - - '144275714590' - 10b75444feae + - '144275714590' + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -174,9 +174,9 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 - - 47e5dbc3e790 - e9f8633db0a2 + - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -188,8 +188,8 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 5b87038565bb - 7861f3b10c68 + - 5b87038565bb - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -202,9 +202,9 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - - 4e1d64e6385f - 9dfda4e310ed + - 4e1d64e6385f + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -216,8 +216,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 523c2aff0376 + - f3936d0632cb - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -230,9 +230,9 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - b41c2c1bcfbf - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea + - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -244,9 +244,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - - c885369b207b - 8d958759cf2a + - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -258,9 +258,9 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 + - 35e38452bb3f - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -274,8 +274,8 @@ tools: owner: devteam revisions: - 54053ea6c77e - - 045f0e1043f7 - 74db4cffab1f + - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -287,9 +287,9 @@ tools: - name: fastq_stats owner: devteam revisions: + - b1cea1b2fcd0 - f86c27295151 - f0e7deab6518 - - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -322,10 +322,10 @@ 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 @@ -337,9 +337,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -351,10 +351,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 - bdf1ce174e39 - - 736b8f6ee456 - 90858c306551 + - cb1e251cac37 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -366,8 +366,8 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - 421f0af4ee95 + - 7ce1891db6f5 - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -380,10 +380,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 - - 02f8a17a4ebd - - 3599f5451ee2 - f984bb114520 + - 3599f5451ee2 + - 02f8a17a4ebd + - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -396,9 +396,9 @@ tools: owner: devteam revisions: - 6027ef51ef91 - - 177f0621c266 - - 0c2907307ba4 - e246088b6e34 + - 0c2907307ba4 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -438,9 +438,9 @@ tools: owner: iuc revisions: - f69501361cec - - 037f0acc7830 - - b4c6f054210a - 2f804526f5fd + - b4c6f054210a + - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -452,8 +452,8 @@ tools: - 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 @@ -473,8 +473,8 @@ tools: - name: seqtk owner: iuc revisions: - - 3da72230c066 - 4b494533146a + - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -500,8 +500,8 @@ tools: owner: iuc revisions: - 71f649c23021 - - d3f58a0dc09d - bf04bd405d5b + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -513,12 +513,12 @@ tools: - name: umi_tools_count owner: iuc revisions: + - b557acca0b56 - 8250ea3a1501 - - a535cf1e5da4 - - e654095ab143 - 71ad4a56c40c - - b557acca0b56 + - e654095ab143 - 24013bf85a6f + - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -530,21 +530,21 @@ tools: - name: umi_tools_dedup owner: iuc revisions: - - c5a2ee07c4e1 - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 7accf7407811 - 015cf18f4a15 + - 7accf7407811 - f3759eec3018 - - 7a7e33d28f62 - - 27ac32a22ad2 - - 6a675c3aa610 - 9fa7803d1c51 + - 6a675c3aa610 - 828dba98cdb4 + - 27ac32a22ad2 + - 7a7e33d28f62 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -563,8 +563,8 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - e4e12f0b3af1 - - 4c8a1c7d3608 - 953b4821b183 + - 4c8a1c7d3608 + - e4e12f0b3af1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 0197b2f00..061f598cb 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,9 +3,9 @@ tools: owner: devteam revisions: - e41385662e5e - - 64e9a6afdd0c - - ce9cd02d5b88 - 7b4468117008 + - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,59 +18,59 @@ tools: - name: fastqc owner: devteam revisions: - - 3d0c7bdf12f5 + - 2c64fded1286 + - e7b2202befea + - f2e8552cf1d0 - 9da02be9c6cc + - 3d0c7bdf12f5 - 2b0c9d9fc6ca - - 2c64fded1286 - - 5ec9f6bceaee - ff9530579d1f - - f2e8552cf1d0 - - e7b2202befea + - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 - 18a51655db17 + - ad116ae3f4d9 - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - - 59003d0543cd - cc0fd298cc17 + - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - 8880fb74ef56 - - a72af9de6bf5 - 1f296803dfa3 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 75c93c70d094 - - 9a913cdee30e + - b2f1f75d49c4 + - bf675f34b056 - 3d93dd18d9f8 + - f7985e0479b9 + - 9a913cdee30e - 1c2db0054039 - - b2f1f75d49c4 - f7e2f1eb3a16 - - bf675f34b056 - abfd8a6544d7 - - f7985e0479b9 + - 75c93c70d094 - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index 929eb4f64..b248d7a64 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 85ef5f5a0562 - 83a19df00eab - 141612f8c3e3 + - 85ef5f5a0562 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 6da72d926..394e068e3 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 @@ -16,30 +16,30 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - - 8f53b238a360 - f2f3bc622a16 + - 8f53b238a360 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 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 @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: + - b2c25142267e - cf61daf064fe - 45296e47d565 - - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,15 +108,15 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query @@ -137,8 +137,8 @@ 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 @@ -158,14 +158,14 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index eb150e512..2a6e45eeb 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee 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 b9fe43a6f..f82c901c7 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - b39347891609 - c1b437242fee - - 983bf725dfc2 - e9df53a75f3c - - b39347891609 + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -18,52 +18,52 @@ 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: + - 1ec814014652 + - 1790dcf3c32d - 69ebb7f46e45 - - e407b9da183a + - 9a776b080193 + - 734abc7ac21d + - 5e6237d58b0c - aad3885b3216 - - 8848455c0270 + - 83c7d564b128 - 6ea73833cf67 - - 5e6237d58b0c - - 4df8de2d0e48 - 4317d3cb6cba - 516a54ddf218 - - f8054ea1c365 - - f5ea3ce9b9b0 - - 1790dcf3c32d - 653e89d73fc4 + - 8848455c0270 + - e407b9da183a + - f8054ea1c365 - ba931a59dd59 - - 734abc7ac21d + - 7068f48d0ef9 + - f5ea3ce9b9b0 + - 4df8de2d0e48 + - 6591f049cf7e - c441583adae5 - - 1ec814014652 - - 9a776b080193 - e08a7ad4378b - - 83c7d564b128 - - 6591f049cf7e - - 7068f48d0ef9 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - 21a560af5913 - - 34758ab8aaa4 + - 9aaa46d45472 - 75b3b3d0adbf + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - 054483e27a35 - - bfdc6a7ffd3a - af5eccf83605 - 468c71dac78a + - bfdc6a7ffd3a 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 2efc088e9..726ab5b04 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: - - fd59d783248a + - c4bde687c846 + - a64dc31ab7f2 + - df7356989ac1 - 7f13dc906cb9 - - ae9994cf526f - 4b519282a05b - - a64dc31ab7f2 + - ae9994cf526f - 290a11559985 - 740057a5126d - - df7356989ac1 - - c4bde687c846 + - fd59d783248a 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: - - 7cf5b1d072b5 - f95284aa2946 + - 7cf5b1d072b5 - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,8 +49,8 @@ tools: owner: iuc revisions: - '566197475670' - - 53460afd5115 - 374e9062d874 + - 53460afd5115 - ca7cb0eaad62 - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data @@ -58,12 +58,12 @@ tools: - name: ggplot2_heatmap owner: iuc revisions: + - 10515715c940 + - d3a9e32672ec - da4c086cff5b - - 3d059e9c2fba - 391a4cc45fea + - 3d059e9c2fba - 1a72f938213e - - d3a9e32672ec - - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -76,19 +76,19 @@ tools: - name: ggplot2_pca owner: iuc revisions: - - b1268b7544d3 - ae344ccf9d62 + - b1268b7544d3 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - 5298e06f14f9 - - e3a675da7fd0 + - 1acf88921176 - d0fc8b746d57 + - e3a675da7fd0 - 299307abd804 - - 1acf88921176 + - 5fe1dc76176e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -107,15 +107,15 @@ 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 owner: iuc revisions: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -134,17 +134,17 @@ tools: - name: jbrowse owner: iuc revisions: - - fd5dbf0f732e - - 836d1aa3e89a + - ca2def38369c - 667e17248bfe - - 4542035c1075 - - a6e57ff585c0 + - 112eb40ba6cf - 1cfc579079a6 - - 6cd09d7b5f37 - 2bb2e07a7a21 + - fd5dbf0f732e - 17359b808b01 - - 112eb40ba6cf - - ca2def38369c + - 6cd09d7b5f37 + - a6e57ff585c0 + - 836d1aa3e89a + - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -162,9 +162,9 @@ tools: - name: pathview owner: iuc revisions: - - 03c13085aecc - - fe154a7af404 - f1691de443a7 + - fe154a7af404 + - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -174,20 +174,26 @@ tools: - bd1416eea1f0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: plot_ragtag_paf + owner: galaxy-australia + revisions: + - 94e0834ae4ed + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f - - 62e3a4e8c54c - 85da91bbdbfb - f234e2e59d76 + - 62e3a4e8c54c + - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -199,9 +205,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - - 6c571966cfb9 - 44c66e8d21e6 + - 6c571966cfb9 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -213,23 +219,23 @@ tools: - name: pygenometracks owner: iuc revisions: + - 4ac4e7083b7e + - 2824d77cd8f8 + - 36b848d5f3ec + - a1abfa420d9d + - 14e7c35f3d00 - 360df4999907 - 326a3db8d9d1 - - 14e7c35f3d00 - - 36b848d5f3ec - 7dd841a32245 - - a1abfa420d9d - - 2824d77cd8f8 - - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - 73b8cb5bddcd - - 2f557f6abbfb - 83c573f2e73c - 44608d0193ed + - 2f557f6abbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 0889e9292..0409223a9 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -63,15 +63,15 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - 64dd8bb151e1 + - 79da59a0b180 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -84,23 +84,23 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - c354af93f567 - 6903bc865d63 + - c354af93f567 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - 9a2f72d7dbd2 + - 94697510d55f - ff6decc0f432 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 @@ -113,15 +113,15 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - d4c9061c8fef + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 1be0fc4d8654 - 7d5c97823f8b + - 1be0fc4d8654 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -141,15 +141,15 @@ 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 @@ -183,23 +183,23 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 0cf90e01d9f8 - 4428dba93375 + - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 - - 0f98603d0116 - ea91cfd0444e + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 2e2711aac..8402f0767 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,51 +2,51 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 29f66c353bcb - ed2cca6b5de4 - - 9edf8894a22d - - 921a2da49a0c - a4c13ddcc8ee + - 921a2da49a0c + - 29f66c353bcb + - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - ec4b948dc6f0 + - 5746d61f0a91 - 755df866ad0c - d404277cc87a - - ec4b948dc6f0 - 78fb5e286609 - - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - 03dd3c16ae4e - - 4d511437b1e5 - 9e357a8b2ec3 - 11fa44ee0603 + - 977dc15add20 + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 41dbf4d162a2 + - 0ba4f56a3613 - 77919cc3618e - 3b5b54ed6392 - c3e5e2cf12b7 - - 0ba4f56a3613 + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 5308ca68ef3d + - b63363075c2e + - 7babd8a46fe0 - 9939786dd9c9 + - 5308ca68ef3d - 12d51d7be66f - - 7babd8a46fe0 - - b63363075c2e 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 813028b51..6996244bc 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,29 +2,29 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 0c777d708acc - 3df9f0a4bf34 - - 8bccb36e055a - - 81f0cbca04a7 - 699a5e9146b3 + - 8bccb36e055a - 7db4fc31dbee - - 0c777d708acc + - 81f0cbca04a7 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 + - 2436a8807ad1 + - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 9d47aabda459 - - e576b73a2e2f - 6ad1d3cfdea1 + - e576b73a2e2f + - 9d47aabda459 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -46,11 +46,11 @@ tools: - name: bfconvert owner: imgteam revisions: - - fcadded98e61 - 10eed33aa9b2 - 85edbb7a436b - f3360fbeda64 - b07f4839ca77 + - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -71,48 +71,48 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: + - 0e4dccaafef5 - e917a2424690 - eb6c08714244 - - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - e7273daa5ae2 - - 6070780813d9 - 670975e92458 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - df3ad3ba5c6f - ef4aed1d34c4 + - cdf8e3c57dae tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 5d28ac336861 - - 2484086dee41 - 6a7da2e5f696 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - bace5a93a97c - 11f177b1a59e - f2ed92b011a9 - - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -126,17 +126,17 @@ tools: - name: cp_gray_to_color owner: bgruening revisions: - - 3245681b2f6d - 31d195bedf6d + - 3245681b2f6d - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - b6eec6087271 - 87d4d92d7487 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -150,64 +150,64 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - 2564f461de62 + - ac5bea85a391 - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - a32c3f810ade - - 20dbb1f7ec7b - 91e03287f285 + - 20dbb1f7ec7b + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - b64af54c5c09 + - 5499dc6f8ac1 - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: + - d3890df07463 - 6f4715b8540a - e972e07c7845 - - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - e52c75a28c4b + - 407925835dd9 - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - acf3aa487283 - d85f11570109 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - b76841ee5560 + - 035a58c7f54a - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,16 +220,16 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 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 + - 27edbb90ab2b - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -270,7 +270,7 @@ 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 513753b80..dc90c9b09 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: - - 78bbd17d0703 - - a38934e303b9 + - f362150bef41 + - 3a72fede57ce - 3e4f434a69c6 - - d6e72da3ec35 - e4ee04da1c19 - e319b5b65879 - - 3a72fede57ce - - f362150bef41 + - a38934e303b9 + - d6e72da3ec35 - 1069f6db0a0e - 40737febe339 + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - 7fe36019c073 - - 618297d23022 + - fcbeda41d0ac + - 9537184d421f - 0135f1d487a0 - 8f8df367470d - - fcbeda41d0ac + - f91cfb73d369 + - c88553ec696e + - 618297d23022 - 72ddd32392cd - 2b95d5c04908 - - c88553ec696e - - f91cfb73d369 - - 9537184d421f tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 - fafb3d685fa9 - - ad0dc9f4c9e2 - 2cf4a1cafc16 + - ad0dc9f4c9e2 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - a1c2aecd7a0d - - 6a1515bb0687 + - 43aac8d29685 + - 5dc33613c288 + - 8d36959b000d + - ee2beb764a7b - 9eaadf03e0df + - a1c2aecd7a0d - 3d18f8c3c0f6 - - bd2a7d1316b9 - - 5dc33613c288 - - 43aac8d29685 - 94df24c6bc00 + - bd2a7d1316b9 - 7f1cfa4c0e32 - 28a6f1908fcc - - ee2beb764a7b - ee29337f905c - - 8d36959b000d + - 6a1515bb0687 - 8c05afb547fa tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 9f978da6528a - - bcaa0d571ce2 + - 86a20ae274fc + - a250929be21b - c092052ed673 - - 8858fa037a15 - - db536ad45f28 - - d37ede8589b2 + - bcaa0d571ce2 + - 9f978da6528a + - 5671e1d3d5ee - 5d6ed46cc101 - - a250929be21b - - cb903c9dc33d + - d37ede8589b2 + - 8858fa037a15 - 364f4ffec275 - - 5671e1d3d5ee - - 86a20ae274fc + - db536ad45f28 - e3bb03cf207a + - cb903c9dc33d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - ed28dd32141c - - 49236b03e4fd - e1a015876aa9 + - 3b6a16d82c1b + - abbc8041e8ec + - 49236b03e4fd + - 584beffa972b + - c5c9f02b6167 - 230b05597996 + - 38b91a3190cd + - ed28dd32141c - 12d66d0d05ac - 194e3ceee923 - - 584beffa972b - - 38b91a3190cd - - abbc8041e8ec - - c5c9f02b6167 - - 3b6a16d82c1b - f95f403841ad 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 3f4e816cb..c0e3dc15c 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: + - f198773344e4 - 0f1724dd59d2 - - b8a457820315 - 17e3b698dd52 - - f198773344e4 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf + - 374cb875d38a - ac092723240d - 22c2a1ac7ae3 + - ba0c40780ecf - a513e3fbb4c5 - - 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 2c65ff23c..afa427ac5 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -10,28 +10,28 @@ tools: - name: keras_model_config owner: bgruening revisions: - - 4d81e3e2fb63 - - f22a9297440f - 8a794e6d3388 + - f22a9297440f + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 818f9b69d8a0 - - b6ef6d0cb6b7 + - 2af1346e68c9 - f1b9a42d6809 - e1317b5502fa - - 2af1346e68c9 + - 818f9b69d8a0 + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - 1588f9076e32 - - 947c2eacccb8 - 8334dc98c48e + - 947c2eacccb8 + - c80db5d6fd8c - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,62 +39,62 @@ tools: owner: bgruening revisions: - 1552b8cb4a94 - - 83228baae3c5 - 9991c4ddde14 - - 29e4122c90de - 25b46af53232 + - 29e4122c90de + - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 060ca94ac049 - - a07ab242b0b5 - - 53616c8b0865 - f3dfa4bdf87e + - a07ab242b0b5 - 1a53edc4b438 + - 060ca94ac049 + - 53616c8b0865 - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 + - 927586a18553 - d4808d5b83da + - dc4b5fd604a6 - 91c4e3331208 - - 927586a18553 - - 40f4447733b2 - 2fc89dcd41c8 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - 7626ea9c2e1b - 36e8d6d5d01b + - c6ae57f774c6 + - 25ab6b4e376e - 301e07345c93 - e5a5ad882f1f - - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 02d2be90dedb - - 4ed102b922cb - f9639b488779 - - 80852884053f - - 0630258dcf35 - b7c3e9a3b954 + - 0630258dcf35 + - 80852884053f + - 4ed102b922cb + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - 14180f9c831e - - caeb57858702 - - 61634a87efc7 - 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 883074181..f30430f84 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -3,16 +3,16 @@ tools: owner: devteam revisions: - d5ceb9f3c25b - - f6877ad76b00 - - 017aba02828d - - cd659e8cc5fa - - 17062a0decb7 - - 3ba8d4563129 - 749c918495f7 - - 937aa69e715f + - 0d4acadabb04 - a6d65b0c67af + - 017aba02828d - 03e9b2fbc005 - - 0d4acadabb04 + - 3ba8d4563129 + - cd659e8cc5fa + - f6877ad76b00 + - 937aa69e715f + - 17062a0decb7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -32,11 +32,11 @@ tools: owner: devteam revisions: - 3fe632431b68 - - dfd8b7f78c37 - - e188dc7a68e6 + - 2477830927ec - 64f11cf59c6e + - e188dc7a68e6 + - dfd8b7f78c37 - 53646aaaafef - - 2477830927ec tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,28 +48,28 @@ tools: - name: lastz owner: devteam revisions: + - e7f19d6a9af8 - 37b497aa133f - - 60afcc2c1d05 - 2ff111fac1d7 - - e7f19d6a9af8 - 3e1ea2facca6 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 037c6e54df11 - - 8c6cd2650d1f - - 5cc34c3f440d - b3eab4b67562 - - c0c2d0941de8 + - be1d967337e4 - 11a0d50a54e6 - - 09b53c1d4ab1 + - 037c6e54df11 - 53c0b7a1a0c3 + - 8c6cd2650d1f + - 6b1e195506a3 + - 5cc34c3f440d - 3f4d6399997b - - be1d967337e4 + - c0c2d0941de8 - f54f5baedfdd - - 6b1e195506a3 + - 09b53c1d4ab1 - 77b2770508f6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,17 +77,17 @@ tools: owner: iuc revisions: - 1cd2511a396e + - 13022c3d3076 + - 9ee34ba73ebf + - e403d27e8f24 - ec9cbd6b9a49 - - 79b885ce78d7 - - 00fbfac99d39 - - 5ef7ec16b04f - 42ce70172b72 - 45795f582ae9 - - 9ee34ba73ebf - - e403d27e8f24 - 178bdbdb6d24 - - 13022c3d3076 + - 5ef7ec16b04f + - 00fbfac99d39 - b8f5f6e87f5c + - 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 1f91d8697..26f5ded07 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -93,15 +93,15 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - c990df6afc24 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 00e66c401366 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -114,8 +114,8 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 9e3c83d2afc3 - 1b09315a3f87 + - 9e3c83d2afc3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -128,8 +128,8 @@ tools: - name: matchms_metadata_match owner: recetox revisions: - - 1d443ed476a1 - 03bc9b7f40f6 + - 1d443ed476a1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -166,8 +166,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7627b40601f6 - 9ff95a1a2705 + - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -241,8 +241,8 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr @@ -255,49 +255,49 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae - 7b42ee54d757 - c53a97599181 + - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 149b9cc7499b - f3a18e020cdd - 18ec7635bac6 + - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - 134be5abb208 - - dfebc82ba1f0 - 481d769e2f7a + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - 02c772a49998 - - 51332c2520c7 - 9064aecc78a7 + - 51332c2520c7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: + - e7305ba0dd38 - b341cfd4baf8 - b3413f335327 - - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - cf061712a184 - - dd7bbc2b99d1 - 17a48d0a80f4 + - dd7bbc2b99d1 + - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals @@ -311,9 +311,9 @@ tools: - name: recetox_aplcms_remove_noise owner: recetox revisions: - - d90187b0f247 - ffbabefbd2e2 - ea0758b41473 + - d90187b0f247 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -375,8 +375,8 @@ tools: - name: use_theoretical_mz_annotations owner: recetox revisions: - - e0cac9994a72 - b3d41b1fcb18 + - e0cac9994a72 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: w4mclassfilter diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index f329df202..13a0bccfa 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,9 +8,9 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - - 0e63d03c8790 - 0094893f5001 + - 0e63d03c8790 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - 7f1aaa1932d8 - a8216def322b + - 7f1aaa1932d8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -95,19 +95,19 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc + - 5b5a7af9fbb4 - 63f86089423e - 76d3d2b10738 - - 5b5a7af9fbb4 + - 65db807336bc - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 1c35dadbe76f - 84fd33a60b35 - 00f5005840fa - - 1c35dadbe76f - 96336c6a2bb7 - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis @@ -115,81 +115,81 @@ tools: - name: dada2_filterandtrim owner: iuc revisions: - - f732237754fc + - 34e55239e68b - addaf9d22850 - e8fba04706d3 - - 34e55239e68b - a9f4a217dcd6 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 0776d824d896 - 5fe3edf19b9c - 04c15826a0b8 - - 0776d824d896 - - 8c202e741d68 - 75403243703a + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - 43c99742158b - 75c8945b0da2 - e96bbb9e24ea - 8470de786d47 + - 43c99742158b + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - 306a40d4bb8f + - 1d75bd0595e2 - 84743da21318 - - 35176674168c - 5c865a382933 + - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 32c9ea835770 - - ac72310b038a - - 78faebd0879c - 8daf4564ccda - 555ccac8a4c5 + - 78faebd0879c + - ac72310b038a + - 32c9ea835770 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - f947b4bb5107 - - cae017b76acb - 7b8cb2b02978 - a58e4a43f49c + - d60df8727f59 + - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 1bc3657cd694 - 073608a50ac3 + - 7136e9ab70db - 7f3b59dee073 - - 1bc3657cd694 - 04144473e59e - - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - a7817705348e - - 0a1224c4b781 - - 19299bb1c6af - d943081510da - 9058d8943303 + - 19299bb1c6af + - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -202,29 +202,29 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 65d52c693b8e - - b907a3c0434f - - 4d9445dff47b - - a68b985913ab - - f8f56dd6449f + - 5c7ba3d85a01 - c4db8c4de66f - dbf1798c0dcc - - 5c7ba3d85a01 + - 4d9445dff47b + - f8f56dd6449f + - b907a3c0434f + - a68b985913ab + - 65d52c693b8e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 654548ae1357 - 6c84982ee6f7 - 6d364c65c946 - - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -237,16 +237,16 @@ tools: owner: iuc revisions: - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -279,8 +279,8 @@ tools: - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table @@ -293,31 +293,31 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - c409a495841f + - 31c6d107e7a5 - 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 - 71ea608ddfa3 - 172920f67a84 + - d24841f5c3d2 - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 12fb63b5f63f + - 2bdd84912a2b - a4d7148ccee4 - - 4137b492233e - a293a742194f - d7e9a3c41657 - - 2bdd84912a2b + - 12fb63b5f63f + - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -329,20 +329,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 75bedfb2078b - - 6fcb8ac37a3e - - 97f7bb0851e7 - cf87759761eb + - 6fcb8ac37a3e - e2c71b852aba - - 64bc7acc22a9 + - 75bedfb2078b + - 97f7bb0851e7 - a92c06a3afa7 + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -354,21 +354,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - 4e5e73d03f0d - 080ea153677c - - c82508e76ad1 - - 2d35528d2141 - 4033827c76b8 + - 5e5a999ffaa9 + - 2d35528d2141 + - c82508e76ad1 + - 4e5e73d03f0d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - 95bf7479d53c - - fc6c328c292f - 6b7622dda516 + - 2cd76b089570 + - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -380,8 +380,8 @@ tools: - name: jellyfish owner: iuc revisions: - - 11658afb8c87 - dcd30574a456 + - 11658afb8c87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single @@ -394,15 +394,15 @@ tools: - name: khmer_abundance_distribution owner: iuc revisions: - - e699e2747356 - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - - b3d513c7093e - 570505540a7b + - b3d513c7093e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions @@ -436,8 +436,8 @@ tools: - name: khmer_partition owner: iuc revisions: - - 5a0fa29951ae - 8388fe31d604 + - 5a0fa29951ae tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kmc @@ -449,10 +449,10 @@ tools: - name: kraken2 owner: iuc revisions: + - 4a9da2b6c2e3 + - cdee7158adf3 - 20e2f64aa1fe - 328c607150ff - - cdee7158adf3 - - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -471,22 +471,22 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1c677354ab18 + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -530,8 +530,8 @@ 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 @@ -567,22 +567,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 7f5d7b0e9884 - - 327d9f4cc95f - 0270541aaf46 + - 327d9f4cc95f + - 7f5d7b0e9884 - 27250f92a01a - - 4fd3b5d8706b - - 2cff76cf35c6 - 3cc4a60615c0 + - 2cff76cf35c6 + - 4fd3b5d8706b - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - - eb50e7eca3dc - 76bc4efa1aeb + - eb50e7eca3dc + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -648,26 +648,26 @@ 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: - - 740fd2d16a28 - - ef65b083bd0c - - 1a037928504c - 2131d7dca455 + - 6dee4abadccb + - 289b3807e80c + - ec368db926f4 + - 1a037928504c + - ef65b083bd0c + - b89b0765695d + - ff8f55893e7d - a16313517e55 - fd69c607b43f - - ff8f55893e7d + - 740fd2d16a28 - a92a632c4d9b - - b89b0765695d - 1a6cdf55390f - - ec368db926f4 - - 289b3807e80c - - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -692,43 +692,43 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 6034c3f3ecf0 - 2f47a294ef49 + - 6034c3f3ecf0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 709adbfcf308 - 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 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 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 + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -747,8 +747,8 @@ 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 @@ -766,8 +766,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 65e5f9caefcc + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -809,12 +809,12 @@ tools: - name: staramr owner: nml revisions: - - 4b9a8031ab74 - - 4d83eccf5f81 - 2fd4d4c9c5c2 - - 141afacabcfa - aeaa20b96ef2 - be818ae858e4 + - 4d83eccf5f81 + - 4b9a8031ab74 + - 141afacabcfa - 3b22de20bd4b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -845,8 +845,8 @@ tools: - name: vsearch owner: iuc revisions: - - 9495df9dd6ef - 576963db5f1b + - 9495df9dd6ef - 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 e826cebe9..383f190e9 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 @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index b5c7802a1..9e040bb7d 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: - - 94b8c6013083 - - 8b67dd48fec1 - - 48c13389050d - - bdfbaf0c10aa - - 9422c5a87ee2 + - cd07731e4434 + - a74dbfee5a86 - 9baa871cb1d1 - 9eeb13a92d79 - - 2263989660f5 + - 94b8c6013083 - 80f03df2e2ce - - cd07731e4434 - - a74dbfee5a86 - 6ae5a7b5a0a2 + - 48c13389050d + - 9422c5a87ee2 + - 8b67dd48fec1 + - 2263989660f5 - 098506c54016 + - bdfbaf0c10aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c44f824c051a - - be78f13134e2 - d7ce0ec78e51 + - be78f13134e2 + - c18157c68134 + - f14193ec1f50 - d390fe1567dc - - aaa0d6a8b808 - - bc3831dd65c1 - - fc2e49f91e52 + - 5abf2c2249aa - 2e093badc689 - - f0af8936ed41 + - 4a60927aaca5 - '764845535798' - 3ff17bad4006 - - c18157c68134 - - 4a60927aaca5 - - 5abf2c2249aa - - f14193ec1f50 + - aaa0d6a8b808 + - fc2e49f91e52 + - f0af8936ed41 + - bc3831dd65c1 + - c44f824c051a tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -60,29 +60,29 @@ tools: - name: gecko owner: iuc revisions: - - 5efbd15675ca - 1de657a3198d + - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - 8e649f27aa0d - f0d493f8f84f - - f1a5908ea2cb + - bf28a8cff401 + - 8e649f27aa0d - c5908940967d - - 15974dd17515 - 6f28e90db932 - - bf28a8cff401 + - f1a5908ea2cb + - 15974dd17515 + - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - fbca557a4847 - b3acbb3a6af0 - e8fdceffea4c - - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -97,15 +97,15 @@ tools: owner: iuc revisions: - 48823c9635a4 - - bcd65de9725b - 57f042937ba7 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae - fb43e8887350 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,8 +120,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - - 959c1f8dae95 - cf3c9489c088 + - 959c1f8dae95 + - b4124df98b26 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 05ec41a24..5e968de74 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,9 +8,9 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 18a8d140ec6f - 7c47b3c9e493 - 28928576e1ea + - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado @@ -29,21 +29,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - fc8804320156 - - 79e9a869f40e - 72b5e9dda577 - 0e9e7fcdd543 + - cb34f00cc10f + - 79e9a869f40e - a7228a7ea146 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae + - fa11aa8103b2 - 18505fe2bdb1 + - d6cddc06aeae - db25ec99c3ea - - fa11aa8103b2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -55,22 +55,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - cc36773a3681 - - 19f3b583a9b3 - - 43815fa60f3a - - ec699520444c - 0f5f4a208660 + - 222669c4afb6 - edf6d4003fad - - eb746fa6f514 - 2bf63b38ee9b - - 222669c4afb6 + - ec699520444c + - 19f3b583a9b3 + - cc36773a3681 + - 43815fa60f3a + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -83,59 +83,59 @@ tools: owner: iuc revisions: - 645159bcee2d - - a38bdcec9e4c + - a02b8b3f5a0c + - 7b379e98b9a9 - 0f1c34698076 + - a38bdcec9e4c - edbb6c5028f5 - a3c4fe6f49ab - - a02b8b3f5a0c - - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - d219b6d8158a + - 85a394edc247 - 3b6f94fc7e1d 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 - - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - - 5f76b20953e5 - 93d623d9979c + - 5f76b20953e5 + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - daf8518d243a + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -147,8 +147,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - d1805f9c4c82 - 47936349f3e9 + - d1805f9c4c82 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -160,8 +160,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 0433aad600e9 + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -180,8 +180,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -211,8 +211,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - c5c5a3e84989 - 64a83664b814 + - c5c5a3e84989 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 319d043ba..dac515b80 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -21,15 +21,15 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 4e85a3a5dbd1 - 71186bb66ca2 + - 4e85a3a5dbd1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 96d2000977ab - 58341ad4fb42 + - 96d2000977ab 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 + - 3e73c97f025d + - d74850cf4e42 + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 83da94c0e4a6 + - 1586b111d2a3 - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -83,11 +83,11 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - edacc4bcd3cb - - 2f27f3b86827 - - ed1518ce2237 - e4b4837f06f5 - 1e34d2e3d285 + - ed1518ce2237 + - edacc4bcd3cb + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -113,9 +113,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - - 48a42ca61006 - 5711fc06a63e + - 48a42ca61006 + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -135,8 +135,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -155,16 +155,16 @@ 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: - - b4b2b284230a - - 5bcf0e24f42c - 172815da3d41 + - 5bcf0e24f42c + - b4b2b284230a - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,8 +178,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -191,16 +191,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - fea85c467896 - 87febc68b45b + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -225,35 +225,35 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 0cb27ea69dc1 - 4ba60cb14cb0 - - 9c43baa60906 + - 5fe20c915fa6 - 2c61c30a57e7 + - 9c43baa60906 + - 0cb27ea69dc1 - d8dc037e3c13 - - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - 14785f8a3725 - d9339bb8127e + - 14785f8a3725 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: + - aec831b54a5b - 9d09724f2bf1 - 0db22932bc39 - - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - 29c738066906 - - df30a2f1db55 - 6e24e79d3d69 + - df30a2f1db55 - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -280,8 +280,8 @@ tools: - 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 @@ -301,9 +301,9 @@ tools: - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - 94a50db37d1a - 9946bc39c834 + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1053,8 +1053,8 @@ 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 @@ -1067,8 +1067,8 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - a22969b08177 - e4b7d1507a75 + - a22969b08177 - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1081,11 +1081,11 @@ tools: - name: salsa owner: iuc revisions: - - f77f7a7f3b83 - 9a22227bb6d0 + - ab5b7f6b7198 - 58a870ef434c - ba7b0f11e470 - - ab5b7f6b7198 + - f77f7a7f3b83 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 aefad48af..598472f7a 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - d033ffc1c161 - '841557158611' - - f04a1264e2a2 - - f73435dc282b - - b89cac5156ec - - cce7b18495e4 - 81e66674859e + - 6a457678efcb - a6619171428e - - d033ffc1c161 - - 8834daeb9892 - - 107d3ba7024a - 3f59ebfbfe3d - 26de3a7b1cb9 - - 5a7c56a5cc08 + - f04a1264e2a2 + - b89cac5156ec + - d7c7ef3353fe - 3b8b5bde0bd9 + - f73435dc282b + - cce7b18495e4 + - 5a7c56a5cc08 + - 8834daeb9892 - c78f3d7dd1db - - 6a457678efcb - - d7c7ef3353fe + - 107d3ba7024a tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 02b8758214b0 - - e75442c7f4da - - b0af57c1a968 - - 6223845127ea - - 6283babe736e - - 4755f52427c4 - - 6a726db04d4b - - aa8cc71438cf - - 5b777002c2de - 5fcd1ece3a6e + - 6283babe736e - 659517798cc4 + - 6a726db04d4b - 88c4aa435ded - - df47d4845b62 - 3b96e92e8ec3 - - a185b079b095 + - 4755f52427c4 + - 02b8758214b0 + - 6223845127ea - 7a2092844346 + - b0af57c1a968 + - aa8cc71438cf + - a185b079b095 + - 5b777002c2de + - e75442c7f4da + - df47d4845b62 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 70acec670c30 + - d1c340a5664b + - b8476e82ac20 - 111bd54f6bc4 + - 24d024316465 + - 524d31add34a - f97743d52b87 - - b8476e82ac20 + - 70acec670c30 - 0878b7fd5260 - - 524d31add34a - - d1c340a5664b - - 24d024316465 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - - 9e10ba792be2 - feb40665d7cd + - 9e10ba792be2 - 4f6349228462 + - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,26 +110,26 @@ tools: - name: pangolin owner: iuc revisions: - - 2fa9d4f1b48f - - 81804a978fc0 + - ca0d8cf80567 + - b7e297c2ede6 + - 5f8727ff21e7 - abf6dbe8c9d7 - - 03ed9524dcd1 + - 3a43c3982401 - 83a69484cb87 - - ca0d8cf80567 - - 7bb8726be37c - - 437e28791761 - 2f1019071464 - - b7e297c2ede6 - - b6abccb1f25b + - 9d61d3fa046c + - 7bb8726be37c + - 42a174224817 - 36912871ccdc + - 437e28791761 - a2099fb98cdb - - ca337cce3888 - - 8ad84c5753ea - - 3a43c3982401 - - 5f8727ff21e7 - - 9d61d3fa046c - 14ae456b8cc5 - - 42a174224817 + - 81804a978fc0 + - b6abccb1f25b + - 2fa9d4f1b48f + - 8ad84c5753ea + - 03ed9524dcd1 + - ca337cce3888 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac - - ba29b5e2a4be - - a4b71be30c3c - 73a469f7dc96 - - b1e68bbe4cef + - a4b71be30c3c - ea30d3089354 + - b1e68bbe4cef + - ba29b5e2a4be + - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - - dbe2b2204555 - 91887494eb97 + - dbe2b2204555 - 809e42326fc2 - - e88a7de55d6e - 9b2b122d0415 + - f1ccc8a6eb05 + - e88a7de55d6e - 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 adbb9d131..0766d34d5 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -3,13 +3,13 @@ tools: owner: devteam revisions: - f6ced08779c4 - - 1aac2a13842a - - 3f254c5ced1d - - f9242e01365a - - a1f0b3f4b781 - - 7d34178f2812 - - fc288950c3b7 - b502c227b5e6 - 881d7645d1bf + - f9242e01365a + - fc288950c3b7 + - 3f254c5ced1d + - 7d34178f2812 + - a1f0b3f4b781 + - 1aac2a13842a 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 e9f494f2b..51893e5e5 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: - - d00e15139065 - - c0e71cb2bd1b - - 6ab1a261520a - - eb085b3dbaf8 - - ca90d17ff51b - - 3bd420ec162d - - 5b85006245f3 - a58f7eb0df2c - 7fbec959cf2b - - e4a053d67e24 - 2f7702fd0a4c + - 5b85006245f3 + - eb085b3dbaf8 + - 6ab1a261520a + - 3bd420ec162d + - c0e71cb2bd1b + - e4a053d67e24 + - d00e15139065 + - ca90d17ff51b 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 6b21258a9..a72150a4a 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,31 +2,31 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 - - f28ad96b76dc - - 0a18ac48ac53 + - 4c177985028a - b574b84afc4d + - 0a18ac48ac53 - 277dc652246e + - f28ad96b76dc - b18329a8ac14 - - 4c177985028a + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - a9a28e46d54a - - 525f201b86c1 - bf06d196e23d - - e988563cc6e5 - e215f71d7983 + - a9a28e46d54a - b41107d8fe89 + - 525f201b86c1 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - 4fbffddde8cd + - 8da3511c9467 - bb6397b94018 - 56da27be956a tool_panel_section_label: Proteomics @@ -34,42 +34,42 @@ tools: - name: cardinal_filtering owner: galaxyp revisions: - - 890845926d4b - b8c79e70516d - - f23d67e28cc8 - 528fb09022be - a8157342d9a3 + - f23d67e28cc8 + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 - - 80600735685d - 59e85306eae5 + - 80600735685d - a95a82eb4d50 - - 25b83cbd596a - ae304a72db7b + - a69865da6f80 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: + - 83aac7741200 + - f1897eb07081 - e0669b1854b1 - ed9ed1e6cca2 - - 83aac7741200 - 798da6bdff3d - - f1897eb07081 - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - - a7fb9b395ddf - d426a9107a6c + - 74b61bf5bc4b - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations @@ -77,19 +77,19 @@ tools: revisions: - cc430977c8ff - df2187f9013b - - 91f0f5922011 - 82f6c2f4332d + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - d2483487e077 - - 10566783d718 - - c5aa9fca18c6 - 043f9c91f686 + - c5aa9fca18c6 - ba92b59cd529 + - 10566783d718 - 1693b2126f30 + - d2483487e077 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - 9fa3dbf06f17 + - bf0728e000cd - ae4dc0c041f9 - ff8c9e0e8a7b - - bf0728e000cd + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,24 +129,24 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - - 4081e4faa4ab - 0fa397f4f40b + - 4081e4faa4ab + - 1c5cbf8f79ce 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: - - 0d2e93e01e68 - ce1a157a41bd - d6a4dfdad269 + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,9 +158,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - e66f552a3c47 - 160538a890a6 - d286ff4600dd - - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -180,15 +180,15 @@ tools: - name: maxquant owner: galaxyp revisions: - - 1f39c833f65f - - f522c08e900c - - 2133b0be850a + - 4d17fcdeb8ff - 97a7f34fcb6a - - 37d669de2828 + - f522c08e900c + - 1f39c833f65f - 837224ad1694 + - 2133b0be850a - 9c52362ae7bb - 7f432d87c82c - - 4d17fcdeb8ff + - 37d669de2828 - e42225f8a659 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,194 +201,194 @@ tools: - name: metaquantome_db owner: galaxyp revisions: + - a72ac2c7cc5b - 85b8866f06d7 - - e63db1aa82ee - 0ed07016d668 - - a72ac2c7cc5b + - e63db1aa82ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 1974224d63c2 - 352b37c66d97 - 767c1d761aaf - 990b4560ead7 - - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - 99450519d727 - 35cc7ca0bdc7 + - deaf035bbe9f - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c7745841de24 - - 06f6826d380c - e79958768a2c + - 06f6826d380c - c1343e3389ca + - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - da986f83631b - d46d64e7964d - d2eac53666f0 + - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - - 1199751329b0 - 9bf325045235 + - 1199751329b0 - 8bd7734309f6 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert owner: galaxyp revisions: - - ab6c14374bc0 - 6153e8ada1ee + - ab6c14374bc0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: + - 28434abe6c5c - 8212e342e482 - - de7593c29499 - 593839e1f2c3 - - 28434abe6c5c + - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - 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39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 34e7afee141d - 1c5f31b8d632 - - 18f93351f8b6 - 8d4db262964c + - 34e7afee141d - f817513840a9 + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability @@ -422,10 +422,10 @@ tools: - name: openms_idscoreswitcher owner: galaxyp revisions: - - 4204882495f2 - - be74a8cd7d66 - 0e52c85f3b15 - 476b5e296979 + - be74a8cd7d66 + - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -447,8 +447,8 @@ tools: - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - 4e66c4e73909 + - d0304fb829c0 - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -464,64 +464,64 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: - - 08488066d588 - a2a6e9551046 + - 08488066d588 - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - 2a9ff56cb279 + - de7a553552a6 - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - c1809c05ae8c - 1bf940c18d93 + - c1809c05ae8c - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - 9f505cd4428f - f861ec9fbe59 - 496cf619e311 - - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - 0bddef8d144e - - c99d5004b74f - d4396637b9f5 + - c99d5004b74f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 8b814eafce2c - 4bb198c0bd3e - 89254095cbf6 - - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: + - 05ec9fb05ed1 - f9ed7e074900 - f82b320ceb90 - - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - d31426ef20f6 + - 6e8cc5ed2a9b - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -536,18 +536,18 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 6b01678ec2fc - - decc397c3b7e - - 5ae104d0da6e - 3d8d4ada5405 + - 5ae104d0da6e + - decc397c3b7e + - 6b01678ec2fc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - d6aca689dd48 - - dd173849c3d8 - 5182338d5e7c + - dd173849c3d8 - e039cc5c7aed - 539a3a4dcc9e tool_panel_section_label: Proteomics @@ -564,33 +564,33 @@ tools: owner: galaxyp revisions: - 43b9ed22e8ce - - 9c70a651a53e - dd71e020e2aa + - 9c70a651a53e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 1b03536aa3c9 - d063e2fe4ba4 - 9020199dba0a - - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - 78c080d36945 - - f036e8cf1a55 - ad2ba3a95a02 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - - fb52e95a370c - 5c2a97a234d6 + - c8b225c69a7f - 7f6a1f27553e + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -616,14 +616,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c - - 07ff622ec007 - - 1beff3ddce58 - da885ca16cb2 - - 3634c90301af - 943a34df6047 - 3ec27b4cee7c + - a72c48001f7c + - 1beff3ddce58 - 7fdd9119cc4f + - 3634c90301af + - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -684,9 +684,9 @@ tools: owner: galaxyp revisions: - a371252a2cf6 - - 1a5690a5eedc - - 265c35540faa - 12692567c7f9 + - 265c35540faa + - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index 274226cda..002b57ee7 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: - - cd5f98911089 - - 110a346daf36 - - 42201b90e3f4 - 289b7d6b69a4 - e345aadf914f + - 110a346daf36 - 2f1d464ebfd2 + - cd5f98911089 + - 42201b90e3f4 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: + - 8501601a118d + - fcce77c09289 - c207119ba5f6 - 0345dbaaa79b - - fcce77c09289 - - 42d9087b4789 - 0cd2df8af811 - - 8501601a118d + - 42d9087b4789 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: - - 33486216eec0 + - 405a212b32ab - ad5ab22ffe24 - - 421c33b8bf17 - 04db7fd6b238 - 89eb29319bf4 - - 405a212b32ab + - 33486216eec0 + - 421c33b8bf17 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 - - fa51dc5e8386 - - f6e91108b7b1 - - 7b72fde3d27e - 1d839ead7ad3 + - 7b72fde3d27e + - fa51dc5e8386 - 7370bb65bad4 + - eb784fa07f80 + - f6e91108b7b1 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: - - c9b77ced9a78 - - 8a55d29c8fcf - - a3e86cd9cac7 - - 3d70c2996730 - 1544278c272e + - 3d70c2996730 - d30e36c48c93 + - a3e86cd9cac7 + - c9b77ced9a78 + - 8a55d29c8fcf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 - - e2db212d64ad - - 887cf585cafc - b242deb58952 - - a5969aa9347e - 564c33e5c3e3 + - a5969aa9347e + - 7b881f5f5ad5 + - 887cf585cafc + - e2db212d64ad tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,8 +105,8 @@ tools: owner: iuc revisions: - b4bab607eb05 - - 8cff84759bf6 - bd5ff77e2036 + - 8cff84759bf6 - 9a171f9a450b - e897c74a48bb tool_panel_section_label: RAD-seq @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 5e10f396979e - - 6dafad990086 - - 4f65e343ecdf - 887e0991eb24 - - adc7a7610d4f + - 4f65e343ecdf + - 6dafad990086 - 33f0793edf93 + - adc7a7610d4f + - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -138,11 +138,11 @@ tools: owner: iuc revisions: - c5d7050e4ad7 - - 4e280b27a831 - c287418eb288 - - 43e3eeb2e0ec - - 97575d01f06b + - 4e280b27a831 - 17d39bf0a63a + - 97575d01f06b + - 43e3eeb2e0ec 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: - - a819ec3b362d - d9bf483266a1 - - 09b8edb56d80 + - a819ec3b362d + - 9586f08634c0 - cd034465d4a4 + - 09b8edb56d80 - 0b8c84a7fdb5 - - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -172,11 +172,11 @@ tools: owner: iuc revisions: - a9c34a289493 + - 95351dd0fd3f - 69842dd5aa48 - - 2645575d1bf2 - bf0e43ab0416 + - 2645575d1bf2 - a4b4bd84f69e - - 95351dd0fd3f 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: - - 8a35a3bc6752 - d033e1ccb386 - - 912f904a6e1e - - d1fda11e602f + - 8a35a3bc6752 - bb0475c884ff + - d1fda11e602f - cfb504394ae1 + - 912f904a6e1e 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: + - 95286af4139b - d504d945a655 - d1fad35bdb4a - - 95286af4139b 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: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c 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 680f7d245..718d91020 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -3,25 +3,25 @@ tools: owner: iuc revisions: - 31f8063eedea - - cf01dd6c6b1f - 7acb00fc980a - 2d4e3aff9dc7 + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - - 7a5a2d28c539 - - 32e542c2a773 - 703a2cb3fb38 + - 32e542c2a773 + - 7a5a2d28c539 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 01ccd366690d + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -70,9 +70,9 @@ tools: - name: cuffcompare owner: devteam revisions: + - e66b9b5b8580 - f648e5180e40 - ad5d061fbdf2 - - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffcompare @@ -99,8 +99,8 @@ tools: owner: devteam revisions: - 86285ddd4512 - - 6a6717a5f421 - cf747d1bd79a + - 6a6717a5f421 - 22cf48ad7b16 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -113,9 +113,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 28b94cfbfdb9 - - 9a854107dbb2 - 6cbfede05833 + - 9a854107dbb2 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -152,9 +152,9 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - - 8f0181aacb7a - e3b16fd7dd08 + - 8f0181aacb7a + - 0693ccd171c4 - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -167,13 +167,13 @@ tools: - name: deseq2 owner: iuc revisions: - - d027d1f4984e + - 6a3a025714d3 - 8fe98f7094de - - 24a09ca67621 - - 9a882d108833 - cd9874cb9019 + - 9a882d108833 - 0696db066a5b - - 6a3a025714d3 + - 24a09ca67621 + - d027d1f4984e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -185,11 +185,11 @@ tools: - name: dexseq owner: iuc revisions: + - 62adf13b86ea + - b47c006d90c5 - 9a7c5b6d8f1e - df929f257179 - - 62adf13b86ea - 2872c633f07e - - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -201,18 +201,18 @@ tools: - name: edger owner: iuc revisions: - - ae2aad0a6d50 - - a8305cf0c951 - - 070900306913 - - 334ce9b1bac5 - - 5bf899c13979 - - 0cb907a2a810 + - f2843df56434 - 555659de7321 - - 9bdff28ae1b1 + - 5bf899c13979 + - ae2aad0a6d50 - df0c8d0a5992 - - 3d89af8a44f0 - 6e53e565fc6a - - f2843df56434 + - 9bdff28ae1b1 + - 3d89af8a44f0 + - 334ce9b1bac5 + - 070900306913 + - 0cb907a2a810 + - a8305cf0c951 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -224,8 +224,8 @@ tools: - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -243,17 +243,17 @@ tools: - name: featurecounts owner: iuc revisions: - - a37612abf7f9 + - af814359d244 - 7db9d3ea71c9 - - 90d16db017d7 - a56fbe2d6ba7 - - e6a2a912677a + - 38b6d12edc68 + - a37612abf7f9 + - 90d16db017d7 - ea04b737afa0 - - af814359d244 - - f9d49f5cb597 - - f3a5f075498f - 6f66ae7c5f7a - - 38b6d12edc68 + - e6a2a912677a + - f3a5f075498f + - f9d49f5cb597 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -283,9 +283,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c5e024a18cf - 3c97c841a443 - 0f710191a66d + - 3c5e024a18cf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -303,12 +303,12 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - 3fb01a8c902d + - d4b55e2beb12 - 6ab42baa56e9 - f4af63aaf57a - - d4b55e2beb12 + - 26371a1df031 - 6c19daec423d + - 3fb01a8c902d - a86e80d3c09c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -328,8 +328,8 @@ tools: owner: lparsons revisions: - 4418229c501e - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -347,11 +347,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - - 5ae5c312d718 - - 1c75aa5de15e - 01247aaf0a10 + - 1c75aa5de15e + - 87c11c05d238 - ce5d418183c5 + - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -363,10 +363,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - c971db6f0fe5 - - 4f9c4e6566e5 - 10c98fab6c5a + - 40985510cd98 + - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -378,14 +378,14 @@ tools: - name: limma_voom owner: iuc revisions: + - 0921444c832d + - d6f5fa4ee473 - 97e06a4c7c75 - - e827f9aae031 - 708348a17fa1 - 58c35179ebf0 - - 32511f586472 - 119b069fc845 - - 0921444c832d - - d6f5fa4ee473 + - e827f9aae031 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -434,8 +434,8 @@ 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 @@ -453,21 +453,21 @@ tools: - name: rgrnastar owner: iuc revisions: + - 5ec75f5dae3c - 0a563fd2f22e - - 7ed2edc1337f + - 99b17b74a8cd + - 980d2a2e1180 + - c772497b2c32 - e132e7d02a3e - b9e04854e2bb - - 4074fc1940e2 - - b0f2be869d6d - - 5ec75f5dae3c - - 980d2a2e1180 - - 99b17b74a8cd + - 4014de1b6daf + - 79de45b5069b - c7c55b694974 - - c772497b2c32 + - 7ed2edc1337f + - 4074fc1940e2 - 4df95e2d7f61 - 3ea5a2a63fa2 - - 4014de1b6daf - - 79de45b5069b + - b0f2be869d6d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -491,14 +491,14 @@ tools: - name: salmon owner: bgruening revisions: - - e3d32471da11 - - 2c0ca397d302 - - cc05793bb896 - - ebab418107f5 - 53e9709776a0 - 15cd64d7c58b - - 49121db48873 - f4d5237a84f6 + - ebab418107f5 + - e3d32471da11 + - 2c0ca397d302 + - 49121db48873 + - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -510,23 +510,23 @@ tools: - name: seurat owner: iuc revisions: - - fab6ff46e019 - 8c28affc7c48 - c0fd285eb553 - 56242ff81c84 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cbf488da3b2c - - 1ebd14235b92 - 914cfcba0ec8 - cef79931dda5 - - dd4df992d93d + - 258d696dbd7e - ae618321f34a + - 1ebd14235b92 + - cbf488da3b2c + - dd4df992d93d - 76d290331481 - - 258d696dbd7e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -577,10 +577,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - ba3720d7e68b - d6a479fd4281 - 74217fbfba4d + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -607,8 +607,8 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - 3f4094b6a565 + - fab23c3b5258 - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -621,10 +621,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - - 34a018cbee9c - - be3f26533209 - 4687ecf0eb2d + - be3f26533209 + - 34a018cbee9c + - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -636,11 +636,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 33406f5a445c - - 05ab8d5e04a2 - - 65e7dea767ea - c5fbddcac63a + - 33406f5a445c - 5192f657f305 + - 65e7dea767ea + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -652,10 +652,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - a35cba31d904 - - e406ac71165d - 6f0fb35b799c - 1fdb25a8384d + - a35cba31d904 + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -667,10 +667,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - c2c039e421af - - 7c7fbf13aadd - 964b7efe2639 + - 37a1129c89d2 + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -683,9 +683,9 @@ tools: owner: iuc revisions: - 24e94d84adc9 + - eafea3083352 - 047c22569787 - 1d689e4e1caf - - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -697,10 +697,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - 1812dbc5bb7b - - 9871104ea630 + - 04bb8bb7c198 - 3a4ac03d1266 + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -724,15 +724,15 @@ tools: - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 - - cee61b3fcf78 + - 32b86cd8eb50 - 48636f857c4b - - d84caa5a98ad - 9fa24d5aac68 - - c9cfec002f71 - - 32b86cd8eb50 - 8f1c3df4dd49 + - d84caa5a98ad + - cee61b3fcf78 - db1f362cca3e + - c9cfec002f71 + - d2bc35f3d1c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -744,10 +744,10 @@ tools: - name: trinotate owner: iuc revisions: - - 6fd16fad465d - 2b093007fab9 - - 9e61bc67866f + - 6fd16fad465d - 4383070d29ed + - 9e61bc67866f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 0693de33b..f1dfdef45 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: + - 1a052c827e88 - 473382134e56 - 080fd5739bb4 - 27e16a30667a - - 1a052c827e88 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 5926c7961..cc913921a 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,8 +2,8 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 3c661e57a88f + - 10184eaa85fc - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -17,9 +17,9 @@ tools: owner: devteam revisions: - cb20f99fd45b + - 993b19f20c76 - 108db6635177 - 1dfd95ee241e - - 993b19f20c76 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -44,8 +44,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 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 + - 19ece8afbaab - e7fd6754d093 - 30a201c9c310 - - 19ece8afbaab + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -123,15 +123,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - 0e60e2dd20af - cf1ffd88f895 + - 0e60e2dd20af tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -149,9 +149,9 @@ tools: - name: samtool_filter2 owner: devteam revisions: + - 56c31114ad4a - 649a225999a5 - dc6ff68ea5e8 - - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -164,9 +164,9 @@ tools: owner: devteam revisions: - 9149ad20699a - - 46c6639921f1 - 6856f8a01905 - 12749212f61b + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: + - 33208952b99d - 26b4f9f98aca - 92ec40abcdcf - 06dc50b7b711 - - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - 720217c23995 - 66e23b11feae - - b3d99709fe1a - b906586a6596 + - b3d99709fe1a + - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -221,8 +221,8 @@ tools: - name: samtools_fixmate owner: iuc revisions: - - d2df79922531 - e5ece8fa99de + - d2df79922531 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -231,8 +231,8 @@ tools: - fefd89ab563c - 22970df7a40e - db17d5321bad - - cc61ade70eb8 - fe34990e5ce7 + - cc61ade70eb8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - 7def34e6cf4d - - 88b8c2916784 - 811fc2d75ad4 - 7a6034296ae9 + - 88b8c2916784 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -260,28 +260,28 @@ tools: - name: samtools_markdup owner: iuc revisions: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 36677f429310 + - b40e2d865d52 + - 740ce0a18f0d - 65a38e8c8e2a - cae2794d2deb - - 740ce0a18f0d - - b40e2d865d52 + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - 583abf29fc8e + - 9da0311ab1dd + - fa7ad9b89f4a - b61f5d6a7f25 - 329deb17a9f7 - - fa7ad9b89f4a - - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - - 85e38b31e8b3 - 30388d878f81 - bb8cfc6f6e0c + - db000c6007a0 + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -327,8 +327,8 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - b8beef827165 - a4a10c7924d1 + - b8beef827165 - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - d54a4df48867 - 6c2c1836728b - - e613c1ad4c4c - cab3f8d35989 + - d54a4df48867 + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - b7f7826ef1cd - 818030fa6bbf - - bd850490c7f1 - bcedabb53ddf - 5d9ae78f34d3 + - 135c85f4cfaf + - bd850490c7f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: + - 1cc79f49b8d5 + - 145f6d74ff5e - 541082d03bef + - 3a0efe14891f - 24c5d43cb545 - 5a08c09b9311 - - 3a0efe14891f - - 1cc79f49b8d5 - - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - b01db2684fa5 - - c370440f901e - 2dce91e11ca7 - 32dc5f781059 + - 5826298f6a73 + - bf328cec6a42 - 0dbf49c414ae + - b72793637686 - 350bbc5c2ffd + - b01db2684fa5 - 6be888be75f9 - - b72793637686 - - 5826298f6a73 - - bf328cec6a42 + - 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 b627117bd..a1fe6435e 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 - - 480d9e9d156b - - 6f6537780379 - - 5cb6146337d8 - - 4aab5ae907b6 - ea5e944f447d - d147d6455873 - 59bb6d34fca6 + - 480d9e9d156b + - 4aab5ae907b6 + - a62c4a11a67d + - 6f6537780379 + - 5cb6146337d8 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 2b122ee48..dc29364e3 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,10 +8,10 @@ tools: - name: alevin owner: bgruening revisions: - - ecb9ea6269ee - - c9944a2600f1 - - e32b215b7c04 - e4c01dcece8b + - e32b215b7c04 + - c9944a2600f1 + - ecb9ea6269ee - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,21 +19,21 @@ tools: owner: iuc revisions: - cfaf5a405371 - - c0b037b12765 - 707023fa62fe - e1c3c2f2a834 + - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - cfc3f5a57dc6 - - 32e547223c9e + - 00712416fdaa - fb9e030ffae4 - - d330b3082107 + - cfc3f5a57dc6 - 93dd15e13e6a - 55e35e9203cf - - 00712416fdaa + - d330b3082107 + - 32e547223c9e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 0bf7fddf90c7 - - ee98d611afc6 - 6f0d0c784f09 - - 39e945f0b2c1 - - 688357ad5e61 - b9fac48532eb + - 688357ad5e61 + - 39e945f0b2c1 - 038e32885fec + - ee98d611afc6 + - 0bf7fddf90c7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: + - b85871dd69f9 + - 43cb7b5a6fe7 + - ed4996a16f7f + - d4af736e7b83 - 3d748954434b - 9bd945a03d7b - - b85871dd69f9 - 7e8c677a7b71 - - d4af736e7b83 - - ed4996a16f7f - - 43cb7b5a6fe7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -81,45 +81,45 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - a4774b7b2e85 - fe75d2414dc0 - 2e8022f1923c + - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 4fff5a293013 - - 02b1fe7aed76 - 769d815e4b0d + - 02b1fe7aed76 + - 4fff5a293013 - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - aa4a6f0916b4 - c29e7bb492bf - - a90f8efe08b4 - 344c2af50552 + - a90f8efe08b4 + - aa4a6f0916b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - 5b7c81b35b89 - - b13d3e4c48e1 + - 050cf43887d3 - c32347702e12 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - 1d77986f9ddc - - 239193b96d72 - - ae969fdb8442 - 02fc39c8610d + - ae969fdb8442 + - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -155,11 +155,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 + - cfe1e6c28d95 - 8855361fcfc5 - - cdf4443d5625 - a9caad671439 - - cfe1e6c28d95 + - cdf4443d5625 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -202,8 +202,8 @@ tools: - 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 @@ -223,8 +223,8 @@ tools: - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - a63e9713c39d - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -251,8 +251,8 @@ tools: - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - e06265d204f6 - 2dccb6bb0add + - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts @@ -265,15 +265,15 @@ 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 @@ -286,8 +286,8 @@ 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 @@ -300,8 +300,8 @@ tools: - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops @@ -321,15 +321,15 @@ 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 @@ -363,8 +363,8 @@ tools: - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -384,15 +384,15 @@ 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: - - 8d203e74869b - 58de3c7c8e89 + - 8d203e74869b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc @@ -405,8 +405,8 @@ tools: - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 36dfa2825a59 - 1d6af10874d5 + - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -431,19 +431,19 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - 59be31ac9dc3 + - 4b0adaa31c95 + - 7784821452ac - eeab712b0b99 - 0f1aaff9b22d - e98619de2776 - - 4b0adaa31c95 - - 7784821452ac - - 59be31ac9dc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -455,9 +455,9 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 282819d09a4f - - 7ffaa0968da3 - 2cfd0db49bbc + - 7ffaa0968da3 + - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -470,8 +470,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 7705cc75ac18 - 8c64a2da3869 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -489,11 +489,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - c4f39bf4a068 - 0bff0ee0683a - - f911a64454fb - - a4b734cd253b - 7e014059a88d + - c4f39bf4a068 + - a4b734cd253b + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -506,9 +506,9 @@ tools: owner: iuc revisions: - 7608d5faee41 + - 43c146e25a43 - d45f092caf24 - b83fbc90161e - - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -521,8 +521,8 @@ tools: owner: iuc revisions: - 37a47c4fd84d - - 2b0d3e2f402a - f3eb2291da05 + - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -548,11 +548,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - e93b008c637a - - 72979cac22b2 - c92d0f9338c5 - - 2af7c5086a96 - 44b935f2271b + - 72979cac22b2 + - e93b008c637a + - 2af7c5086a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -576,16 +576,16 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 6f83f8fd381f - aaa5da8e73a9 - - 6acb08931836 - - edec35114f72 - 77b91b9bdf52 - - 38db3fef7aad + - f9353ee6a0d4 - 4d8f983cd751 - - b2df381a6004 + - 38db3fef7aad + - 6f83f8fd381f - cb43c5d3acd3 - - f9353ee6a0d4 + - 6acb08931836 + - b2df381a6004 + - edec35114f72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -597,15 +597,15 @@ tools: - name: scanpy_filter owner: iuc revisions: + - 72a6bebab2a5 + - a97abb8cd15b + - fc0321c000a3 - 277313130da5 - b409c2486353 - - a97abb8cd15b - - a03ff8633507 - - 72a6bebab2a5 - - 8cb783c81905 - d636ce5cde16 - - fc0321c000a3 - 3c86f71498bc + - 8cb783c81905 + - a03ff8633507 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -618,16 +618,16 @@ tools: owner: iuc revisions: - 5e9171dc8244 - - 18262103fa61 - - c0a80a16560f - - 6bd82ed14acd - f54f0f0598ad - - cc0deb593fc8 - - 4338bf96809e - 6c145a6868cc - - 3081ff5c84a3 + - c0a80a16560f - 5c3ebe2adc77 + - 18262103fa61 - c5d3684f7c4c + - 3081ff5c84a3 + - 4338bf96809e + - cc0deb593fc8 + - 6bd82ed14acd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -639,16 +639,16 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - d844935c906c - - 94c19fb1281c + - ab55fe8030b6 - a407e7f8bdc1 + - 7b9fafe32c86 + - 146ae5d70b47 - c9cb76cf8d6c - - 56c0d4acef02 + - d844935c906c + - 94c19fb1281c - 3bcd5445cd7a - - 146ae5d70b47 - 9f354c7c8c92 - - ab55fe8030b6 - - 7b9fafe32c86 + - 56c0d4acef02 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -660,17 +660,17 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 6f5349dd5c49 - 0185bd174ea0 + - dbbe1ea8ecb1 + - f7446fd8d5e7 - 1072ce66b426 - - 6adf98e782f3 - - 7647e5cd1b8b - - aa0c474463c2 + - 6f5349dd5c49 - 9b0cdb8cf6be - - f7446fd8d5e7 + - aa0c474463c2 + - 7647e5cd1b8b + - 6adf98e782f3 - 40812a65a78b - 95777145cb92 - - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -682,16 +682,16 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - 73ab2ac53d06 - - fe8f16c594ec + - a39040ae0a38 - 9fb627495ec2 + - d18e7a6e5cd4 - bf2017df9837 + - fe8f16c594ec - 458e8f43a775 - c65fce500915 + - 73ab2ac53d06 - 215733a383f2 - - a39040ae0a38 - f2f6c703da06 - - d18e7a6e5cd4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -703,9 +703,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - - fd808de478b1 - b834074a9aff + - fd808de478b1 + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -717,8 +717,8 @@ tools: - name: scater_filter owner: iuc revisions: - - 652923ce664f - 7a365ec81b52 + - 652923ce664f - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -737,9 +737,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - 81e5bdff4853 - ef4c80837bc5 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -757,9 +757,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - 46fc6751d746 - 9e5c0bb18d08 + - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -988,8 +988,8 @@ tools: - name: sinto_fragments owner: iuc revisions: - - 03a04f48b922 - 29e6bfb2cf49 + - 03a04f48b922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -1008,22 +1008,22 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 88192fe25375 - 588c811fdd48 + - 88192fe25375 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - 370d45e0d1a8 - fecf9664c885 + - 370d45e0d1a8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -1035,8 +1035,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 3f8e29f9b..de251468d 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 419027d822d6 - 746e8e4bf929 - - 4c07ddedc198 - 562f3c677828 - 2f3c6f2dcf39 + - 4c07ddedc198 + - 419027d822d6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -56,8 +56,8 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - 7a15159140d1 - 6c29c7e347e8 - cb1c59d69557 + - 7a15159140d1 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: + - 9c3e1d3235c8 + - 840f29aad145 - 7442b94d6a1e - 4c4ec859c31a - - 840f29aad145 - b1eda492f063 - aef56d0e7a61 - - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 30d21a6041f6 + - d0352e8b4c10 - 07843f917990 - 9fda0b82f419 - - d0352e8b4c10 - 375bbd555f4a + - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d - 8b1b2b91f8d0 - - 4cc980df6265 - - 2c58b83c9bad + - 7ae443e6217d - cd02bf168d23 + - 2c58b83c9bad + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - 4bbaf77573ef - - ad7e0b4291ee + - e10e776f2109 - 1dd433d2c92c - 7dd3fb35904f - - e10e776f2109 - bb9fc9d46ea4 + - 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 0c46810b2..d55ec68b2 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -35,14 +35,14 @@ tools: owner: devteam revisions: - 9cd341095afd - - be25c075ed54 - 464b9305180e - 626658afe4cb + - 6595517c2dd8 + - 02026300aa45 - aff5135563c6 - 6e8d94597139 + - be25c075ed54 - 13b6f0007d9e - - 02026300aa45 - - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 557ec8d7087d - - 9cc411a62277 - - 90f657745fea - 37cde8134c6a + - 9cc411a62277 + - 557ec8d7087d - 34d29339abab + - 90f657745fea tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - f2aac0c5c60d - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 83069b38aa85 - - 33d61c89fb8d + - 623f3eb7aa48 + - cf4397560712 - cf34c344508d - - 2e8f945f7285 + - 83069b38aa85 - 3a6b78c39dca + - 2e8f945f7285 - 1ea4e668bf73 - - 623f3eb7aa48 - - cf4397560712 + - 33d61c89fb8d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 503bcd6ebe4b - 399da6b5ec21 - ae8c4b2488e7 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -143,30 +143,30 @@ tools: owner: iuc revisions: - bce29ec10b78 + - f768f6183386 - b722161a845a - c4d18aa4ec4a - - f768f6183386 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - 9ff72e942410 - fbf99087e067 - d698c222f354 + - 74a8bef53a00 + - 9ff72e942410 + - ddf54b12c295 + - 86755160afbf + - 12615d397df7 - 0a8c6b61f0f4 - a6f147a050a2 - - 86755160afbf - f46f0e4f75c4 - - ddf54b12c295 - - 74a8bef53a00 - - 12615d397df7 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 803e3c616..4e0018af0 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,9 +14,9 @@ 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 @@ -34,58 +34,58 @@ tools: - name: freebayes owner: devteam revisions: - - ef2c525bd8cd - 156b60c1530f - - a5937157062f - 04fa42777df9 - 57def2d7c093 + - a5937157062f + - ef2c525bd8cd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - 791f73caa0c8 - - e61c9ac190ad - 435b157bed6d - 09d6e4693887 + - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 3b4b2121842f - - e1461b5c52a0 + - 4805fe3d8fda - 074d44697036 + - 65432c3abf6c - dfadc322b065 - - 4805fe3d8fda - - 03627f24605f - b11e8e9c23bf - - 65432c3abf6c + - 03627f24605f + - e1461b5c52a0 + - 3b4b2121842f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - - 9cb929f21cfa - 701d134358ad + - 9cb929f21cfa + - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: + - 971e07ca4456 - f4473557ffc7 - - 426d707dfc47 - c27549b9aa1f - - 971e07ca4456 + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: + - aa35ee7f3ab2 - cdaab621d454 - dbd9f2db9ed8 - - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -104,11 +104,11 @@ tools: - name: snippy owner: iuc revisions: + - d220115f882b + - 9bccc8404a3c - 5bbf9eada9c2 - c9a8ef2aa380 - fa016f1eea1a - - 9bccc8404a3c - - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -150,21 +150,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 3b1e7c170b10 - e7aff4a85df5 - 40f0591deda0 - - 32f14a2723ec - ee4a90760848 - - 3b1e7c170b10 + - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 02d81b994ef5 - - 42818629ec4c - 9793bc5d741b - - adc0645b945c - 4934c0ac6197 + - 42818629ec4c + - adc0645b945c + - 02d81b994ef5 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 002fed5d8..0a4dcec2b 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,14 +2,14 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - 2c372041ed8c - - b7ea370b8f5d - - 6a88248893c4 - 265fe0f9ea64 + - 6a88248893c4 - 8a2e296c07ef + - ebe5fc018e72 + - 2c372041ed8c - e075b1be5abb - 95815a0bb307 - - ebe5fc018e72 + - b7ea370b8f5d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 22637b1a55bf + - 21687e35f066 + - 544cb432072b - 1001172b5089 - - c37b684e7f4e + - 22637b1a55bf - b03984136ce4 - - 21687e35f066 + - c37b684e7f4e - 0fba2c15b40d - - 544cb432072b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - ccb83bf54de0 + - 8408bffd5616 - 8627b2b383b4 - bf1f4994f104 + - 143796b504eb + - ccb83bf54de0 - 0238f68ad641 + - 01d6b7d6365e - 8ca3647c90fd - - 8408bffd5616 - 3a7084316a6e - - 01d6b7d6365e - - 143796b504eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,14 +59,14 @@ tools: - name: bcftools_concat owner: iuc revisions: - - 03e0645395d2 - abd489215f73 - f430a1ec7ee4 - 6b6c992d3a14 - d144af39073a + - 81426b3cf18b - 62ca6da715bf + - 03e0645395d2 - 9b5abbf50d23 - - 81426b3cf18b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: + - 1829900b5dcd + - e522022137f6 + - 95c6f3f4c77f + - 1171446da5db - d37e313a41be - 2363ef414c9b - - d3081540d175 - 8aa352093d73 - - 1829900b5dcd - - 1171446da5db - - 95c6f3f4c77f - - e522022137f6 + - d3081540d175 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 1137ce8efc1e - - 92c0aff8b53e + - d58d2e8c7a57 - 9b29129fb491 - - b14ff40958cb - 09f37afb3621 - - 012656fd329f - 348cd212dbad - - d58d2e8c7a57 + - 1137ce8efc1e + - b14ff40958cb + - 012656fd329f + - 92c0aff8b53e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: + - de68c11034f6 - 367ba501b6eb + - ecc9192912b8 - 7291189e98b4 + - 1f2183a23823 - cfd81f17580b - - ecc9192912b8 - 55c0e906c14c - - de68c11034f6 - - 1f2183a23823 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 64a8f7dae3ad - - e6f4badbe6f3 - 039ea3f1dea9 - - 7cbf3c66d4ad + - e6f4badbe6f3 + - 64a8f7dae3ad + - ae68ceb4cca3 - d237eaef451f + - 7cbf3c66d4ad - 6c790a091c7c - - ae68ceb4cca3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 277719af4dd7 - - 963a3635b2e1 - cdb7b4927742 - - 6ea7170a016d - 5d6653c989cb - - e7452697afd9 - 46fcafba49ec + - 6ea7170a016d + - 277719af4dd7 - 33bd9301568c + - 963a3635b2e1 + - e7452697afd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 5a321fab1fe4 - - 7b4454382d39 - 26d97cdd5410 + - 5a321fab1fe4 + - 91c1e57d5c7f + - b7f0f59baa7e - a1213a0b7b66 + - 7b4454382d39 - a29a2f40b665 - - 91c1e57d5c7f - 501bfb078342 - - b7f0f59baa7e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 39bca000353d + - 709dd8291b83 - 768d04526638 - - 5f27e814a119 - - c803c34361e0 - - 15da1ddcfeff - 97d19c008d15 + - 5f27e814a119 + - 39bca000353d - 81e4014fa809 - - 709dd8291b83 + - c803c34361e0 - d7d1663559e9 + - 15da1ddcfeff tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,14 +210,14 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 86296490704e + - b1eba148b35b - b931e65638b8 - - b84fda8ebef0 - - 5b006286a458 - - 2215287d5cc9 - 7ba36babba2d - 85ee7e6c4204 - - b1eba148b35b + - 86296490704e + - 2215287d5cc9 + - b84fda8ebef0 + - 5b006286a458 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - cf06b44624c7 - - f506df85c652 - - 56556e1267de - 5660b21a0dbd - - 37757ffb4c5f - - 31ea13dfe5e6 - 4e1d23e5c691 - - 0a5dcc9a8ec2 - - ce9396ddcb2b + - 31ea13dfe5e6 + - f506df85c652 - 9c711df3258d + - cf06b44624c7 + - 56556e1267de + - ce9396ddcb2b + - 0a5dcc9a8ec2 + - 37757ffb4c5f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -250,12 +250,12 @@ tools: - name: bcftools_norm owner: iuc revisions: - - a404f786a94c - - 48291658fdf6 - - 021693fdadaa - 6deb4d549bc9 - - 19905c025d2a + - a404f786a94c - 1ca7418e46ee + - 19905c025d2a + - 021693fdadaa + - 48291658fdf6 - 271965b55437 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 3f6fadf8b8ff - - 97e8145d7e30 - - 71c78e0eea52 - - dadbd61dc4cf - - f7879f1e77f9 - - 69d8b7567281 - 5ad5d4243987 + - 69d8b7567281 - c450406f722b + - f7879f1e77f9 + - 97e8145d7e30 + - dadbd61dc4cf + - 3f6fadf8b8ff + - 71c78e0eea52 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 52f9e4a660e3 + - 79f7a1acc2cd + - cc7f9a4e186b + - d31a2e310a52 - 6cf13a657cf6 + - 52f9e4a660e3 - 0fe007201caf - 2514e684f8a3 - - d31a2e310a52 - - 79f7a1acc2cd - 283911fe7e1a - - cc7f9a4e186b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: + - 1411bef27a75 - 0a62420cb9cd - - 80e6e399ccd0 - 75ddd081f608 - - a12844ca467a - - 026a989b7cee - - 1411bef27a75 - - 6963a6841d22 - 230e424bde67 + - 80e6e399ccd0 + - 6963a6841d22 + - 026a989b7cee + - a12844ca467a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - b10d1510fa84 - e493702b19eb - - bca7ce81688f + - 450a265f92e8 + - b10d1510fa84 - 5acfca5a76af + - 5808f77b2bb6 - 444e6a756c35 + - bca7ce81688f - ba20340426fe - - 5808f77b2bb6 - - 450a265f92e8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 157ffcdd3fa7 - 68fec03a63b7 - - 12152af85697 - - dd72ff87cfd0 - d52b8947b269 - - c43399f161f4 + - 157ffcdd3fa7 - 4d236c696844 - f2482aa4862e + - dd72ff87cfd0 + - 12152af85697 + - c43399f161f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 8dbce095986c - - 29ba253e2e05 - cbe39e530cbf - - 75becf493cd3 - - 8f2fc0ab30fb - 6f8e223f78f3 + - 8f2fc0ab30fb - 0e5d11004815 + - 8dbce095986c + - 75becf493cd3 + - 29ba253e2e05 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,11 +381,11 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - e0a856def0b0 - 8f5962c43868 - 9708e3086f32 - - 88bb477f45f7 - a8630d4fbaf8 + - 88bb477f45f7 + - e0a856def0b0 - 3ff5654b4e7d - a367a15c6de5 - f544f71adb73 @@ -401,13 +401,13 @@ tools: owner: iuc revisions: - 6ce175385dd9 - - 34dc0bbc7e93 - - 03e30f06f15f - - 96d0145c041a - - 31c096c6b156 - - 8b260d252ff4 - 4ed46189d6c6 - 5c9729d54721 + - 03e30f06f15f + - 34dc0bbc7e93 + - 8b260d252ff4 + - 31c096c6b156 + - 96d0145c041a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 46eb13bc2c73 - - 2c4941386820 - a1aad8b559c6 - - 681bdf1e22ff - - 09f5e45a8212 + - 46eb13bc2c73 - a730269af659 - - 11af7fce71cf - 40daf124be88 + - 11af7fce71cf + - 681bdf1e22ff + - 2c4941386820 + - 09f5e45a8212 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 3897eaadfbff - - 12038f59c0f4 + - 882b2e649602 + - f272b8ba0983 - 743cd1472aeb + - 12038f59c0f4 - 8cb121b6a1d2 - - f272b8ba0983 - - 882b2e649602 - - 0594ea1417c8 - - b74b8cbfc1f1 - 6cbb9c47795c + - b74b8cbfc1f1 + - 3897eaadfbff + - 0594ea1417c8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,12 +458,12 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - adee7e8b746f - - 238f78e38a8b - a9826db86d9a + - dba06328556a + - adee7e8b746f - cced6715f926 + - 238f78e38a8b - 18cf9de1cf73 - - dba06328556a - eccb508bb678 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - 9f36041495a3 - - e0ad88dec40d + - 31a1b89eab9b - c9935c9e8a24 - - fdec14f69010 + - e0ad88dec40d - f64e7ca2efd2 - - 31a1b89eab9b - e53501abf992 + - 9f36041495a3 - 3ce32adc55b2 + - fdec14f69010 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - 3b7b1fe7b937 + - d68c43202172 - fd3539749127 - d43eb39b989e - - 2331ddcbd5aa + - b7be725976b6 - 79489d5685dd + - 2331ddcbd5aa + - 3b7b1fe7b937 - 4db0695a6fc7 - - b7be725976b6 - - d68c43202172 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 58091e1be01b + - 1ccf0e7fb4f6 - 6a636d58dfc2 + - 78cd8b69da4c + - b0d39ef600a7 + - 58091e1be01b - 1a989b4110da - 5296d26b0373 - - b0d39ef600a7 - - 78cd8b69da4c - - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,13 +532,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - '388983871932' - - baa8823f8073 - - 4d3ce9dc1525 - 591cc8518033 + - b641062a2587 - bf8325a07ce7 + - baa8823f8073 + - 4d3ce9dc1525 - e8af591435d1 - - b641062a2587 + - '388983871932' - b17394940c7a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - d1f8f55f564d - - e6b5cbbf449b + - 3a233c8eb814 - 3ca3de4e5291 - - 38d75661c235 - - 1a2ef636f48e - 59fa8742285e - c2ab91a0d506 - - 3a233c8eb814 + - d1f8f55f564d + - e6b5cbbf449b + - 1a2ef636f48e + - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -577,8 +577,8 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -605,8 +605,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -619,8 +619,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -647,8 +647,8 @@ tools: - name: vcffilter owner: devteam revisions: - - 6b935ab36d7b - 4bdc111b2470 + - 6b935ab36d7b - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -697,8 +697,8 @@ tools: - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -711,8 +711,8 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 06370d956..15250eab7 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 18aad692772a - 9def47f3c1e4 + - 18aad692772a tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 93869f322..857f6d150 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,9 +2,9 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - c2ef298da409 - 78c75f134c16 + - 3f3e247c053d - 4efdca267d51 - 6e9aea89e388 tool_panel_section_label: Annotation @@ -33,23 +33,23 @@ tools: - name: aegean_parseval owner: iuc revisions: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 1aae04680c4b - - 133f36c29579 - - a79ee60b6926 - - f29602ae449e - - cd2480f35935 - 44018dd6b447 - - 4f2967b27e67 - - 3e1f6f6d557e - b5d8e5475247 + - a79ee60b6926 + - 4f2967b27e67 + - 1aae04680c4b - fe3ca740a485 + - f29602ae449e + - 133f36c29579 + - 3e1f6f6d557e + - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,26 +62,26 @@ tools: - name: augustus_training owner: bgruening revisions: - - 7be22100e5e1 - - f1e653756174 - dc027fa56d55 - 6519ebe25019 + - 7be22100e5e1 + - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - bd0e53f3a891 - 28433faa6e42 + - 09855551d713 - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - d77802fe76f7 + - da5f1924bb2e - 92eee5f31117 - 728dacaf08a9 tool_panel_section_label: Annotation @@ -89,9 +89,9 @@ tools: - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,16 +116,16 @@ tools: - name: cpat owner: bgruening revisions: - - 8e9e228c54c4 - 7ccc6234b54e + - 8e9e228c54c4 - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - 63662ae295d6 + - d9c3016f7283 - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -150,35 +150,35 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 9c15ca7e764e + - b6b5cd37f2a2 - 14f588312c56 - - 3bbe70fef6df - 582fd74dc2a1 - - 756376aeb1ae - 9f2455341fac - - 9c15ca7e764e - - b6b5cd37f2a2 + - 3bbe70fef6df + - 756376aeb1ae tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 0ffe5be70caf - - 73428a792541 + - 8e1ace8f77c6 - 989f7c061f35 - 30fb23d4c31c - - 8e1ace8f77c6 - a230ea445788 - 1691af4a0d17 + - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 30f08d74024f - 57c6718cbfcc - - 5a5ae61da69c - - 494f0bb4a993 - e94187d661df + - 30f08d74024f + - 494f0bb4a993 + - 5a5ae61da69c - 0418d28136de - 563a19373357 tool_panel_section_label: Annotation @@ -186,25 +186,25 @@ tools: - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 - d6c7106b7b2e - - f77d7b685bb3 + - 2bba2ff070d9 - 4b96ced19f75 - 7abc5f6dd595 - 1bc5a03faf2e + - f77d7b685bb3 - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - fed64e676186 - 520e30695ec3 - - d77fdcca400e - - b3cf4684e9c7 - - d3af38b9c7e1 - 54961e026fe4 + - fed64e676186 - 52af33194019 + - b3cf4684e9c7 + - d77fdcca400e + - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -216,9 +216,9 @@ tools: - name: gff_to_prot owner: iuc revisions: + - 07d7991bf205 - 2aea122fbd25 - 79261884facd - - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -230,10 +230,10 @@ tools: - name: goseq owner: iuc revisions: - - 8b3e3657034e - ef2ad746b589 - - 602de62d995b - 43798b4caee0 + - 602de62d995b + - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -257,16 +257,16 @@ 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: - - 74810db257cc - 98cafcbd2578 - c55643c3d813 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -291,19 +291,19 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 + - c8ac28e8ac44 - 033755194fe9 - - e95d52d295d7 + - 624606f7c996 - b815ec682418 - - c8ac28e8ac44 + - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -352,9 +352,9 @@ tools: owner: crs4 revisions: - d643e3b03500 + - bf68eb663bc3 - 8a22554cdde2 - a17498c603ec - - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -366,8 +366,8 @@ 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 @@ -398,29 +398,29 @@ tools: - name: snpeff owner: iuc revisions: - - 268d162b9c49 + - 5b80f544c67f + - 6322be79bd8e - 8f92c2b26e6d - - cfcf33df7fc0 - 68693743661e - 5c7b70713fb5 - - 5b80f544c67f + - cfcf33df7fc0 + - 268d162b9c49 - 5a29ab10dba6 - - 6322be79bd8e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 09d6806c609e + - 5fab4f81391d - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -432,16 +432,16 @@ tools: - name: tbprofiler owner: iuc revisions: - - 037a11682176 - - ba6f87115e13 - - e1a9d6fd258d - - 51dd22484644 - - 809dfc93d593 - - d03af1c7002c - 45083d070fb8 + - e1a9d6fd258d - ac8250086ac3 + - 809dfc93d593 + - 51dd22484644 - 37213cf56392 + - d03af1c7002c + - ba6f87115e13 - 200c378d85f3 + - 037a11682176 - 4839e590cb26 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 6161aaf8c..30ee18bf0 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,79 +2,79 @@ tools: - name: abyss owner: iuc revisions: - - 553bfe8bd0b5 - - 841084c5fc46 - - 0e93176640ac - - d6d5ccc2c581 - - 8f1b150a2487 - 7547fcab5d19 - 0124fce4654a + - d6d5ccc2c581 + - 0e93176640ac - a929ce596a34 - 890b794c997d - fa5259cc561b + - 553bfe8bd0b5 + - 8f1b150a2487 + - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b9e31c5c01c7 - 21e491ad532a - 067592b6b312 + - 94fe43e75ddc - b2860df42e16 + - b9e31c5c01c7 - ddddce450736 - - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - 3371c5bdc17a - - faee8629b460 - a7f16f24e9a1 + - 5258e18bbe23 - 22286dab5aa1 + - faee8629b460 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: - - bb935709506a - - 602fb8e63aa7 - - 1e62c28ba91d - - 4048d82f0c88 - - 0d243f458b53 - 46ae58b1d792 - - e4bd1e99bacf + - 2babe6d5c561 + - cf13a1e03e5b - ea8146ee148f + - 2dd755c1c6ff + - 602fb8e63aa7 - 1440ae06552f - - 41030a6c03b7 - e824f5d958d0 - - cf13a1e03e5b - - 2dd755c1c6ff - - 5ecdeca79a0d - - 2babe6d5c561 + - bb935709506a + - e4bd1e99bacf + - 4048d82f0c88 + - 1e62c28ba91d + - 41030a6c03b7 + - 0d243f458b53 - 94170eee0ad8 + - 5ecdeca79a0d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - 86f150c8019d + - 5732f959936a - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -88,41 +88,41 @@ tools: owner: bgruening revisions: - e27815e82dd4 + - 291923e6f276 - 3ee0ef312022 - 1ce9b1d72ec3 - - 3e4f8642c77e - - cb8dfd28c16f - - 291923e6f276 - 8d4f03b5fe9d - - 276f5d8712d5 + - 3e4f8642c77e - 1f0769f0b56b + - 276f5d8712d5 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - b2f674562a18 - 460fad600dce - - 3169a38c2656 - 01210c4e9144 - - b2f674562a18 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - 7348b69e5109 - ba88bc5a6446 + - 8b330a577046 - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - - 5127a713de83 - 3fba9c77550a + - 5127a713de83 - 3ef480892a9f + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -134,23 +134,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 3f7be05a1597 - - ec9e21e9c71b - - 41cea2aa2dce - - da9d8bf98802 - - 6505bd37670d - - 5f625c63b8bc - - f3c89da3af16 + - 60024a528cbd - 2061fb3b81b4 + - df25d4fb79b7 - 366a11d316a7 - - 60024a528cbd - - 0ee0c3089254 + - f3c89da3af16 + - da9d8bf98802 + - 41cea2aa2dce + - 3f7be05a1597 - 045c7c3d8e59 - - 71740308d412 - - 284a1cb82b61 + - 5f625c63b8bc - 9ef6920c3089 - - df25d4fb79b7 + - 6505bd37670d - 5bec28269d95 + - 284a1cb82b61 + - 0ee0c3089254 + - 71740308d412 + - ec9e21e9c71b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,20 +174,20 @@ tools: - name: megahit owner: iuc revisions: + - 14ddfc8ffb93 - 7518ee87b53d - de387b2b2803 - - 14ddfc8ffb93 - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - eb7b00ec347d - - 9d79beb19ac3 - - d7edbc9c3a07 - f8113c25bc6b + - d7edbc9c3a07 - 39edec572bae + - 9d79beb19ac3 + - eb7b00ec347d - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -195,22 +195,22 @@ tools: owner: iuc revisions: - 51c2360aa807 - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - e731ea24e48d - - 2ecf5a570907 - - f369ef5f210b - - fd128c111ab0 - - eb7a370f6588 - - f338e9942b27 - 99ecfdafc64f + - f369ef5f210b + - e731ea24e48d - 3ca2d2a9068c + - eb7a370f6588 - 606b09cc9860 + - fd128c111ab0 + - 2ecf5a570907 + - f338e9942b27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -222,10 +222,10 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d - 8b6d0d85252b - a7b889b90140 - 73a3846701e1 + - 8dee0218ac7d - b799a615995d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -244,9 +244,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 15200570e926 - 7c2f5268d01c + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -261,43 +261,43 @@ tools: - bbe19ef04a74 - d256a51a656b - 79b48f02db49 - - 2b16ba799da9 - dfb8a4497339 - - 8fef980d48b5 + - 2b16ba799da9 - 02831bf9e95f + - 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 + - 3061c8b029e5 - 875d0f36d66f + - 342a1d1fed7b - 6fcbee531de6 - 72472698a2df - - 3061c8b029e5 + - 7594365c546b + - 675488238c96 - 59db8ea8c845 - - 342a1d1fed7b - ebb0dcdb621a - - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 - - 39bed8de8017 - - 78c533842eeb - cd06929b224b - d865b62f501c + - a199cd7ac344 + - 78c533842eeb - aa39b19ca11e + - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -309,31 +309,31 @@ tools: - name: raven owner: iuc revisions: + - f8564b2d7f63 - 5c55448d0f33 - - f11b994b7eb2 + - 33b7d8481a76 - 3edba9afc9bc - - f8564b2d7f63 - 2b2a352488fa - - 33b7d8481a76 + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 378e55aeeb25 + - 53c2bc8c2ae3 + - 1d06c8b38e77 - e122f9101584 - 28189050e437 - - 53c2bc8c2ae3 - - ef69617ecb42 + - 378e55aeeb25 - 5fc94b3a4704 - - 1d06c8b38e77 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -345,78 +345,78 @@ tools: - name: shovill owner: iuc revisions: - - 865119fcb694 - - f698c7604b3b - - d9f6a00b6db7 - - 83ead2be47b2 - - ee17a294d3a3 - 196a599ec43d + - d9f6a00b6db7 + - f698c7604b3b - ad80238462c1 + - 865119fcb694 + - ee17a294d3a3 + - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - - 24e471d13fe9 - 5e0825476fb7 + - 24e471d13fe9 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - c33a476f4001 - 904bf932cf78 - - 1fc82fe7ebef + - 051fd2db8a27 + - 604782a8a53a - 7490b213baa9 + - 1fc82fe7ebef - 1bb12736175c - - 604782a8a53a - - 051fd2db8a27 - - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - fee85957cebe - d6e617c4e338 - - 808b3a0a6716 - - 9678993ca5bd + - fee85957cebe - 34305b013402 - - ad8b536d1caa - 655fa188c3cc + - 9678993ca5bd + - 808b3a0a6716 + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - - 037f9927c4ff - 7e27faaad80e + - b8002c3f7141 + - 8d4b90bf9caf + - 21da31ed41a1 - 6b5a5842531e + - 037f9927c4ff - e5a3b75a271f - - 21da31ed41a1 - - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - 7922870efcca - - 2a10645aeadd - 328aa71f0f3c - f1532cb33c75 - - 9de69775f512 - - 5b26685e5d3b - 86f66ab58e14 + - 2a10645aeadd + - 5b26685e5d3b + - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 340bc17f49cf - - e41dcb0e913b - - 85fb02c43042 - 1708851f8804 + - 85fb02c43042 + - e41dcb0e913b - 8cc856b935ee - 6aad515a5270 tool_panel_section_label: Assembly @@ -424,109 +424,109 @@ tools: - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 + - d159735a6a9f - d5fb354f745d + - b65a43f70b99 - 6357b127161e - - de1260f8a300 - - d159735a6a9f - b3490b036c5a - 249f6a28c751 + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d5887ace0dd4 - - 7897763d14ec - - d2d1df21dfb9 + - dd7ad84f3943 - a90db5dbaaf3 + - d2d1df21dfb9 + - d5887ace0dd4 + - 9006e5836729 - 33368fec3b70 + - 7897763d14ec - b7829778729f - - 9006e5836729 - - dd7ad84f3943 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 189e837009c9 - - 505a9833ab5d - - 6f4c8ad6ea01 - - 8f631679571f - ed2425b9fd27 + - 505a9833ab5d - ced385aa976d + - 8f631679571f + - 189e837009c9 + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e + - f31d376ce725 - 356afed970b4 - 9ded6109434a - - 19bdfd1e6fe3 - e59bee4565b3 - - f31d376ce725 + - 19bdfd1e6fe3 + - d40ed4eb0c0e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - af40e971a8cc - - b23249f81bc4 + - 4688ae3b49b5 - ebd801e712bc - - 6dd935e4984b - 80a17897564d - - 4688ae3b49b5 + - b23249f81bc4 + - af40e971a8cc + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b64696992ee9 - cb1e3db43020 - - bb11fefb23a3 - b5e35a2ca4f3 - - 937ea677d437 - 59bd28f6265d + - bb11fefb23a3 + - b64696992ee9 + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6bfab4a4a988 - - 2628f6790eda - 6015aa0303f2 - - cb4768eeca3b + - 2628f6790eda - 383bb5ad32e2 + - 6bfab4a4a988 - 05bd7504fdb2 + - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 8f9f06995f98 - 6e26c9afd301 + - 3e44ef016b45 + - 8f9f06995f98 + - e92675014ac9 - 9e3e80cc4ad4 - 0a3a602cd1e3 - e022dff952df - - e92675014ac9 - - 3e44ef016b45 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 5da9a0e2fb2d + - 8d09f8be269e - 920677cd220f - 08256557922f - - 8d09f8be269e - - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 37d88f41c810 - 4a53b89fa703 + - 37d88f41c810 - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -539,8 +539,8 @@ tools: - name: yahs owner: iuc revisions: - - 425e63adcc5d - ff4031bfaa22 - 39495e107274 + - 425e63adcc5d 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 7b5384b80..26bea9656 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -3,25 +3,25 @@ tools: owner: iuc revisions: - 1ae00120dd24 - - bfd290fe1588 - 4768f7f8e93f + - bfd290fe1588 - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 1f5641a52664 - ded48b36f3b7 - - 8e8dc9a1e3e5 - 31812e7a1315 + - 8e8dc9a1e3e5 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - - 24a7a95867b0 - 17fcac7ddf54 + - 24a7a95867b0 + - 5c8ff92e38a9 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 8c04ebbf9..6a6f9fe38 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 + - 1c427e24fb79 - d1f62024a08b - - 7beb76ffbc0f - a9c9d768b751 - - 1c427e24fb79 - - 204a131e47db + - 7beb76ffbc0f - 0840ba83860c + - 159b04e36791 + - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index e6eaf0052..e2c0e74bb 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - a68aa6c1204a - - b28e0cfa7ba1 - - a1a923cd89e8 + - 0a5c785ac6db - 07e8b80f278c - - e19bebe96cd2 - - a8eabd2838f6 - dde39ba9c031 + - 87ee588b3d45 + - a8eabd2838f6 + - b28e0cfa7ba1 + - a68aa6c1204a + - e19bebe96cd2 + - 64e2edfe7a2c - ce3c7f062223 - - 0a5c785ac6db + - a1a923cd89e8 - 589e7e57fd6d - - 64e2edfe7a2c - - 87ee588b3d45 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 1c06d97ec..df3ac39a5 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: + - e8ac2b53f262 - 54f751e413f4 - 62c9df8382c2 - - e8ac2b53f262 - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - e25d3acf6e68 + - 0e3cf9594bb7 - d999e774072a - - 5edc472ec434 - - a52d2d93e595 + - e25d3acf6e68 + - cbf3f518b668 - 6f386c5dc4fb + - 5edc472ec434 - acf4e47b734c + - a52d2d93e595 - 2889433c7ae1 - - 0e3cf9594bb7 - - cbf3f518b668 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 7eb6ddedc..ea8ed51e5 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 - - 710301bc46fa - 095ad4d096d1 - - c8cdde00b105 + - 710301bc46fa - 27ee142314a9 + - da6bd1975a71 - f4230f116196 + - c8cdde00b105 - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - bfb65cb551d8 - - 0fac8e2afc13 - 79cfd9ead848 - - 3b8a9d5ced85 - 88076940fa94 + - 3b8a9d5ced85 + - 0fac8e2afc13 + - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - eb6564a60136 - - 55918daa5651 + - 715cd0e87781 - f5d979cb4b54 - b46d4b4d995c + - eb6564a60136 - d532b7e5f64b - - 715cd0e87781 + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 5579659312e6 - dae135dfd519 + - fdf2cc80adb5 - d2f955aea23a + - 5579659312e6 - f26afd1b7104 - - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - 319a28774da9 - - bc31d02be922 - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 4da9ee404eab - 2c349b027a01 + - 4da9ee404eab + - cac1886249a2 - 070e3ecc3fda - ed736e6eee39 - - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 807aa4c9293d - - da8753545526 - - c0c9a5024177 - - 525ca7c8065f + - f197e34c33a9 - 2e219a2d9327 + - 525ca7c8065f + - c0c9a5024177 - 73008ef1f487 + - 807aa4c9293d - d1f803b5943c - - f197e34c33a9 + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - 1809414a9454 - - 7568ae18908a - c4fbab8e03c5 - 2c8ed1b52bf7 - - 61094e01eff9 - 27ea4e1a3f95 + - 61094e01eff9 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 + - 79e8ab8f1e81 + - 730ef07b90ae - ba83f0923369 + - d7ec25187599 - ccfbd956a2d3 - - 730ef07b90ae - - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -269,8 +269,8 @@ tools: owner: bgruening revisions: - e2c36f62e22f - - e6011617c748 - 4242b4d68e9c + - e6011617c748 - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -351,9 +351,9 @@ tools: owner: bgruening revisions: - 9b48456a96fe + - d4c67ced6abc - 85fad59f8168 - bf99565cec1f - - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 8da32525d..ae0972bad 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: - - 163688bb8f73 - - 2605cbdaa7d8 - - c97a786e8fb5 - f907216064f6 - fa56d93f7980 + - 2605cbdaa7d8 + - c97a786e8fb5 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -25,11 +25,11 @@ tools: - name: macs2 owner: iuc revisions: - - 86e2413cf3f8 + - 640d3af5d833 - 424aefbd7777 - 495a4173006f - f5d67c722d67 - - 640d3af5d833 + - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index c5a664587..02e426c53 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 90981f86000f - 830961c48e42 - - 25136a2b0cfe + - 90981f86000f - 33151a38533a + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - - 2dae863c8f42 - baabc30154cd - 6cbe2f30c2d7 + - 0046692724f9 + - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index c301ea401..d1766bc1a 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 0b3c3ad92827 - - 5e1240a87bcb - - f3a19509108a - - e3cbd2287f63 + - 4a6ee918c13a - ab9350a8ab4d - 367b1ed91207 - - 4a6ee918c13a + - 5e1240a87bcb + - e3cbd2287f63 - 3b6f97e7094c + - f3a19509108a - a3b86937ead6 - 6ef0b5664c69 + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 091bb5922a82 - 33c99804a32f + - 501c21cce614 - 72ed72122deb - - 1b5fc03380d4 + - 584008e574b2 + - e177a8ea0bf1 - 54ccb7e1f49a - - 501c21cce614 + - d4d4e9febf5c + - 091bb5922a82 - bd46669113b9 + - 1b5fc03380d4 - e525f9ffb9ac - - e177a8ea0bf1 - - 584008e574b2 - - d4d4e9febf5c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -65,9 +65,9 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 8979c288aefb - - 77b41c89d856 - 186b8d913e6c + - 77b41c89d856 + - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -94,8 +94,8 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d + - 4dea02886337 - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,8 +121,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - 18dbde5680c0 - b9ea85dfaf45 + - 18dbde5680c0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -135,18 +135,18 @@ tools: owner: devteam revisions: - 68f57cc8fad0 - - 2dcfbbf9071a - 78fb18899c99 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - 19e45916daf9 + - 26c6706bfb07 - b9b385097f13 - 92ac8e086317 - - 19e45916daf9 - 63769c4217a7 - - 26c6706bfb07 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 cd84e3727..1b0360a8f 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - a1ca9bccc7f2 + - de72ba3ed6f2 - 29451af70c52 - 268e91e540ee - 5f6d123679f4 - - c929a006727f - e821645ef8fc - - a1ca9bccc7f2 - - de72ba3ed6f2 + - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - bb1e4f63e0e6 - - 5d11599b8a7d - 2d2cf5c1ea8a - - 12af64f93288 - 0e49b109abc2 - - 0e143b4c3987 - 7a7fd0f5f15d + - 0e143b4c3987 + - 5d11599b8a7d + - 12af64f93288 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 195e98217334 - dc059492a995 + - 195e98217334 + - 81b1e3e1fc6c - c06951d10364 - 7c1beb6d6eca - 1d848bc4585f - - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - 71aa86af6762 + - bfff7454b59a - 07418a30ed01 - 3d211717a775 + - 93eb012d9eed - 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tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - d57251071381 - - 2da482e408b8 - 23f7c5f1fdaf + - 2da482e408b8 + - b88ebb3672a1 + - d57251071381 - f8fc4e5aff9d - 793665fff0f8 - - b88ebb3672a1 - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - ba6efa77fb79 - - a7849312d328 + - e4c7985d4585 + - 25d830337d31 + - 010e58e9d822 - 512155688d98 - c60570fa602f + - ba6efa77fb79 - a4dfb122e52b - - 010e58e9d822 - - e4c7985d4585 - - 25d830337d31 + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 4d678170d29b - - 00d869ea03a1 - - 443d9a9d6d11 - aa200e4f3939 - 69264da0ce77 - c899e0ccff8c + - 443d9a9d6d11 + - 00d869ea03a1 - 38e3f226248b + - 4d678170d29b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 6662b1a8d326 - - 10301d137111 - - a2d70c4fd406 - d806504e96d9 - aac8444d6681 - c361b12d207a + - 6662b1a8d326 + - 10301d137111 + - a2d70c4fd406 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 04fa04399..69d156f58 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: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -30,8 +30,8 @@ tools: - 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 @@ -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: - - c0f7b58b4ce4 - d4bea99366f9 + - c0f7b58b4ce4 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 f664232e7..08bf8c016 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 832c20329690 - - 63dd26468588 - dba489bfcd62 + - 63dd26468588 + - 832c20329690 - ce385837c160 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 3d7570e88..cf8b05588 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 29bdbc353f20 - - cf1322aeb137 - 62f5fab76dfb - - 6da3972210ee + - cf1322aeb137 - d82648ad25a3 + - 6da3972210ee + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 156245560..29136720e 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,33 +8,33 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5eb7e84243f2 - - 093678460093 - 660cffd8d92a - - e4691e1589d3 - - c5e2e5902201 - - 5915ea1ec9b1 - - 64172f1c1202 - - 48f587c13075 - - b1c926deaa2d - de6cebe3c043 - - fe74900d6dc7 - - 4e5056fefd88 + - 64172f1c1202 - 8665bcc8b847 - - 44e2cc14f75b - 135b80fb1ac2 + - 49370cb85f0f - c4b82dce8335 + - e4691e1589d3 + - 288f97432497 + - c5e2e5902201 - c053d4cad713 - - 49370cb85f0f - 8c0175e03cee - - 288f97432497 + - 4e5056fefd88 + - 48f587c13075 + - 5915ea1ec9b1 + - 093678460093 + - fe74900d6dc7 + - b1c926deaa2d + - 44e2cc14f75b + - 5eb7e84243f2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - f666895cbebd - 8889eb864cef + - f666895cbebd - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 @@ -75,44 +75,44 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - f81d4362b6c1 - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - cd0874854f51 - - 9c620a950d3a - 0dbb995c7d35 - 56022eb50bbd + - cd0874854f51 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - 65b93b623c77 - dbf9c561ef29 + - d60c3f704da0 - c59d48774d03 - 1d8fe9bc4cb0 - - d60c3f704da0 + - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 - 9115b978ce10 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: + - '144275714590' - 10b75444feae - 81a9090d6df3 - - '144275714590' tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -126,48 +126,48 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 5b87038565bb - e30352e889fe - 7861f3b10c68 + - 5b87038565bb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 4e1d64e6385f + - 9dfda4e310ed - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 523c2aff0376 - f3936d0632cb + - 523c2aff0376 - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - b41c2c1bcfbf - 3e396e702cea - 2ccb8dcabddc + - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - 8d958759cf2a + - 09a2199cd356 - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 397dc333436b - 35e38452bb3f + - 397dc333436b - 249c8393f2d4 - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ @@ -175,93 +175,93 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - - 74db4cffab1f - 045f0e1043f7 + - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - f86c27295151 + - f0e7deab6518 - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: + - 33794bdb7fe0 - f0b18efb97f1 - b63b2bfb3ea3 - - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - - 297962e79f39 - ac3fed111eb6 + - 297962e79f39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: + - 529bccd5e4a1 + - 567d5b3c52b1 - d5e9e83cd3d8 - 09070cacefd8 - - 567d5b3c52b1 - - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - 736b8f6ee456 - - bdf1ce174e39 - - cb1e251cac37 - 90858c306551 + - cb1e251cac37 + - bdf1ce174e39 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser 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: - - 3599f5451ee2 - - f984bb114520 - - 02f8a17a4ebd - b29d37ca9e41 + - 02f8a17a4ebd + - f984bb114520 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 0c2907307ba4 + - 177f0621c266 - 6027ef51ef91 + - 0c2907307ba4 - e246088b6e34 - - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 61b4cedc8934 - 547e8d00f11c - - 73194cdd4f57 + - 61b4cedc8934 - 377ac2829eac + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -273,17 +273,17 @@ tools: - name: pear owner: iuc revisions: + - 037f0acc7830 - b4c6f054210a - - f69501361cec - 2f804526f5fd - - 037f0acc7830 + - f69501361cec 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 @@ -296,8 +296,8 @@ 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 @@ -317,19 +317,19 @@ tools: - name: ucsc_fasplit owner: iuc revisions: + - bf04bd405d5b - 71f649c23021 - d3f58a0dc09d - - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: + - 24013bf85a6f - 71ad4a56c40c + - b557acca0b56 - a535cf1e5da4 - - 24013bf85a6f - e654095ab143 - - b557acca0b56 - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -343,14 +343,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 015cf18f4a15 - - 828dba98cdb4 - - 27ac32a22ad2 - f3759eec3018 + - 27ac32a22ad2 - 7accf7407811 - - 7a7e33d28f62 - 6a675c3aa610 - 9fa7803d1c51 + - 7a7e33d28f62 + - 828dba98cdb4 + - 015cf18f4a15 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -363,8 +363,8 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 953b4821b183 - e4e12f0b3af1 + - 953b4821b183 - 4c8a1c7d3608 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 987f75524..4c9ddda74 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,9 +2,9 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - - 7b4468117008 - ce9cd02d5b88 + - 7b4468117008 + - 64e9a6afdd0c - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,13 +19,13 @@ tools: owner: devteam revisions: - 2c64fded1286 - - ff9530579d1f - - e7b2202befea - 9da02be9c6cc - - f2e8552cf1d0 + - e7b2202befea - 5ec9f6bceaee + - ff9530579d1f - 2b0c9d9fc6ca - 3d0c7bdf12f5 + - f2e8552cf1d0 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -39,47 +39,47 @@ tools: - 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: + - 59003d0543cd - 7306ec78632a - cc0fd298cc17 - - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - 8880fb74ef56 - 1f296803dfa3 - a72af9de6bf5 - - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - c1a4b5f3b432 - - b2f1f75d49c4 - - 1c2db0054039 + - f7e2f1eb3a16 + - 75c93c70d094 - 5e33b465d8d5 - - bf675f34b056 - abfd8a6544d7 - - 9a913cdee30e - - 75c93c70d094 + - c1a4b5f3b432 + - bf675f34b056 - 3d93dd18d9f8 - - f7e2f1eb3a16 + - b2f1f75d49c4 + - 9a913cdee30e + - 1c2db0054039 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - - 949f01671246 - cd7e644cae1d + - 949f01671246 + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 35dc8cde4..1dc6b6ca8 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ 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 @@ -16,8 +16,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 85ef5f5a0562 - 83a19df00eab + - 85ef5f5a0562 - 141612f8c3e3 tool_panel_section_label: Filter and Sort 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 c076ea8a5..e4f053657 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,23 +9,23 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - - f2f3bc622a16 - 8f53b238a360 + - f2f3bc622a16 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -86,8 +86,8 @@ tools: - name: gemini_load owner: iuc revisions: - - b2c25142267e - cf61daf064fe + - b2c25142267e - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: - - 666f60a9331a - - da74170c55c7 - 840fb4850be3 + - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -151,8 +151,8 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index dd5bc64db..9844ff03b 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,15 +2,15 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -23,8 +23,8 @@ tools: - 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 3b7d67575..a8b11c03f 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - 983bf725dfc2 - e9df53a75f3c - b39347891609 - c1b437242fee - - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: + - 1c58de56d587 - 28587613264f - e063168e0a81 - - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 5e6237d58b0c - - 9a776b080193 - - 7068f48d0ef9 - - 653e89d73fc4 - - 1ec814014652 - - 8848455c0270 - - e08a7ad4378b - - 6591f049cf7e - 1790dcf3c32d - - 734abc7ac21d - - 6ea73833cf67 - - ba931a59dd59 - - c441583adae5 - 516a54ddf218 - - e407b9da183a - 69ebb7f46e45 - - f8054ea1c365 - - aad3885b3216 + - 4df8de2d0e48 - f5ea3ce9b9b0 + - 653e89d73fc4 + - 6591f049cf7e + - aad3885b3216 + - 1ec814014652 + - 9a776b080193 + - 734abc7ac21d + - e407b9da183a + - 6ea73833cf67 - 83c7d564b128 + - 7068f48d0ef9 + - 5e6237d58b0c + - f8054ea1c365 + - c441583adae5 + - 8848455c0270 + - ba931a59dd59 + - e08a7ad4378b - 4317d3cb6cba - - 4df8de2d0e48 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 75b3b3d0adbf - 9aaa46d45472 - 34758ab8aaa4 - 21a560af5913 - - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 468c71dac78a - bfdc6a7ffd3a - af5eccf83605 - - 054483e27a35 - 95fb5712344f + - 468c71dac78a + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 9a2b4a404..ff1324d5d 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: + - 4b519282a05b + - df7356989ac1 - a64dc31ab7f2 + - ae9994cf526f + - 740057a5126d - fd59d783248a - 7f13dc906cb9 - - ae9994cf526f - - 290a11559985 - c4bde687c846 - - 4b519282a05b - - df7356989ac1 - - 740057a5126d + - 290a11559985 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,8 +28,8 @@ 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 @@ -42,21 +42,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - 3b37b1b1c3a7 - '566197475670' - 374e9062d874 + - 3b37b1b1c3a7 + - 53460afd5115 - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 1a72f938213e - - da4c086cff5b + - 10515715c940 - 391a4cc45fea + - da4c086cff5b + - 1a72f938213e - 3d059e9c2fba - - 10515715c940 - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,19 +77,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - d0fc8b746d57 - 5298e06f14f9 - - 5fe1dc76176e + - d0fc8b746d57 - 1acf88921176 - - e3a675da7fd0 + - 5fe1dc76176e - 299307abd804 + - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 17b666467c32 - 0e7290688b50 + - 17b666467c32 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -101,15 +101,15 @@ 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: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -127,17 +127,17 @@ tools: - name: jbrowse owner: iuc revisions: - - fd5dbf0f732e + - 112eb40ba6cf - 1cfc579079a6 - - 667e17248bfe - - 836d1aa3e89a - - 4542035c1075 - - a6e57ff585c0 - 6cd09d7b5f37 - - ca2def38369c + - fd5dbf0f732e + - 836d1aa3e89a - 17359b808b01 - 2bb2e07a7a21 - - 112eb40ba6cf + - 667e17248bfe + - ca2def38369c + - a6e57ff585c0 + - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -155,23 +155,23 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - 03c13085aecc + - f1691de443a7 - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - 594b85e4237a - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c - 85da91bbdbfb + - 62e3a4e8c54c - 1c5dcef5ce0f - f234e2e59d76 tool_panel_section_label: Graph/Display Data @@ -192,9 +192,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - 44c66e8d21e6 - 6c571966cfb9 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -206,22 +206,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - 360df4999907 - a1abfa420d9d + - 14e7c35f3d00 - 36b848d5f3ec + - 7dd841a32245 + - 2824d77cd8f8 - 326a3db8d9d1 - 4ac4e7083b7e - - 2824d77cd8f8 - - 14e7c35f3d00 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 73b8cb5bddcd - 2f557f6abbfb - 44608d0193ed - - 73b8cb5bddcd - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 5ea495385..0f8d4aa06 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 @@ -28,8 +28,8 @@ tools: - 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 @@ -42,8 +42,8 @@ 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 @@ -56,15 +56,15 @@ tools: - name: scanpy_find_markers owner: ebi-gxa revisions: - - 0a8e527d1517 - d8f5224005bb + - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -77,8 +77,8 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 3c47bc560688 - 352cdf3b2f75 + - 3c47bc560688 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony @@ -91,9 +91,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - - 9a2f72d7dbd2 - ff6decc0f432 + - 9a2f72d7dbd2 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -148,15 +148,15 @@ tools: - 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: - - 79cc06a557b0 - 6a6364b488db + - 79cc06a557b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -197,9 +197,9 @@ 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 diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index e390430ac..2a8edcea3 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,51 +2,51 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - a4c13ddcc8ee - - 9edf8894a22d - - 921a2da49a0c - ed2cca6b5de4 - 29f66c353bcb + - 921a2da49a0c + - a4c13ddcc8ee + - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - d404277cc87a + - ec4b948dc6f0 - 78fb5e286609 - 755df866ad0c - - ec4b948dc6f0 - - d404277cc87a - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 4d511437b1e5 - - 03dd3c16ae4e - - 977dc15add20 - - 11fa44ee0603 - 9e357a8b2ec3 + - 11fa44ee0603 + - 977dc15add20 + - 03dd3c16ae4e + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - c3e5e2cf12b7 + - 3b5b54ed6392 - 77919cc3618e - - 0ba4f56a3613 - 41dbf4d162a2 + - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 9939786dd9c9 + - 12d51d7be66f + - 7babd8a46fe0 - 5308ca68ef3d - b63363075c2e - - 7babd8a46fe0 - - 12d51d7be66f 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 e30610fa2..949718097 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,45 +2,45 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 81f0cbca04a7 - - 8bccb36e055a - - 699a5e9146b3 - - 3df9f0a4bf34 - 0c777d708acc + - 3df9f0a4bf34 + - 8bccb36e055a - 7db4fc31dbee + - 81f0cbca04a7 + - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: + - 5bc8cdc17fd0 - 0a53256b48c6 - 5791a7f65275 - 2436a8807ad1 - - 5bc8cdc17fd0 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - - 6ad1d3cfdea1 - 9d47aabda459 + - 6ad1d3cfdea1 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 77f7159d775a - - b1c2c210813c - 70316d792fc9 + - b1c2c210813c + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - dba87c4b32d3 - - d51310ab328a - f70b215d155c + - d51310ab328a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_split_binaryimage_by_watershed @@ -52,11 +52,11 @@ tools: - name: bfconvert owner: imgteam revisions: - - fcadded98e61 - f3360fbeda64 - - 85edbb7a436b - - 10eed33aa9b2 + - fcadded98e61 - b07f4839ca77 + - 10eed33aa9b2 + - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -70,111 +70,111 @@ tools: owner: imgteam revisions: - b58447a2eed2 - - 5bf8eb50b280 - 664232d2a3f7 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - 0e4dccaafef5 + - e917a2424690 - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - e7273daa5ae2 - - 670975e92458 - 6070780813d9 + - 670975e92458 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - df3ad3ba5c6f + - cdf8e3c57dae - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 2484086dee41 - - 6a7da2e5f696 - 5d28ac336861 + - 6a7da2e5f696 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - 11f177b1a59e - bace5a93a97c + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: + - d0178bdcd00e - f8fa0f6718a3 - f24c370e5ea4 - - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 3245681b2f6d - - 31d195bedf6d - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: + - b6eec6087271 - 87d4d92d7487 - 993faa34333b - - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - c09dcda1143f + - 6100a22bf4f2 - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 667a513e67e4 - b178453ea8d1 + - 667a513e67e4 - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: + - 2564f461de62 - a1a961c46d4b - ac5bea85a391 - - 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 @@ -188,8 +188,8 @@ tools: - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - e972e07c7845 + - d3890df07463 - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -197,24 +197,24 @@ tools: owner: bgruening revisions: - 407925835dd9 - - 980aed9e8fd5 - e52c75a28c4b + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - 79e10d12d90a - - d85f11570109 - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - b76841ee5560 - - 80b200ae516b - 035a58c7f54a + - 80b200ae516b + - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -227,16 +227,16 @@ 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: - - 33f4fa1413fb - 27edbb90ab2b + - 33f4fa1413fb - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -263,8 +263,8 @@ tools: - name: image_info owner: imgteam revisions: - - 7b6d9412c7f8 - 236ec78b2e53 + - 7b6d9412c7f8 - f8b4eada923c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index dca7585c1..fae443492 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - e319b5b65879 - - 3e4f434a69c6 - - e4ee04da1c19 - d6e72da3ec35 - - f362150bef41 - - 78bbd17d0703 + - 40737febe339 - 3a72fede57ce - 1069f6db0a0e + - 78bbd17d0703 - a38934e303b9 - - 40737febe339 + - e4ee04da1c19 + - f362150bef41 + - 3e4f434a69c6 + - e319b5b65879 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - 7fe36019c073 - - fcbeda41d0ac - - 8f8df367470d - - f91cfb73d369 - 0135f1d487a0 - - 9537184d421f - 618297d23022 + - 8f8df367470d + - fcbeda41d0ac - 72ddd32392cd - - c88553ec696e + - 9537184d421f - 2b95d5c04908 + - c88553ec696e + - f91cfb73d369 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - d7e79eb3bcb3 - fafb3d685fa9 - ad0dc9f4c9e2 - 2cf4a1cafc16 - - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - - ee29337f905c - - 5dc33613c288 - - 43aac8d29685 - 7f1cfa4c0e32 - 6a1515bb0687 + - 3d18f8c3c0f6 + - bd2a7d1316b9 - ee2beb764a7b - - 94df24c6bc00 - - a1c2aecd7a0d - 9eaadf03e0df + - a1c2aecd7a0d + - 5dc33613c288 - 28a6f1908fcc - - 3d18f8c3c0f6 - - bd2a7d1316b9 + - 94df24c6bc00 + - 43aac8d29685 - 8d36959b000d + - 8c05afb547fa + - ee29337f905c tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 9f978da6528a - - cb903c9dc33d - - 364f4ffec275 + - a250929be21b + - 5671e1d3d5ee - db536ad45f28 - - d37ede8589b2 - 86a20ae274fc - - 5d6ed46cc101 - - e3bb03cf207a - - 5671e1d3d5ee - - c092052ed673 + - d37ede8589b2 - bcaa0d571ce2 + - c092052ed673 + - 364f4ffec275 + - cb903c9dc33d + - e3bb03cf207a + - 9f978da6528a - 8858fa037a15 - - a250929be21b + - 5d6ed46cc101 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - 584beffa972b - 12d66d0d05ac + - f95f403841ad + - 230b05597996 - 194e3ceee923 - 3b6a16d82c1b + - e1a015876aa9 - 49236b03e4fd - - 230b05597996 - - 584beffa972b - c5c9f02b6167 - abbc8041e8ec - ed28dd32141c - - e1a015876aa9 - 38b91a3190cd - - f95f403841ad 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 6ac8ba469..61e1d35d7 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - 17e3b698dd52 - f198773344e4 + - b8a457820315 - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - ba0c40780ecf - a513e3fbb4c5 - 22c2a1ac7ae3 - 374cb875d38a - ac092723240d - - 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 b31af29ae..302787147 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,99 +2,99 @@ 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 owner: bgruening revisions: - - f22a9297440f - - 4d81e3e2fb63 - 8a794e6d3388 + - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 818f9b69d8a0 - - b6ef6d0cb6b7 + - f1b9a42d6809 - 2af1346e68c9 + - b6ef6d0cb6b7 + - 818f9b69d8a0 - e1317b5502fa - - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - 1588f9076e32 - 8334dc98c48e - 947c2eacccb8 + - c80db5d6fd8c - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - 83228baae3c5 - 9991c4ddde14 - - 25b46af53232 - 29e4122c90de + - 25b46af53232 + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 - a07ab242b0b5 - - 53616c8b0865 - - 1a53edc4b438 - f3dfa4bdf87e + - 1a53edc4b438 + - 841a6cc5fc58 + - 53616c8b0865 - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 - - d4808d5b83da - 2fc89dcd41c8 - - 40f4447733b2 - 91c4e3331208 + - d4808d5b83da + - 40f4447733b2 + - dc4b5fd604a6 - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 7626ea9c2e1b - 36e8d6d5d01b - - c6ae57f774c6 + - 25ab6b4e376e - 301e07345c93 + - c6ae57f774c6 + - 7626ea9c2e1b - e5a5ad882f1f - - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 + - 0630258dcf35 + - 02d2be90dedb + - f9639b488779 - 80852884053f + - b7c3e9a3b954 - 4ed102b922cb - - f9639b488779 - - 02d2be90dedb - - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - - 14180f9c831e - - 61634a87efc7 - ec69cbe34b73 + - 61634a87efc7 + - 14180f9c831e + - caeb57858702 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 e76415e72..9405789b0 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 03e9b2fbc005 - - f6877ad76b00 - - 017aba02828d - - 0d4acadabb04 - - cd659e8cc5fa - 937aa69e715f - - a6d65b0c67af - - 3ba8d4563129 - 749c918495f7 - - 17062a0decb7 + - 3ba8d4563129 + - 017aba02828d + - cd659e8cc5fa + - 03e9b2fbc005 + - f6877ad76b00 - d5ceb9f3c25b + - 17062a0decb7 + - a6d65b0c67af + - 0d4acadabb04 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,18 +24,18 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: + - 64f11cf59c6e - e188dc7a68e6 - - 53646aaaafef - - 2477830927ec - dfd8b7f78c37 - - 64f11cf59c6e + - 2477830927ec + - 53646aaaafef - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - 37b497aa133f - 3e1ea2facca6 + - 37b497aa133f - 60afcc2c1d05 - - e7f19d6a9af8 - 2ff111fac1d7 + - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - c0c2d0941de8 + - f54f5baedfdd - 11a0d50a54e6 - - 09b53c1d4ab1 - - 037c6e54df11 - - 53c0b7a1a0c3 - 6b1e195506a3 - - 5cc34c3f440d - 3f4d6399997b - - f54f5baedfdd - - 8c6cd2650d1f - - be1d967337e4 - - b3eab4b67562 + - 5cc34c3f440d + - 09b53c1d4ab1 - 77b2770508f6 + - b3eab4b67562 + - 53c0b7a1a0c3 + - be1d967337e4 + - 037c6e54df11 + - 8c6cd2650d1f + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - e403d27e8f24 - ec9cbd6b9a49 - - 9ee34ba73ebf - - 79b885ce78d7 - 42ce70172b72 - - 5ef7ec16b04f + - 178bdbdb6d24 - 1cd2511a396e + - e403d27e8f24 - 00fbfac99d39 - - 178bdbdb6d24 - b8f5f6e87f5c + - 9ee34ba73ebf - 45795f582ae9 - 13022c3d3076 + - 5ef7ec16b04f + - 79b885ce78d7 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 289129e6b..710532e67 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 90dc951da294 - 6cd2a9e6ac49 + - 90dc951da294 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -75,29 +75,29 @@ tools: - name: matchms_convert owner: recetox revisions: - - c990df6afc24 - b9cc12600553 + - c990df6afc24 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - d7b517f2c5fe + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - 9e3c83d2afc3 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -148,8 +148,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 9ff95a1a2705 - 7627b40601f6 + - 9ff95a1a2705 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -168,8 +168,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - b5467dead5b1 - 90745ecc5e9f + - b5467dead5b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -217,78 +217,78 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae - 7b42ee54d757 - c53a97599181 + - 79ad928a0dae tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 18ec7635bac6 - 149b9cc7499b + - 18ec7635bac6 - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: + - 134be5abb208 - 481d769e2f7a - dfebc82ba1f0 - - 134be5abb208 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 9064aecc78a7 - - 51332c2520c7 - 02c772a49998 + - 51332c2520c7 + - 9064aecc78a7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b341cfd4baf8 - - b3413f335327 - e7305ba0dd38 + - b3413f335327 + - b341cfd4baf8 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - 17a48d0a80f4 - - dd7bbc2b99d1 - cf061712a184 + - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - 99d118321d5f - - d7f5878a98c3 - 24278c6b6d1c + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - d90187b0f247 - ffbabefbd2e2 + - d90187b0f247 - ea0758b41473 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 f5c8a7977..ecc37c47a 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,15 +2,15 @@ tools: - name: bracken owner: iuc revisions: - - 1d4bd12f01cf - 0c7b6eb7e752 + - 1d4bd12f01cf tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: - - 0094893f5001 - 0e63d03c8790 + - 0094893f5001 - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,10 +90,10 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - 65db807336bc - - 76d3d2b10738 - 7c2100246a2f + - 5b5a7af9fbb4 + - 76d3d2b10738 - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -102,28 +102,28 @@ tools: revisions: - 84fd33a60b35 - 18a502a9d287 - - 00f5005840fa - 1c35dadbe76f - 96336c6a2bb7 + - 00f5005840fa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - e8fba04706d3 - - addaf9d22850 - f732237754fc - 34e55239e68b + - e8fba04706d3 + - addaf9d22850 - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 75403243703a - 0776d824d896 - - 8c202e741d68 - 5fe3edf19b9c - - 75403243703a + - 8c202e741d68 - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -131,48 +131,48 @@ tools: owner: iuc revisions: - 8470de786d47 - - 43c99742158b - - 75c8945b0da2 - e96bbb9e24ea + - 75c8945b0da2 + - 43c99742158b - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 35176674168c - 1d75bd0595e2 + - 35176674168c - 306a40d4bb8f - - 5c865a382933 - 84743da21318 + - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 32c9ea835770 - - 78faebd0879c - 555ccac8a4c5 - - 8daf4564ccda - ac72310b038a + - 78faebd0879c + - 8daf4564ccda + - 32c9ea835770 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - 7b8cb2b02978 + - d60df8727f59 - a58e4a43f49c - cae017b76acb - - d60df8727f59 + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 1bc3657cd694 - 7136e9ab70db - 073608a50ac3 + - 1bc3657cd694 - 7f3b59dee073 - 04144473e59e tool_panel_section_label: Metagenomic Analysis @@ -180,9 +180,9 @@ tools: - name: dada2_seqcounts owner: iuc revisions: - - d943081510da - 19299bb1c6af - 9058d8943303 + - d943081510da - 0a1224c4b781 - a7817705348e tool_panel_section_label: Metagenomic Analysis @@ -198,28 +198,28 @@ tools: owner: iuc revisions: - 65d52c693b8e - - 4d9445dff47b + - f8f56dd6449f - a68b985913ab - b907a3c0434f - - f8f56dd6449f - - 5c7ba3d85a01 - c4db8c4de66f - dbf1798c0dcc + - 4d9445dff47b + - 5c7ba3d85a01 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: - 654548ae1357 - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - 6aad8ca3918b - e66ab198ec15 - bd7a9c6efb10 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 9704f1a3b32d - 7f208f1eb64f + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -274,45 +274,45 @@ tools: - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - 79706f10d680 + - 31c6d107e7a5 - e88b731dad59 - c409a495841f - - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - d24841f5c3d2 + - 094ad9c068af + - 172920f67a84 - 714d5a28cc5c - 71ea608ddfa3 - - 172920f67a84 - - 094ad9c068af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - 12fb63b5f63f - a4d7148ccee4 - - a293a742194f - 4137b492233e + - d7e9a3c41657 - 2bdd84912a2b + - a293a742194f + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -324,20 +324,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - 75bedfb2078b + - 6fcb8ac37a3e + - cf87759761eb + - a92c06a3afa7 - 97f7bb0851e7 - e2c71b852aba - 64bc7acc22a9 - - a92c06a3afa7 - - cf87759761eb - - 75bedfb2078b - - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -350,20 +350,20 @@ tools: owner: iuc revisions: - 080ea153677c - - 4033827c76b8 + - c82508e76ad1 - 5e5a999ffaa9 - - 2d35528d2141 + - 4033827c76b8 - 4e5e73d03f0d - - c82508e76ad1 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - - 2cd76b089570 - fc6c328c292f + - 2cd76b089570 - 6b7622dda516 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -376,43 +376,43 @@ tools: - name: khmer_abundance_distribution_single owner: iuc revisions: - - 385a965c6f87 - 65b382bf9b7c + - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution owner: iuc revisions: - - e699e2747356 - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - - b3d513c7093e - 570505540a7b + - b3d513c7093e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions owner: iuc revisions: - - adb3dd5a899f - 1061711538c6 + - adb3dd5a899f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: - - b86562b4f3fd - 29a4d6e2ae9c + - b86562b4f3fd tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 19607c740d19 - 00f7064c564b + - 19607c740d19 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median @@ -425,8 +425,8 @@ tools: - name: khmer_partition owner: iuc revisions: - - 8388fe31d604 - 5a0fa29951ae + - 8388fe31d604 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kmc @@ -438,17 +438,17 @@ tools: - name: kraken2 owner: iuc revisions: + - 20e2f64aa1fe - cdee7158adf3 - 328c607150ff - - 20e2f64aa1fe - 4a9da2b6c2e3 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 @@ -460,8 +460,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 67236d921e83 - 5bee9adae474 + - 67236d921e83 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -506,8 +506,8 @@ 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 @@ -519,8 +519,8 @@ 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 @@ -556,22 +556,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 3cc4a60615c0 + - 327d9f4cc95f + - e073891b2afc + - 4fd3b5d8706b - 27250f92a01a - 0270541aaf46 - - 3cc4a60615c0 - 2cff76cf35c6 - - 4fd3b5d8706b - - 327d9f4cc95f - 7f5d7b0e9884 - - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - eb50e7eca3dc - - 76bc4efa1aeb - 708abf08a626 + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -637,33 +637,33 @@ 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: - - 289b3807e80c - - 740fd2d16a28 - - ef65b083bd0c - - 1a6cdf55390f + - 1a037928504c + - a16313517e55 - ec368db926f4 - - b89b0765695d + - 1a6cdf55390f + - a92a632c4d9b - 6dee4abadccb + - b89b0765695d - fd69c607b43f - - 1a037928504c - - a16313517e55 - ff8f55893e7d - - a92a632c4d9b + - ef65b083bd0c - 2131d7dca455 + - 289b3807e80c + - 740fd2d16a28 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 @@ -694,22 +694,22 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 709adbfcf308 - 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 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -722,8 +722,8 @@ tools: - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -761,8 +761,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 65e5f9caefcc - 2e62e32d4f33 + - 65e5f9caefcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -792,20 +792,20 @@ tools: - name: staramr owner: nml revisions: - - 141afacabcfa - 2fd4d4c9c5c2 - 4d83eccf5f81 - 3b22de20bd4b - - 4b9a8031ab74 - - be818ae858e4 - aeaa20b96ef2 + - be818ae858e4 + - 141afacabcfa + - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - b3c7199d8786 - 9495df9dd6ef - 576963db5f1b + - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index dbd37638b..aeb746c63 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index e1f385cdd..c70964317 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: + - a74dbfee5a86 - 2263989660f5 - bdfbaf0c10aa - - 6ae5a7b5a0a2 - - 48c13389050d - 94b8c6013083 + - 9baa871cb1d1 + - cd07731e4434 - 9eeb13a92d79 + - 48c13389050d + - 80f03df2e2ce + - 8b67dd48fec1 - 9422c5a87ee2 + - 6ae5a7b5a0a2 - 098506c54016 - - a74dbfee5a86 - - 8b67dd48fec1 - - cd07731e4434 - - 9baa871cb1d1 - - 80f03df2e2ce tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c18157c68134 - - f14193ec1f50 - - f0af8936ed41 - - be78f13134e2 - - '764845535798' - - d7ce0ec78e51 - - d390fe1567dc + - c44f824c051a - 5abf2c2249aa - aaa0d6a8b808 - - 4a60927aaca5 - - fc2e49f91e52 + - '764845535798' + - d7ce0ec78e51 - bc3831dd65c1 - - c44f824c051a - - 2e093badc689 + - 4a60927aaca5 - 3ff17bad4006 + - f0af8936ed41 + - 2e093badc689 + - d390fe1567dc + - c18157c68134 + - f14193ec1f50 + - be78f13134e2 + - fc2e49f91e52 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -67,61 +67,61 @@ tools: - name: mafft owner: rnateam revisions: - - 6f28e90db932 - - f0d493f8f84f - - a65296ffb4a0 - - f1a5908ea2cb - - 15974dd17515 - bf28a8cff401 + - f1a5908ea2cb - 8e649f27aa0d + - 6f28e90db932 + - 15974dd17515 + - f0d493f8f84f - c5908940967d + - a65296ffb4a0 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 - name: mummer_dnadiff owner: iuc revisions: + - 60698466facd - 5561a1193611 - c9685bc0407c - - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - bcd65de9725b - - 48823c9635a4 - 57f042937ba7 + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: + - 4fc0cb2ac8ae - ebe3b0f84de9 - fb43e8887350 - - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 7cd7a55a678d + - e18267f90096 - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - cf3c9489c088 - - b4124df98b26 - 959c1f8dae95 + - b4124df98b26 + - 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 610595e99..db4bf8ccc 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -8,37 +8,37 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: + - 18a8d140ec6f - 28928576e1ea - 7c47b3c9e493 - - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: - - fc5b6491cf78 - 99c9427219d3 + - fc5b6491cf78 - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: + - cb34f00cc10f + - 79e9a869f40e - 72b5e9dda577 - - 0e9e7fcdd543 - fc8804320156 - - cb34f00cc10f - a7228a7ea146 - - 79e9a869f40e + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - 18505fe2bdb1 - - d6cddc06aeae - - db25ec99c3ea - fa11aa8103b2 + - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -50,22 +50,22 @@ tools: - name: medaka_variant owner: iuc revisions: + - cc36773a3681 - 43815fa60f3a - - 2bf63b38ee9b - edf6d4003fad + - 2bf63b38ee9b + - 0f5f4a208660 - eb746fa6f514 - 222669c4afb6 - - cc36773a3681 - - 19f3b583a9b3 - - 0f5f4a208660 - ec699520444c + - 19f3b583a9b3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -77,10 +77,10 @@ tools: - name: nanoplot owner: iuc revisions: - - a02b8b3f5a0c - - 7b379e98b9a9 - - 645159bcee2d - a3c4fe6f49ab + - 645159bcee2d + - 7b379e98b9a9 + - a02b8b3f5a0c - a38bdcec9e4c - 0f1c34698076 - edbb6c5028f5 @@ -89,41 +89,41 @@ tools: - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - - d219b6d8158a - 3b6f94fc7e1d + - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - be95355fef8d - 90a922f32523 - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - - 449e9aeded2d - d376944466bf + - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - bec636361cfd - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 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 @@ -155,8 +155,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 0433aad600e9 + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -175,8 +175,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -206,8 +206,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 7262f7abd..d49b79582 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: - - adfd6bf710bd - 3e73c97f025d - - d74850cf4e42 - 97b1b5ad1cda - baceff842902 + - adfd6bf710bd + - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - - 9dd107db92c2 - 1586b111d2a3 + - 9dd107db92c2 + - 83da94c0e4a6 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 - - e4b4837f06f5 - - 19b6a2f0dbe2 - 2f27f3b86827 + - e4b4837f06f5 - ed1518ce2237 + - 13851aefa67a - 1e34d2e3d285 + - 19b6a2f0dbe2 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 @@ -75,8 +75,8 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 @@ -111,8 +111,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - b1bc53e9bbc5 - 4d3eff1bc421 + - b1bc53e9bbc5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -132,9 +132,9 @@ tools: owner: iuc revisions: - 172815da3d41 - - 27a6a256cd23 - - 52b6a4d98009 - b4b2b284230a + - 52b6a4d98009 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -146,8 +146,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -160,8 +160,8 @@ tools: owner: iuc revisions: - 19bbd19b74b3 - - fea85c467896 - 87febc68b45b + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -193,12 +193,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - d8dc037e3c13 - - 4ba60cb14cb0 - - 0cb27ea69dc1 + - 2c61c30a57e7 - 5fe20c915fa6 - 9c43baa60906 - - 2c61c30a57e7 + - 4ba60cb14cb0 + - d8dc037e3c13 + - 0cb27ea69dc1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -212,17 +212,17 @@ tools: owner: iuc revisions: - 0db22932bc39 - - 9d09724f2bf1 - aec831b54a5b + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 29c738066906 - - df30a2f1db55 - ed7a967cb11b - 6e24e79d3d69 + - df30a2f1db55 + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -240,16 +240,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - 1865e693d8b2 - 3e4d45aca422 - ad90c2da4f38 - - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -261,17 +261,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - c520a52b5174 - d63c1442407f - 64deddb6a8ec - - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - 9946bc39c834 - - 94a50db37d1a - 625fd9476402 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -795,11 +795,11 @@ tools: - name: salsa owner: iuc revisions: - - 58a870ef434c - ba7b0f11e470 - - ab5b7f6b7198 - 9a22227bb6d0 - f77f7a7f3b83 + - ab5b7f6b7198 + - 58a870ef434c 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 35e28ae30..75456a5f0 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - d7c7ef3353fe - - 26de3a7b1cb9 - - f04a1264e2a2 - - 5a7c56a5cc08 - - 81e66674859e - - f73435dc282b - - '841557158611' - - 3f59ebfbfe3d - - d033ffc1c161 - b89cac5156ec + - f73435dc282b - a6619171428e + - 6a457678efcb + - 5a7c56a5cc08 + - d033ffc1c161 - 8834daeb9892 + - '841557158611' + - cce7b18495e4 + - 3f59ebfbfe3d + - 3b8b5bde0bd9 - c78f3d7dd1db + - 26de3a7b1cb9 + - f04a1264e2a2 - 107d3ba7024a - - 3b8b5bde0bd9 - - cce7b18495e4 - - 6a457678efcb + - d7c7ef3353fe + - 81e66674859e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 02b8758214b0 - - aa8cc71438cf - - df47d4845b62 - - 7a2092844346 - - 88c4aa435ded - 659517798cc4 + - aa8cc71438cf - 6283babe736e - 4755f52427c4 - - 5b777002c2de - - a185b079b095 + - 6223845127ea + - 7a2092844346 + - 3b96e92e8ec3 - 6a726db04d4b + - 5b777002c2de - b0af57c1a968 - - e75442c7f4da - - 3b96e92e8ec3 - 5fcd1ece3a6e - - 6223845127ea + - 88c4aa435ded + - e75442c7f4da + - a185b079b095 + - df47d4845b62 + - 02b8758214b0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: + - 0878b7fd5260 + - 111bd54f6bc4 - c1d53e95327f - - 70acec670c30 + - d1c340a5664b - b8476e82ac20 - - 111bd54f6bc4 - - 24d024316465 - - 0878b7fd5260 - f97743d52b87 - - d1c340a5664b + - 24d024316465 + - 70acec670c30 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - feb40665d7cd - - 4f6349228462 - - 9e10ba792be2 - daddf188c13f + - 9e10ba792be2 + - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: + - 8ad84c5753ea + - 14ae456b8cc5 + - ca0d8cf80567 + - ca337cce3888 + - 7bb8726be37c + - abf6dbe8c9d7 - 9d61d3fa046c - 3a43c3982401 - - ca0d8cf80567 - - 81804a978fc0 + - 5f8727ff21e7 + - b7e297c2ede6 - 42a174224817 - 2f1019071464 - - abf6dbe8c9d7 - - b7e297c2ede6 - - 03ed9524dcd1 - - b6abccb1f25b - - 8ad84c5753ea - - 5f8727ff21e7 - - 7bb8726be37c - - 2fa9d4f1b48f - - ca337cce3888 - - 14ae456b8cc5 - - 437e28791761 - 36912871ccdc - a2099fb98cdb + - 2fa9d4f1b48f - 83a69484cb87 + - 81804a978fc0 + - 437e28791761 + - b6abccb1f25b + - 03ed9524dcd1 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - ba29b5e2a4be + - ea30d3089354 - b1e68bbe4cef + - ba29b5e2a4be + - a4b71be30c3c - 73a469f7dc96 - - ea30d3089354 - 29ff6a849eac - - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: + - f1ccc8a6eb05 - e88a7de55d6e - 91887494eb97 - 9b2b122d0415 - - 809e42326fc2 - 15ac71df11a0 + - 809e42326fc2 - dbe2b2204555 - - f1ccc8a6eb05 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 3c4b2e3ef..7bcec9799 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - a1f0b3f4b781 - - fc288950c3b7 - - b502c227b5e6 - - 3f254c5ced1d - - 1aac2a13842a - 881d7645d1bf - f9242e01365a - - 7d34178f2812 - f6ced08779c4 + - 1aac2a13842a + - 7d34178f2812 + - b502c227b5e6 + - a1f0b3f4b781 + - fc288950c3b7 + - 3f254c5ced1d 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 678766279..b7d478b7e 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: - - 6ab1a261520a - - a58f7eb0df2c - - d00e15139065 - - 5b85006245f3 + - ca90d17ff51b - eb085b3dbaf8 - - 2f7702fd0a4c - 7fbec959cf2b - e4a053d67e24 - - ca90d17ff51b + - d00e15139065 + - 2f7702fd0a4c - c0e71cb2bd1b - 3bd420ec162d + - a58f7eb0df2c + - 6ab1a261520a + - 5b85006245f3 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 edde958ad..767f3091a 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -3,92 +3,92 @@ tools: owner: galaxyp revisions: - 4c177985028a - - f28ad96b76dc - - b574b84afc4d - - 0a18ac48ac53 - b18329a8ac14 + - 0a18ac48ac53 + - f28ad96b76dc - 277dc652246e - ece627528a78 + - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - a9a28e46d54a + - e215f71d7983 - bf06d196e23d - 525f201b86c1 - b41107d8fe89 - - e215f71d7983 - e988563cc6e5 - - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - 4fbffddde8cd - bb6397b94018 - 56da27be956a - - 4fbffddde8cd - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - a8157342d9a3 - 890845926d4b - - f23d67e28cc8 - b8c79e70516d + - f23d67e28cc8 + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 - ae304a72db7b - - a95a82eb4d50 - - 59e85306eae5 + - a69865da6f80 - 25b83cbd596a - 80600735685d + - a95a82eb4d50 + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - ed9ed1e6cca2 - - 798da6bdff3d - - e0669b1854b1 - f1897eb07081 - 611d80c0e29d + - 798da6bdff3d + - e0669b1854b1 + - ed9ed1e6cca2 - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - d426a9107a6c - 5a35e3a8d013 - 74b61bf5bc4b + - d426a9107a6c - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 91f0f5922011 - 82f6c2f4332d - df2187f9013b - cc430977c8ff + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 1693b2126f30 - 043f9c91f686 + - d2483487e077 - ba92b59cd529 - 10566783d718 - - 1693b2126f30 - - d2483487e077 - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -108,9 +108,9 @@ tools: owner: galaxyp revisions: - ae4dc0c041f9 - - 9fa3dbf06f17 - - ff8c9e0e8a7b - bf0728e000cd + - ff8c9e0e8a7b + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,17 +122,17 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f - eac99effe86f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - 1c5cbf8f79ce - 4081e4faa4ab + - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -145,9 +145,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: + - 0d2e93e01e68 - ce1a157a41bd - d6a4dfdad269 - - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd + - 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 @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: + - f522c08e900c - 1f39c833f65f - 2133b0be850a - - 837224ad1694 + - 4d17fcdeb8ff - e42225f8a659 - - 37d669de2828 + - 837224ad1694 - 97a7f34fcb6a + - 37d669de2828 - 7f432d87c82c - 9c52362ae7bb - - 4d17fcdeb8ff - - f522c08e900c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,17 +202,17 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - 85b8866f06d7 - a72ac2c7cc5b + - 0ed07016d668 - e63db1aa82ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 767c1d761aaf - 352b37c66d97 + - 767c1d761aaf - 1974224d63c2 - 990b4560ead7 tool_panel_section_label: Proteomics @@ -220,19 +220,19 @@ tools: - name: metaquantome_filter owner: galaxyp revisions: - - 35cc7ca0bdc7 + - 99450519d727 - deaf035bbe9f + - 35cc7ca0bdc7 - 4f359549383c - - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - e79958768a2c - - 06f6826d380c - c7745841de24 + - 06f6826d380c + - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat @@ -247,10 +247,10 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - 944b43462104 - - 8bd7734309f6 - 9bf325045235 + - 8bd7734309f6 + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -270,10 +270,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 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tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 111c3a00136d - 986e03d3201e - - c69f69d7867a - 5d9f175dff81 + - 111c3a00136d + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 4204882495f2 - - 0e52c85f3b15 - be74a8cd7d66 - 476b5e296979 + - 0e52c85f3b15 + - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter @@ -441,49 +441,49 @@ tools: - name: openms_multiplexresolver owner: galaxyp revisions: - - 021fdb80f204 - d0304fb829c0 - 4e66c4e73909 + - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - bf32e0bcf554 - ee860980edc6 - 2735db4dd8d9 + - bf32e0bcf554 - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - 08488066d588 + - a2a6e9551046 - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - - 8c01da82292c - 2a9ff56cb279 + - 8c01da82292c + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - 1bf940c18d93 - c1809c05ae8c + - 1bf940c18d93 - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - f861ec9fbe59 - 9f505cd4428f + - f861ec9fbe59 - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -499,99 +499,99 @@ tools: owner: galaxyp revisions: - 89254095cbf6 - - 8b814eafce2c - 4bb198c0bd3e + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - f82b320ceb90 - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - d31426ef20f6 - - 18826fb8e5db - 6e8cc5ed2a9b + - 18826fb8e5db + - d31426ef20f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - 2aebe58de46e - - 4a7b96835140 - bc63b4d12779 + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - 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 - 539a3a4dcc9e + - dd173849c3d8 - e039cc5c7aed - - d6aca689dd48 - 5182338d5e7c + - d6aca689dd48 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - d426affe977c - 8a45fd5a608a + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: + - 9c70a651a53e - dd71e020e2aa - 43b9ed22e8ce - - 9c70a651a53e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 9020199dba0a - d063e2fe4ba4 - 1b03536aa3c9 - - 9020199dba0a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - f036e8cf1a55 + - 78c080d36945 - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - 5c2a97a234d6 - - fb52e95a370c + - 7f6a1f27553e - c8b225c69a7f + - fb52e95a370c 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: pepquery2 @@ -610,14 +610,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 3ec27b4cee7c + - 7fdd9119cc4f - 3634c90301af - a72c48001f7c - 07ff622ec007 - - 943a34df6047 - - 7fdd9119cc4f - - 1beff3ddce58 - da885ca16cb2 + - 1beff3ddce58 + - 943a34df6047 + - 3ec27b4cee7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,10 +677,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 + - a371252a2cf6 - 265c35540faa - 1a5690a5eedc - - a371252a2cf6 + - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 29de61b79..a1e1ae682 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,131 +2,131 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - e345aadf914f - - 2f1d464ebfd2 + - cd5f98911089 + - 110a346daf36 - 289b7d6b69a4 + - 2f1d464ebfd2 - 42201b90e3f4 - - 110a346daf36 - - cd5f98911089 + - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - c207119ba5f6 - - 42d9087b4789 - - 0345dbaaa79b - - 0cd2df8af811 - 8501601a118d + - 0cd2df8af811 + - 42d9087b4789 - fcce77c09289 + - 0345dbaaa79b + - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 89eb29319bf4 + - 405a212b32ab + - 04db7fd6b238 + - 421c33b8bf17 - ad5ab22ffe24 - 33486216eec0 - - 421c33b8bf17 - - 04db7fd6b238 - - 405a212b32ab + - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - 7370bb65bad4 + - eb784fa07f80 + - f6e91108b7b1 - fa51dc5e8386 - 7b72fde3d27e - 1d839ead7ad3 - - f6e91108b7b1 - - eb784fa07f80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - c9b77ced9a78 + - a3e86cd9cac7 - 3d70c2996730 - 1544278c272e - 8a55d29c8fcf - d30e36c48c93 - - a3e86cd9cac7 + - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 + - 564c33e5c3e3 + - 887cf585cafc - e2db212d64ad - b242deb58952 - - 887cf585cafc - - 564c33e5c3e3 - a5969aa9347e + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - b4bab607eb05 - - e897c74a48bb - 9a171f9a450b - 8cff84759bf6 + - e897c74a48bb + - b4bab607eb05 - bd5ff77e2036 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 4f65e343ecdf - 33f0793edf93 - - 5e10f396979e - - 6dafad990086 + - 4f65e343ecdf - 887e0991eb24 - adc7a7610d4f + - 5e10f396979e + - 6dafad990086 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: + - 43e3eeb2e0ec - c287418eb288 + - 17d39bf0a63a - 4e280b27a831 - - 43e3eeb2e0ec - c5d7050e4ad7 - - 17d39bf0a63a - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 0b8c84a7fdb5 - 9586f08634c0 - cd034465d4a4 + - d9bf483266a1 + - 0b8c84a7fdb5 - a819ec3b362d - 09b8edb56d80 - - d9bf483266a1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - a4b4bd84f69e - - 2645575d1bf2 - 69842dd5aa48 - - bf0e43ab0416 - 95351dd0fd3f + - bf0e43ab0416 + - a4b4bd84f69e + - 2645575d1bf2 - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - - cfb504394ae1 - bb0475c884ff + - cfb504394ae1 - 912f904a6e1e - d1fda11e602f + - d033e1ccb386 - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - 95286af4139b - d504d945a655 - d1fad35bdb4a - - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 0ea9fe25f..22a50fd15 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,26 +2,26 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 2d4e3aff9dc7 - 7acb00fc980a - - cf01dd6c6b1f + - 2d4e3aff9dc7 - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - - 32e542c2a773 - 7a5a2d28c539 - 125d20cb23d7 + - 703a2cb3fb38 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -33,8 +33,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: chira_collapse @@ -82,17 +82,17 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - ad5d061fbdf2 + - f648e5180e40 - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - - 6926716bbfb5 - d080005cffe1 + - 6926716bbfb5 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -100,8 +100,8 @@ tools: revisions: - 22cf48ad7b16 - 6a6717a5f421 - - cf747d1bd79a - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -115,8 +115,8 @@ tools: - name: cuffquant owner: devteam revisions: - - 93148c05136f - 679d93c99757 + - 93148c05136f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cummerbund @@ -134,56 +134,56 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - - 8f0181aacb7a - 3b36efd62b3e + - 8f0181aacb7a + - 0693ccd171c4 - e3b16fd7dd08 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 24a09ca67621 - - d027d1f4984e - 8fe98f7094de - - cd9874cb9019 - - 9a882d108833 - 0696db066a5b + - d027d1f4984e + - 9a882d108833 + - 24a09ca67621 - 6a3a025714d3 + - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: + - 2872c633f07e + - 62adf13b86ea - b47c006d90c5 - df929f257179 - - 2872c633f07e - 9a7c5b6d8f1e - - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 6e53e565fc6a - - 9bdff28ae1b1 + - df0c8d0a5992 + - f2843df56434 + - 3d89af8a44f0 - 0cb907a2a810 - 5bf899c13979 - - 555659de7321 + - 070900306913 - ae2aad0a6d50 - - df0c8d0a5992 + - 555659de7321 - a8305cf0c951 - - 3d89af8a44f0 - - f2843df56434 + - 9bdff28ae1b1 + - 6e53e565fc6a - 334ce9b1bac5 - - 070900306913 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -195,17 +195,17 @@ tools: - name: featurecounts owner: iuc revisions: + - af814359d244 + - a56fbe2d6ba7 + - e6a2a912677a + - f3a5f075498f + - ea04b737afa0 - 90d16db017d7 + - a37612abf7f9 - 7db9d3ea71c9 - - ea04b737afa0 + - 38b6d12edc68 - 6f66ae7c5f7a - - a37612abf7f9 - - af814359d244 - f9d49f5cb597 - - e6a2a912677a - - a56fbe2d6ba7 - - 38b6d12edc68 - - f3a5f075498f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -229,8 +229,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 + - 0f710191a66d - 3c5e024a18cf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -243,21 +243,21 @@ tools: - name: hisat2 owner: iuc revisions: - - a86e80d3c09c - - 6ab42baa56e9 - - 6c19daec423d - 3fb01a8c902d - f4af63aaf57a + - 6c19daec423d - 26371a1df031 + - a86e80d3c09c - d4b55e2beb12 + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - 4418229c501e - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -269,33 +269,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: + - 1c75aa5de15e + - 01247aaf0a10 + - ce5d418183c5 - 5ae5c312d718 - 87c11c05d238 - - ce5d418183c5 - - 01247aaf0a10 - - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - 40985510cd98 - - 10c98fab6c5a - 4f9c4e6566e5 + - 10c98fab6c5a - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 0921444c832d - - 58c35179ebf0 - e827f9aae031 + - 0921444c832d + - 708348a17fa1 - d6f5fa4ee473 - - 119b069fc845 - 32511f586472 + - 58c35179ebf0 + - 119b069fc845 - 97e06a4c7c75 - - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -332,8 +332,8 @@ 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 @@ -351,20 +351,20 @@ tools: - name: rgrnastar owner: iuc revisions: - - 79de45b5069b - - 3ea5a2a63fa2 - - 7ed2edc1337f + - 4014de1b6daf - 0a563fd2f22e - - b0f2be869d6d - - 4df95e2d7f61 - 980d2a2e1180 - - 5ec75f5dae3c - - e132e7d02a3e - 4074fc1940e2 - - 4014de1b6daf - - 99b17b74a8cd + - 5ec75f5dae3c + - b0f2be869d6d + - 4df95e2d7f61 + - 79de45b5069b + - 3ea5a2a63fa2 - c7c55b694974 + - e132e7d02a3e - b9e04854e2bb + - 99b17b74a8cd + - 7ed2edc1337f - c772497b2c32 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -378,35 +378,35 @@ tools: owner: bgruening revisions: - e3d32471da11 - - f4d5237a84f6 + - 15cd64d7c58b + - 53e9709776a0 - cc05793bb896 - ebab418107f5 + - f4d5237a84f6 - 49121db48873 - - 15cd64d7c58b - - 53e9709776a0 - 2c0ca397d302 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - fab6ff46e019 + - 8c28affc7c48 - 56242ff81c84 - c0fd285eb553 - - 8c28affc7c48 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 914cfcba0ec8 - 258d696dbd7e - - cef79931dda5 - ae618321f34a - - 76d290331481 + - cef79931dda5 + - 1ebd14235b92 - dd4df992d93d - cbf488da3b2c - - 1ebd14235b92 + - 76d290331481 + - 914cfcba0ec8 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -436,26 +436,26 @@ tools: - name: transdecoder owner: iuc revisions: + - ffd1300599a1 + - 0db979fead3a - c6334cb383ff - d0d4cef4f967 - - 0db979fead3a - - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d - - bcc5f03f1900 - ba3720d7e68b + - bcc5f03f1900 - d6a479fd4281 + - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 2fb4ee002432 - 478f36effca1 + - 2fb4ee002432 - c2b82a94493e - 56162e446004 tool_panel_section_label: RNA-seq @@ -463,63 +463,63 @@ 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_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 + - 870ac06dff8e - 34a018cbee9c - 4687ecf0eb2d - - 870ac06dff8e + - be3f26533209 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 + - 05ab8d5e04a2 - 5192f657f305 - - c5fbddcac63a - 33406f5a445c - - 05ab8d5e04a2 + - 65e7dea767ea + - 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 + - e406ac71165d + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - 964b7efe2639 - - 37a1129c89d2 - - 7c7fbf13aadd - c2c039e421af + - 7c7fbf13aadd + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - 24e94d84adc9 - - 047c22569787 - eafea3083352 - 1d689e4e1caf + - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: + - 04bb8bb7c198 - 3a4ac03d1266 - 1812dbc5bb7b - - 04bb8bb7c198 - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -538,15 +538,15 @@ tools: - name: trinity owner: iuc revisions: + - d84caa5a98ad + - d2bc35f3d1c5 - 48636f857c4b - 9fa24d5aac68 - - 32b86cd8eb50 - - d84caa5a98ad - - db1f362cca3e - - 8f1c3df4dd49 - cee61b3fcf78 - - d2bc35f3d1c5 + - 8f1c3df4dd49 + - db1f362cca3e - c9cfec002f71 + - 32b86cd8eb50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index 9eed3b471..233430f7b 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - - 080fd5739bb4 - 27e16a30667a + - 080fd5739bb4 - 473382134e56 + - 1a052c827e88 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 75765e69f..b88aaf9ce 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: + - 10184eaa85fc - 3c661e57a88f - 88eedb4abea0 - - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - 993b19f20c76 - - cb20f99fd45b - 1dfd95ee241e + - 108db6635177 + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -32,8 +32,8 @@ 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: bamtools @@ -75,10 +75,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 30a201c9c310 - 19ece8afbaab - - 5f8e69cc4c6e + - 30a201c9c310 - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -130,19 +130,19 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - - 12749212f61b - 46c6639921f1 - 6856f8a01905 + - 12749212f61b + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 26b4f9f98aca - - 92ec40abcdcf - - 06dc50b7b711 - 33208952b99d + - 06dc50b7b711 + - 92ec40abcdcf + - 26b4f9f98aca tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,38 +160,38 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e + - b3d99709fe1a + - 66e23b11feae - b906586a6596 - 720217c23995 - - 66e23b11feae - - b3d99709fe1a + - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 - - 22970df7a40e - - cc61ade70eb8 - db17d5321bad - fefd89ab563c + - cc61ade70eb8 + - 22970df7a40e + - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: + - 811fc2d75ad4 - fa5d3e61e429 - 7def34e6cf4d - - 7a6034296ae9 - 88b8c2916784 - - 811fc2d75ad4 + - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -204,21 +204,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 - - cae2794d2deb - - b40e2d865d52 - 65a38e8c8e2a - 740ce0a18f0d + - cae2794d2deb + - 36677f429310 + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 9da0311ab1dd - - 583abf29fc8e - - b61f5d6a7f25 - 329deb17a9f7 + - b61f5d6a7f25 + - 9da0311ab1dd - 8da515fbc1bf + - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -246,54 +246,54 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - a4a10c7924d1 - b8beef827165 - 344fc91e1bfd - - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - cab3f8d35989 - 6c2c1836728b - - d54a4df48867 + - cab3f8d35989 - e613c1ad4c4c + - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - b7f7826ef1cd + - bd850490c7f1 + - bcedabb53ddf - 5d9ae78f34d3 - - 135c85f4cfaf - 818030fa6bbf - - bcedabb53ddf - - bd850490c7f1 + - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: + - 24c5d43cb545 - 5a08c09b9311 - - 3a0efe14891f - 145f6d74ff5e - - 24c5d43cb545 - - 1cc79f49b8d5 + - 3a0efe14891f - 541082d03bef + - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 6be888be75f9 - 350bbc5c2ffd + - b01db2684fa5 + - 2dce91e11ca7 + - 6be888be75f9 + - 0dbf49c414ae + - c370440f901e + - 5826298f6a73 - bf328cec6a42 - 32dc5f781059 - - 2dce91e11ca7 - b72793637686 - - 5826298f6a73 - - b01db2684fa5 - - c370440f901e - - 0dbf49c414ae 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 c82223770..4cea33b64 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: - - 480d9e9d156b - - 6f6537780379 - - a62c4a11a67d - 4aab5ae907b6 - - 59bb6d34fca6 + - 6f6537780379 + - 480d9e9d156b - ea5e944f447d - - d147d6455873 + - 59bb6d34fca6 - 5cb6146337d8 + - a62c4a11a67d + - d147d6455873 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 f72931d06..a27d277a3 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,90 +8,90 @@ tools: - name: alevin owner: bgruening revisions: + - e32b215b7c04 + - f2000bc73102 - c9944a2600f1 - ecb9ea6269ee - - e32b215b7c04 - e4c01dcece8b - - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - cfaf5a405371 - - 707023fa62fe - e1c3c2f2a834 - c0b037b12765 + - cfaf5a405371 + - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - d330b3082107 + - 32e547223c9e - cfc3f5a57dc6 - - 55e35e9203cf - - 00712416fdaa - 93dd15e13e6a + - 55e35e9203cf - fb9e030ffae4 - - d330b3082107 - - 32e547223c9e + - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - b9fac48532eb - - ee98d611afc6 - 0bf7fddf90c7 - - 39e945f0b2c1 - - 688357ad5e61 - 6f0d0c784f09 + - 688357ad5e61 + - ee98d611afc6 - 038e32885fec + - 39e945f0b2c1 + - b9fac48532eb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b + - 3d748954434b - d4af736e7b83 - - b85871dd69f9 - 43cb7b5a6fe7 - - 3d748954434b - - 7e8c677a7b71 - ed4996a16f7f + - 9bd945a03d7b + - 7e8c677a7b71 + - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - 2e8022f1923c - fe75d2414dc0 - a4774b7b2e85 + - 2e8022f1923c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 0e70b2dfe4be - 4fff5a293013 - - 769d815e4b0d - 02b1fe7aed76 + - 0e70b2dfe4be + - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - - 344c2af50552 - a90f8efe08b4 - aa4a6f0916b4 + - c29e7bb492bf + - 344c2af50552 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - 050cf43887d3 - c32347702e12 - b13d3e4c48e1 - - 050cf43887d3 - 5b7c81b35b89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -100,8 +100,8 @@ tools: revisions: - 02fc39c8610d - 1d77986f9ddc - - ae969fdb8442 - 239193b96d72 + - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -138,10 +138,10 @@ tools: owner: iuc revisions: - cdf4443d5625 - - a9caad671439 - 8855361fcfc5 - - cfe1e6c28d95 - 2c1200fba922 + - a9caad671439 + - cfe1e6c28d95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -171,8 +171,8 @@ 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 @@ -185,15 +185,15 @@ tools: - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - 163fd744e235 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -206,8 +206,8 @@ tools: - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 45a386d18509 - 640e0e45518a + - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel @@ -220,43 +220,43 @@ 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 owner: bgruening revisions: - - f0216498a666 - b05f662f9f35 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - e03780179ee5 - 3ee5332bf57c + - e03780179ee5 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 @@ -269,8 +269,8 @@ tools: - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate @@ -297,8 +297,8 @@ tools: - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 972dcccb5bbc - 6c5097f6d41e + - 972dcccb5bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops @@ -311,15 +311,15 @@ tools: - 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 owner: bgruening revisions: - - c261b6b05ee3 - 55b013e59018 + - c261b6b05ee3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains @@ -332,15 +332,15 @@ tools: - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - ed900cd4a0a9 - 1511a8ebe906 + - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 6d042c96aceb + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -360,8 +360,8 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -400,8 +400,8 @@ 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 @@ -414,12 +414,12 @@ tools: - name: modify_loom owner: iuc revisions: + - 59be31ac9dc3 - 4b0adaa31c95 - - 7784821452ac - - e98619de2776 - eeab712b0b99 + - e98619de2776 - 0f1aaff9b22d - - 59be31ac9dc3 + - 7784821452ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -431,16 +431,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 282819d09a4f - 2cfd0db49bbc - 7ffaa0968da3 - - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 2ba99a52bd44 - 56371b5a2da9 + - 2ba99a52bd44 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -465,46 +465,46 @@ tools: - name: raceid_clustering owner: iuc revisions: + - f911a64454fb + - 0bff0ee0683a - a4b734cd253b - - 7e014059a88d - c4f39bf4a068 - - 0bff0ee0683a - - f911a64454fb + - 7e014059a88d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - 43c146e25a43 - d45f092caf24 - b83fbc90161e + - 43c146e25a43 - 7608d5faee41 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - - 69018f285aa3 - a6821f856a1e + - 69018f285aa3 + - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - 2af7c5086a96 + - 72979cac22b2 - e93b008c637a - - c92d0f9338c5 + - 2af7c5086a96 - 44b935f2271b - - 72979cac22b2 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -522,106 +522,106 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 4d8f983cd751 - b2df381a6004 - - 77b91b9bdf52 - - 38db3fef7aad - - 6f83f8fd381f - 6acb08931836 - aaa5da8e73a9 - - cb43c5d3acd3 - f9353ee6a0d4 + - cb43c5d3acd3 + - 6f83f8fd381f + - 38db3fef7aad + - 77b91b9bdf52 + - 4d8f983cd751 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - a03ff8633507 - - 3c86f71498bc - - fc0321c000a3 - - a97abb8cd15b - b409c2486353 + - fc0321c000a3 - d636ce5cde16 - - 72a6bebab2a5 - - 8cb783c81905 - 277313130da5 + - a97abb8cd15b + - 8cb783c81905 + - 3c86f71498bc + - 72a6bebab2a5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 4338bf96809e - f54f0f0598ad - - 18262103fa61 - 3081ff5c84a3 + - c0a80a16560f - 6c145a6868cc - - 5c3ebe2adc77 - - 6bd82ed14acd - 5e9171dc8244 + - 18262103fa61 + - 6bd82ed14acd + - 4338bf96809e - c5d3684f7c4c - - c0a80a16560f + - 5c3ebe2adc77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - c9cb76cf8d6c - 146ae5d70b47 - - 7b9fafe32c86 - 94c19fb1281c - - 9f354c7c8c92 - a407e7f8bdc1 - - d844935c906c - - 3bcd5445cd7a + - 7b9fafe32c86 + - 9f354c7c8c92 + - c9cb76cf8d6c - 56c0d4acef02 - ab55fe8030b6 + - d844935c906c + - 3bcd5445cd7a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 1072ce66b426 - - 6f5349dd5c49 - - f7446fd8d5e7 - - 0185bd174ea0 - - 6adf98e782f3 - 9b0cdb8cf6be - 7647e5cd1b8b - 95777145cb92 - aa0c474463c2 + - 6adf98e782f3 + - 0185bd174ea0 + - 1072ce66b426 + - f7446fd8d5e7 - dbbe1ea8ecb1 - 40812a65a78b + - 6f5349dd5c49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 458e8f43a775 - - 9fb627495ec2 + - fe8f16c594ec - f2f6c703da06 - - bf2017df9837 - a39040ae0a38 + - 215733a383f2 + - bf2017df9837 - c65fce500915 + - 9fb627495ec2 - 73ab2ac53d06 - - 215733a383f2 + - 458e8f43a775 - d18e7a6e5cd4 - - fe8f16c594ec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - - 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 - - 7a365ec81b52 - 652923ce664f + - 7a365ec81b52 + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -647,9 +647,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - - c99ba278dfa9 - 9e5c0bb18d08 + - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -891,15 +891,15 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - afb90d3485df - 8f8bef61fd0b + - afb90d3485df tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 88192fe25375 - 588c811fdd48 + - 88192fe25375 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -912,8 +912,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - fef8f61cb34c - cec3e76eaf05 + - fef8f61cb34c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -925,8 +925,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 90e95e9ee190 - 883c33ef3372 + - 90e95e9ee190 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 278fb0915..dcd70136a 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 + - 562f3c677828 + - 746e8e4bf929 - 419027d822d6 - 4c07ddedc198 - - 746e8e4bf929 - - 562f3c677828 + - 2f3c6f2dcf39 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 @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: + - cb1c59d69557 - 6c29c7e347e8 - 7a15159140d1 - - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,12 +114,12 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - aef56d0e7a61 + - 9c3e1d3235c8 - 4c4ec859c31a - - 7442b94d6a1e + - aef56d0e7a61 - 840f29aad145 - b1eda492f063 - - 9c3e1d3235c8 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes @@ -127,30 +127,30 @@ tools: revisions: - d0352e8b4c10 - 30d21a6041f6 + - 375bbd555f4a - 9fda0b82f419 - 07843f917990 - - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d - 8b1b2b91f8d0 - - 2c58b83c9bad - - cd02bf168d23 - 4cc980df6265 + - cd02bf168d23 + - 2c58b83c9bad + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 7dd3fb35904f - - e10e776f2109 + - 1dd433d2c92c + - ad7e0b4291ee - 4bbaf77573ef - bb9fc9d46ea4 - - ad7e0b4291ee - - 1dd433d2c92c + - e10e776f2109 + - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index e0c06a339..cc2e4f7fc 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -27,21 +27,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: + - 9cd341095afd + - 13b6f0007d9e + - 6595517c2dd8 - 02026300aa45 - - 464b9305180e - - be25c075ed54 - 6e8d94597139 - - 9cd341095afd + - 464b9305180e - aff5135563c6 - - 6595517c2dd8 - - 13b6f0007d9e + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,10 +78,10 @@ tools: - name: filter_tabular owner: iuc revisions: - - 34d29339abab - 9cc411a62277 - 90f657745fea - 557ec8d7087d + - 34d29339abab - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -106,28 +106,28 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - ae7843d06f8f + - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - cf34c344508d - - 3a6b78c39dca - - cf4397560712 - - 83069b38aa85 - 623f3eb7aa48 - 1ea4e668bf73 + - cf4397560712 - 2e8f945f7285 + - 3a6b78c39dca + - cf34c344508d - 33d61c89fb8d + - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - 399da6b5ec21 + - ae8c4b2488e7 - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -140,30 +140,30 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - c4d18aa4ec4a - b722161a845a - bce29ec10b78 - - c4d18aa4ec4a - f768f6183386 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - 74a8bef53a00 - - 86755160afbf - - ddf54b12c295 - - 9ff72e942410 - - fbf99087e067 - 12615d397df7 - - f46f0e4f75c4 + - fbf99087e067 + - ddf54b12c295 - d698c222f354 + - f46f0e4f75c4 - a6f147a050a2 + - 86755160afbf + - 9ff72e942410 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index 4f15e149a..7f02efb36 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,9 +14,9 @@ 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 @@ -34,33 +34,33 @@ tools: - name: freebayes owner: devteam revisions: - - 156b60c1530f - - 57def2d7c093 - - a5937157062f - 04fa42777df9 - ef2c525bd8cd + - 57def2d7c093 + - 156b60c1530f + - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - e61c9ac190ad - 09d6e4693887 - 435b157bed6d - 791f73caa0c8 - - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - - dfadc322b065 - - 074d44697036 - - 4805fe3d8fda - - 03627f24605f - b11e8e9c23bf - - 65432c3abf6c + - dfadc322b065 - 3b4b2121842f + - 65432c3abf6c + - e1461b5c52a0 + - 03627f24605f + - 4805fe3d8fda + - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -83,9 +83,9 @@ tools: - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - aa35ee7f3ab2 - dbd9f2db9ed8 + - cdaab621d454 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -97,8 +97,8 @@ tools: - name: sniffles owner: iuc revisions: - - 93c4b04a0769 - 43fffeed243f + - 93c4b04a0769 tool_panel_section_label: Variant 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