From ad9d1c4d56c41a4f7bc9c692fe4eddc38b3bffec Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 16 Oct 2024 00:02:39 +0000 Subject: [PATCH] Jenkins install build 1677. --- automated_tool_installation_log.tsv | 1 + requests/plot_ragtag_paf@latest.yml | 4 - staging.gvl.org.au/annotation.yml | 126 ++++---- staging.gvl.org.au/assembly.yml | 250 ++++++++-------- staging.gvl.org.au/bacterial_typing.yml | 14 +- staging.gvl.org.au/bb_tools.yml | 8 +- staging.gvl.org.au/bed.yml | 14 +- staging.gvl.org.au/blast.yml | 10 +- staging.gvl.org.au/chemicaltoolbox.yml | 62 ++-- staging.gvl.org.au/chip_seq.yml | 10 +- staging.gvl.org.au/collection_operations.yml | 10 +- staging.gvl.org.au/convert_formats.yml | 53 ++-- staging.gvl.org.au/deeptools.yml | 102 +++---- staging.gvl.org.au/dna_metabarcoding.yml | 8 +- staging.gvl.org.au/emboss.yml | 2 +- staging.gvl.org.au/epigenetics.yml | 4 +- staging.gvl.org.au/fastafastq.yml | 100 +++---- staging.gvl.org.au/fastq_quality_control.yml | 36 +-- .../fetch_alignmentssequences.yml | 2 +- staging.gvl.org.au/filter_and_sort.yml | 4 +- staging.gvl.org.au/gemini_tools.yml | 22 +- staging.gvl.org.au/genome_editing.yml | 4 +- staging.gvl.org.au/get_data.yml | 40 +-- staging.gvl.org.au/graphdisplay_data.yml | 63 ++-- staging.gvl.org.au/hca_single_cell.yml | 28 +- staging.gvl.org.au/hicexplorer.yml | 22 +- staging.gvl.org.au/imaging.yml | 50 ++-- staging.gvl.org.au/ivar.yml | 76 ++--- .../join_subtract_and_group.yml | 6 +- staging.gvl.org.au/machine_learning.yml | 44 +-- staging.gvl.org.au/mapping.yml | 56 ++-- staging.gvl.org.au/metabolomics.yml | 32 +- staging.gvl.org.au/metagenomic_analysis.yml | 172 +++++------ staging.gvl.org.au/mothur.yml | 6 +- staging.gvl.org.au/multiple_alignments.yml | 56 ++-- staging.gvl.org.au/nanopore.yml | 51 ++-- staging.gvl.org.au/none.yml | 52 ++-- staging.gvl.org.au/phylogenetics.yml | 100 +++---- staging.gvl.org.au/picard.yml | 10 +- staging.gvl.org.au/proteomic_ai.yml | 16 +- staging.gvl.org.au/proteomics.yml | 200 ++++++------- staging.gvl.org.au/rad_seq.yml | 70 ++--- staging.gvl.org.au/rna_seq.yml | 194 ++++++------ staging.gvl.org.au/rseqc.yml | 4 +- staging.gvl.org.au/sambam.yml | 86 +++--- staging.gvl.org.au/send_data.yml | 10 +- staging.gvl.org.au/single_cell.yml | 196 ++++++------ staging.gvl.org.au/statistics.yml | 30 +- staging.gvl.org.au/text_manipulation.yml | 46 +-- staging.gvl.org.au/variant_calling.yml | 40 +-- staging.gvl.org.au/vcfbcf.yml | 278 ++++++++--------- usegalaxy.org.au/annotation.yml | 128 ++++---- usegalaxy.org.au/assembly.yml | 240 +++++++-------- usegalaxy.org.au/bacterial_typing.yml | 10 +- usegalaxy.org.au/bb_tools.yml | 6 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 16 +- usegalaxy.org.au/chemicaltoolbox.yml | 60 ++-- usegalaxy.org.au/chip_seq.yml | 14 +- usegalaxy.org.au/collection_operations.yml | 12 +- usegalaxy.org.au/convert_formats.yml | 50 ++-- usegalaxy.org.au/deeptools.yml | 120 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 112 +++---- usegalaxy.org.au/fastq_quality_control.yml | 42 +-- usegalaxy.org.au/filter_and_sort.yml | 4 +- usegalaxy.org.au/gemini_tools.yml | 20 +- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 44 +-- usegalaxy.org.au/graphdisplay_data.yml | 56 ++-- usegalaxy.org.au/hca_single_cell.yml | 34 +-- usegalaxy.org.au/hicexplorer.yml | 16 +- usegalaxy.org.au/imaging.yml | 62 ++-- usegalaxy.org.au/ivar.yml | 78 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 12 +- usegalaxy.org.au/machine_learning.yml | 40 +-- usegalaxy.org.au/mapping.yml | 48 +-- usegalaxy.org.au/metabolomics.yml | 28 +- usegalaxy.org.au/metagenomic_analysis.yml | 174 +++++------ usegalaxy.org.au/mothur.yml | 4 +- usegalaxy.org.au/multiple_alignments.yml | 60 ++-- usegalaxy.org.au/nanopore.yml | 38 +-- usegalaxy.org.au/none.yml | 56 ++-- usegalaxy.org.au/phylogenetics.yml | 88 +++--- usegalaxy.org.au/picard.yml | 8 +- usegalaxy.org.au/proteomic_ai.yml | 10 +- usegalaxy.org.au/proteomics.yml | 216 +++++++------- usegalaxy.org.au/qiime_2.yml | 2 +- usegalaxy.org.au/rad_seq.yml | 60 ++-- usegalaxy.org.au/rna_seq.yml | 176 +++++------ usegalaxy.org.au/rseqc.yml | 4 +- usegalaxy.org.au/sambam.yml | 78 ++--- usegalaxy.org.au/send_data.yml | 10 +- usegalaxy.org.au/single_cell.yml | 178 +++++------ usegalaxy.org.au/statistics.yml | 32 +- usegalaxy.org.au/text_manipulation.yml | 48 +-- usegalaxy.org.au/variant_calling.yml | 28 +- usegalaxy.org.au/vcfbcf.yml | 282 +++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 100 files changed, 2860 insertions(+), 2852 deletions(-) delete mode 100644 requests/plot_ragtag_paf@latest.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index a9340252f..91d5cafa8 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7944,3 +7944,4 @@ Update 213 09/10/24 20:35:18 umi_tools_whitelist False Installed iuc e4e12f0b3af 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 +Install 1677 16/10/24 00:02:20 plot_ragtag_paf True Installed galaxy-australia c1bed78b9ed5 latest 3/3 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1677/install_log.txt diff --git a/requests/plot_ragtag_paf@latest.yml b/requests/plot_ragtag_paf@latest.yml deleted file mode 100644 index f948aa97b..000000000 --- a/requests/plot_ragtag_paf@latest.yml +++ /dev/null @@ -1,4 +0,0 @@ -tools: -- name: plot_ragtag_paf - owner: galaxy-australia - tool_panel_section_label: Graph/Display Data diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index eb15ad45b..5047144df 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,25 +2,25 @@ tools: - name: abricate owner: iuc revisions: + - 3f3e247c053d + - 78c75f134c16 - 4efdca267d51 - c2ef298da409 - - 78c75f134c16 - 6e9aea89e388 - - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval owner: iuc revisions: - - 1dd7adc21b6d - 8dc7512c9dc9 + - 1dd7adc21b6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus @@ -33,30 +33,30 @@ 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: - - b5d8e5475247 - - 44018dd6b447 - - 1aae04680c4b - - cd2480f35935 - a79ee60b6926 - - f29602ae449e - 3e1f6f6d557e + - b5d8e5475247 + - cd2480f35935 + - 4f2967b27e67 + - 1aae04680c4b - 133f36c29579 - fe3ca740a485 - - 4f2967b27e67 + - f29602ae449e + - 44018dd6b447 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -71,10 +71,10 @@ tools: - name: augustus owner: bgruening revisions: + - 28433faa6e42 + - bd0e53f3a891 - ca6d970d931c - 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 - - d77802fe76f7 - 728dacaf08a9 + - d77802fe76f7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - fe48aa4ccd5e - - 7355bbf5e05f - 8fd427007e93 + - 7355bbf5e05f + - fe48aa4ccd5e 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 @@ -116,17 +116,17 @@ tools: - name: cpat owner: bgruening revisions: + - 1ac12c0cc7a0 - 7ccc6234b54e - 8e9e228c54c4 - - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - 9d1fbff733cf - - d9c3016f7283 - 63662ae295d6 + - d9c3016f7283 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: - - 756376aeb1ae - 3bbe70fef6df - - 582fd74dc2a1 + - 14f588312c56 - b6b5cd37f2a2 + - 756376aeb1ae + - 582fd74dc2a1 - 9c15ca7e764e - 9f2455341fac - - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - a230ea445788 - - 30fb23d4c31c - - 989f7c061f35 + - 1691af4a0d17 + - 0ffe5be70caf - 73428a792541 + - 30fb23d4c31c - 8e1ace8f77c6 - - 0ffe5be70caf - - 1691af4a0d17 + - 989f7c061f35 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 57c6718cbfcc - - e94187d661df - 0418d28136de + - 57c6718cbfcc + - 30f08d74024f - 563a19373357 - - 5a5ae61da69c + - e94187d661df - 494f0bb4a993 - - 30f08d74024f + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - d6c7106b7b2e - - 2bba2ff070d9 - 1bc5a03faf2e - - f31125bb85ea + - 2bba2ff070d9 - 7abc5f6dd595 - f77d7b685bb3 - 4b96ced19f75 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 54961e026fe4 - - b3cf4684e9c7 - - d3af38b9c7e1 - 520e30695ec3 - - d77fdcca400e - fed64e676186 + - 54961e026fe4 + - d3af38b9c7e1 + - b3cf4684e9c7 - 52af33194019 + - d77fdcca400e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -230,8 +230,8 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - 43798b4caee0 + - 602de62d995b - ef2ad746b589 - 8b3e3657034e tool_panel_section_label: Annotation @@ -242,12 +242,6 @@ 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: @@ -270,9 +264,9 @@ tools: - 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 @@ -290,25 +284,25 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - 3c1a01127868 - d46d803ca6cc - 370c210d9541 + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - 033755194fe9 - - 624606f7c996 - b815ec682418 - c8ac28e8ac44 + - 624606f7c996 - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -351,11 +345,11 @@ tools: - name: prokka owner: crs4 revisions: - - eaee459f3d69 + - bf68eb663bc3 - 8a22554cdde2 - - d643e3b03500 - a17498c603ec - - bf68eb663bc3 + - d643e3b03500 + - eaee459f3d69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -367,8 +361,8 @@ 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 @@ -399,22 +393,22 @@ tools: - name: snpeff owner: iuc revisions: + - cfcf33df7fc0 + - 268d162b9c49 + - 5b80f544c67f + - 8f92c2b26e6d - 5a29ab10dba6 - 6322be79bd8e - - 8f92c2b26e6d - - 5b80f544c67f - - 5c7b70713fb5 - - 268d162b9c49 - - cfcf33df7fc0 - 68693743661e + - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - - 09d6806c609e - 5fab4f81391d + - 09d6806c609e + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -426,8 +420,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -439,24 +433,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 - 037a11682176 - ac8250086ac3 - - 809dfc93d593 + - 37213cf56392 - ba6f87115e13 + - 809dfc93d593 + - e1a9d6fd258d - 200c378d85f3 - 51dd22484644 - - e1a9d6fd258d - - 37213cf56392 - - 4839e590cb26 + - 45083d070fb8 - d03af1c7002c + - 4839e590cb26 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 15ea9dce6..99b03f6f2 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: - - fa5259cc561b - - 8f1b150a2487 - - 841084c5fc46 + - 890b794c997d - 0124fce4654a - 553bfe8bd0b5 - - 7547fcab5d19 - - 890b794c997d + - 8f1b150a2487 + - a929ce596a34 - d6d5ccc2c581 - 0e93176640ac - - a929ce596a34 + - 841084c5fc46 + - fa5259cc561b + - 7547fcab5d19 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - 21e491ad532a + - b2860df42e16 - 067592b6b312 + - b9e31c5c01c7 - 94fe43e75ddc - ddddce450736 - - b2860df42e16 - - b9e31c5c01c7 - - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,10 +35,10 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 3371c5bdc17a + - faee8629b460 - 22286dab5aa1 - a7f16f24e9a1 - - faee8629b460 + - 3371c5bdc17a - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -52,31 +52,31 @@ tools: - name: busco owner: iuc revisions: - - 41030a6c03b7 - - e824f5d958d0 - - 2dd755c1c6ff - - 1440ae06552f - - ea8146ee148f - - e4bd1e99bacf - - 602fb8e63aa7 + - 94170eee0ad8 - 4048d82f0c88 - - 46ae58b1d792 - - cf13a1e03e5b + - 2dd755c1c6ff - 5ecdeca79a0d - - 2babe6d5c561 - f18f0b887c31 - - 94170eee0ad8 - bb935709506a - - 1e62c28ba91d + - cf13a1e03e5b + - 1440ae06552f + - 41030a6c03b7 + - 602fb8e63aa7 + - 2babe6d5c561 - 0d243f458b53 + - e824f5d958d0 + - ea8146ee148f + - 1e62c28ba91d + - 46ae58b1d792 + - e4bd1e99bacf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - 86f150c8019d - c5b7390290b1 - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -88,41 +88,41 @@ tools: - name: flye owner: bgruening revisions: + - e27815e82dd4 - 3e4f8642c77e - - 3ee0ef312022 - - 1f0769f0b56b - 276f5d8712d5 - - cb8dfd28c16f - - 1ce9b1d72ec3 - 291923e6f276 - - e27815e82dd4 - 8d4f03b5fe9d + - cb8dfd28c16f + - 1f0769f0b56b + - 3ee0ef312022 + - 1ce9b1d72ec3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 460fad600dce - 3169a38c2656 - b2f674562a18 - 01210c4e9144 - - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 8b330a577046 - ba88bc5a6446 - - 06bcf65179fb - 7348b69e5109 - - 8b330a577046 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - 3ef480892a9f - - 3fba9c77550a - 690c2caa367e + - 3fba9c77550a - 5127a713de83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -135,23 +135,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - f3c89da3af16 + - 284a1cb82b61 + - 5f625c63b8bc + - 60024a528cbd + - 41cea2aa2dce - ec9e21e9c71b - - 0ee0c3089254 + - 71740308d412 - df25d4fb79b7 + - 0ee0c3089254 + - 366a11d316a7 + - f3c89da3af16 - 9ef6920c3089 + - da9d8bf98802 - 2061fb3b81b4 - - 3f7be05a1597 - - 5bec28269d95 - - 60024a528cbd - - 284a1cb82b61 - - 5f625c63b8bc - 6505bd37670d - - 71740308d412 - - da9d8bf98802 - - 41cea2aa2dce - 045c7c3d8e59 - - 366a11d316a7 + - 5bec28269d95 + - 3f7be05a1597 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -169,18 +169,18 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - - 7518ee87b53d - 14ddfc8ffb93 + - 7518ee87b53d - de387b2b2803 + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b - 9d79beb19ac3 - d7edbc9c3a07 + - f8113c25bc6b - 39edec572bae - 09c589057ee8 - eb7b00ec347d @@ -189,23 +189,23 @@ tools: - name: meryl owner: iuc revisions: - - eadfd71dde37 - 51c2360aa807 - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - e731ea24e48d - - 99ecfdafc64f + - f338e9942b27 + - eb7a370f6588 + - 2ecf5a570907 + - 3ca2d2a9068c - f369ef5f210b - fd128c111ab0 - - 2ecf5a570907 + - 99ecfdafc64f - 606b09cc9860 - - 3ca2d2a9068c - - f338e9942b27 - - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -217,10 +217,10 @@ tools: - name: miniasm owner: iuc revisions: - - b799a615995d - a7b889b90140 - - 8dee0218ac7d - 73a3846701e1 + - 8dee0218ac7d + - b799a615995d - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,9 +239,9 @@ tools: - name: novoplasty owner: iuc revisions: + - 64a1c751d99b - 7c2f5268d01c - 15200570e926 - - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -254,34 +254,34 @@ tools: owner: iuc revisions: - d256a51a656b - - 8fef980d48b5 - 79b48f02db49 - - 02831bf9e95f - bbe19ef04a74 - 2b16ba799da9 + - 8fef980d48b5 + - 02831bf9e95f - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - 76d4cbefff85 - e9bd16ba5ebd - a315c25dc813 - - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 6fcbee531de6 - 342a1d1fed7b - - 72472698a2df - - 59db8ea8c845 - - 3061c8b029e5 - - 7594365c546b - 675488238c96 - - ebb0dcdb621a + - 7594365c546b - 875d0f36d66f + - 59db8ea8c845 + - ebb0dcdb621a + - 3061c8b029e5 + - 6fcbee531de6 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon @@ -289,10 +289,10 @@ tools: revisions: - d865b62f501c - a199cd7ac344 - - aa39b19ca11e - - 39bed8de8017 - 78c533842eeb - cd06929b224b + - 39bed8de8017 + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -310,31 +310,31 @@ tools: - name: raven owner: iuc revisions: + - 33b7d8481a76 - 2b2a352488fa + - 3edba9afc9bc + - f11b994b7eb2 - 5c55448d0f33 - f8564b2d7f63 - - f11b994b7eb2 - - 33b7d8481a76 - - 3edba9afc9bc 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 - - 1d06c8b38e77 - - e122f9101584 - - 53c2bc8c2ae3 - 28189050e437 + - 378e55aeeb25 - 5fc94b3a4704 + - 53c2bc8c2ae3 - ef69617ecb42 + - e122f9101584 + - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,43 +346,43 @@ tools: - name: shovill owner: iuc revisions: - - 865119fcb694 - - d9f6a00b6db7 - ee17a294d3a3 - - ad80238462c1 + - 196a599ec43d + - d9f6a00b6db7 - 83ead2be47b2 + - 865119fcb694 - f698c7604b3b - - 196a599ec43d + - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 24e471d13fe9 + - 5e0825476fb7 - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 - c33a476f4001 + - 1fc82fe7ebef - 7490b213baa9 + - 904bf932cf78 + - 051fd2db8a27 - 604782a8a53a - 1bb12736175c - - 904bf932cf78 - - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 34305b013402 - d6e617c4e338 - - 9678993ca5bd - - 655fa188c3cc - 808b3a0a6716 + - 655fa188c3cc + - 9678993ca5bd + - 34305b013402 - fee85957cebe - ad8b536d1caa tool_panel_section_label: Assembly @@ -390,146 +390,146 @@ tools: - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - - 7e27faaad80e - e5a3b75a271f - 6b5a5842531e - 037f9927c4ff - - b8002c3f7141 - 21da31ed41a1 + - 7e27faaad80e + - 8d4b90bf9caf + - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 5b26685e5d3b - 86f66ab58e14 - 2a10645aeadd - - f1532cb33c75 - 328aa71f0f3c - 9de69775f512 + - f1532cb33c75 + - 5b26685e5d3b - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - e41dcb0e913b - - 8cc856b935ee - 85fb02c43042 - 340bc17f49cf - 6aad515a5270 + - 8cc856b935ee + - e41dcb0e913b - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 6357b127161e - - b3490b036c5a - - d159735a6a9f - 249f6a28c751 - - d5fb354f745d - b65a43f70b99 + - d159735a6a9f + - b3490b036c5a + - d5fb354f745d - de1260f8a300 + - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - 33368fec3b70 - - 9006e5836729 - - 7897763d14ec - d5887ace0dd4 + - 7897763d14ec + - a90db5dbaaf3 + - b7829778729f - d2d1df21dfb9 + - 9006e5836729 - dd7ad84f3943 - - b7829778729f - - a90db5dbaaf3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 6f4c8ad6ea01 - - 189e837009c9 - - ced385aa976d - ed2425b9fd27 - - 8f631679571f + - ced385aa976d + - 6f4c8ad6ea01 - 505a9833ab5d + - 8f631679571f + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 9ded6109434a - 19bdfd1e6fe3 - - f31d376ce725 - - e59bee4565b3 + - 9ded6109434a + - d40ed4eb0c0e - 356afed970b4 + - e59bee4565b3 + - f31d376ce725 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 4688ae3b49b5 - b23249f81bc4 - - af40e971a8cc + - ebd801e712bc + - 4688ae3b49b5 - 80a17897564d - 6dd935e4984b - - ebd801e712bc + - af40e971a8cc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 937ea677d437 - - cb1e3db43020 - b5e35a2ca4f3 - b64696992ee9 - - 59bd28f6265d - bb11fefb23a3 + - 937ea677d437 + - cb1e3db43020 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 05bd7504fdb2 - cb4768eeca3b - - 6bfab4a4a988 - - 6015aa0303f2 - 2628f6790eda - 383bb5ad32e2 - - 05bd7504fdb2 + - 6015aa0303f2 + - 6bfab4a4a988 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 9e3e80cc4ad4 + - 8f9f06995f98 - 6e26c9afd301 - - 0a3a602cd1e3 + - 9e3e80cc4ad4 - e92675014ac9 - - e022dff952df - 3e44ef016b45 - - 8f9f06995f98 + - 0a3a602cd1e3 + - e022dff952df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 08256557922f + - 5da9a0e2fb2d - 920677cd220f - 8d09f8be269e - - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - - 0e2b4e3f9ca1 - d81360ea69d8 + - 82398ba86ba7 - 4a53b89fa703 + - 0e2b4e3f9ca1 - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 7cf4e390b..7cb40766e 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - - bfd290fe1588 - 392f100eebcd + - bfd290fe1588 - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - ded48b36f3b7 - - 8e8dc9a1e3e5 - - 31812e7a1315 - 1f5641a52664 + - 31812e7a1315 + - 8e8dc9a1e3e5 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - - 17fcac7ddf54 - 24a7a95867b0 + - 17fcac7ddf54 + - 5c8ff92e38a9 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 569544ee9..db3982246 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,12 +2,12 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 1c427e24fb79 - - a9c9d768b751 - - 0840ba83860c + - 7beb76ffbc0f - d1f62024a08b + - 0840ba83860c + - a9c9d768b751 + - 1c427e24fb79 - 204a131e47db - - 7beb76ffbc0f - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 594eb9d6e..e00db7d32 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: - - a68aa6c1204a - - 87ee588b3d45 + - 589e7e57fd6d - dde39ba9c031 - - b28e0cfa7ba1 - - a8eabd2838f6 - 07e8b80f278c + - ce3c7f062223 - 0a5c785ac6db - - a1a923cd89e8 + - a8eabd2838f6 + - a68aa6c1204a + - b28e0cfa7ba1 - e19bebe96cd2 - - 589e7e57fd6d - 64e2edfe7a2c - - ce3c7f062223 + - a1a923cd89e8 + - 87ee588b3d45 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 e1a887906..3d44867c0 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - e8ac2b53f262 - 62c9df8382c2 - 54f751e413f4 + - f921014aba5a 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: + - a52d2d93e595 - d999e774072a + - 0e3cf9594bb7 - 5edc472ec434 - acf4e47b734c - - e25d3acf6e68 - - 0e3cf9594bb7 - 6f386c5dc4fb - - cbf3f518b668 + - e25d3acf6e68 - 2889433c7ae1 - - a52d2d93e595 + - cbf3f518b668 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 e1a4a2471..586b02e6f 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: + - 710301bc46fa + - da6bd1975a71 - 095ad4d096d1 - - 27ee142314a9 - f4230f116196 - - c8cdde00b105 - 6ca543ec1bf8 - - da6bd1975a71 - - 710301bc46fa + - c8cdde00b105 + - 27ee142314a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - - 3b8a9d5ced85 + - 0fac8e2afc13 - bfb65cb551d8 + - 88076940fa94 - 79cfd9ead848 - - 0fac8e2afc13 + - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - f5d979cb4b54 + - b46d4b4d995c - d532b7e5f64b + - eb6564a60136 - 715cd0e87781 + - f5d979cb4b54 - 55918daa5651 - - eb6564a60136 - - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 - - fdf2cc80adb5 - - 5579659312e6 - 97872d87ba80 + - 5579659312e6 - d2f955aea23a + - f26afd1b7104 + - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - d1d0efda35c0 - bc31d02be922 - 319a28774da9 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - ed736e6eee39 + - cac1886249a2 + - 4da9ee404eab - 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 - d1f803b5943c - - da8753545526 - - 525ca7c8065f + - c0c9a5024177 - 2e219a2d9327 + - 73008ef1f487 + - 525ca7c8065f + - da8753545526 + - f197e34c33a9 + - 807aa4c9293d tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 - - 2c8ed1b52bf7 - 1809414a9454 + - 27ea4e1a3f95 - 7568ae18908a - - c4fbab8e03c5 - 61094e01eff9 + - 2c8ed1b52bf7 + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -210,10 +210,10 @@ tools: owner: chemteam revisions: - 730ef07b90ae - - ccfbd956a2d3 - - d7ec25187599 - 79e8ab8f1e81 - ba83f0923369 + - ccfbd956a2d3 + - d7ec25187599 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -269,9 +269,9 @@ tools: owner: bgruening revisions: - b59c91adeac1 + - 1400d1977e7b - 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 + - 85fad59f8168 + - 9b48456a96fe 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 328651e97..d55c3c7e4 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: - - f907216064f6 - fa56d93f7980 - 163688bb8f73 - c97a786e8fb5 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -31,10 +31,10 @@ tools: owner: iuc revisions: - f5d67c722d67 + - 424aefbd7777 + - 640d3af5d833 - 495a4173006f - 86e2413cf3f8 - - 640d3af5d833 - - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -46,16 +46,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 - 4a14714649b4 + - 5c2cc3b58c7d 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 245bdf800..c4d526138 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -11,15 +11,15 @@ tools: revisions: - 33151a38533a - 90981f86000f - - 830961c48e42 - 25136a2b0cfe + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd - - 0046692724f9 - 6cbe2f30c2d7 - 2dae863c8f42 + - 0046692724f9 + - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b 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 3e9a3fe3c..be162739b 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - ab9350a8ab4d - - 4a6ee918c13a - - 367b1ed91207 - - 0b3c3ad92827 + - 3b6f97e7094c + - e3cbd2287f63 - 5e1240a87bcb - - f3a19509108a - 6ef0b5664c69 - - 3b6f97e7094c + - 367b1ed91207 + - 4a6ee918c13a + - ab9350a8ab4d + - 0b3c3ad92827 - a3b86937ead6 - - e3cbd2287f63 + - f3a19509108a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 501c21cce614 - - 72ed72122deb + - 584008e574b2 + - bd46669113b9 - e525f9ffb9ac - 1b5fc03380d4 - - d4d4e9febf5c - - 33c99804a32f - - bd46669113b9 - - 584008e574b2 + - 72ed72122deb - 091bb5922a82 - - e177a8ea0bf1 - 54ccb7e1f49a + - d4d4e9febf5c + - e177a8ea0bf1 + - 33c99804a32f + - 501c21cce614 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -67,16 +67,16 @@ tools: owner: devteam revisions: - 186b8d913e6c - - 77b41c89d856 - 8979c288aefb + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 43807a65369f - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa + - 43807a65369f 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: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -101,8 +101,8 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - 154d00cbbf2d + - 3e436657dcd0 - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -115,28 +115,29 @@ tools: - name: intermine_galaxy_exchange owner: iuc revisions: + - c24014d80001 - faef2b1622a3 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: mz_to_sqlite owner: galaxyp revisions: - - 705821bf30d2 - f5c632894818 + - 705821bf30d2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq @@ -150,9 +151,9 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 63769c4217a7 - 26c6706bfb07 - b9b385097f13 + - 63769c4217a7 - 19e45916daf9 - 92ac8e086317 tool_panel_section_label: Convert Formats @@ -166,15 +167,15 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 3c6f9e8a4c17 - 8067dfa00ed2 + - 3c6f9e8a4c17 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - 98704d357ede - a2f83a375bf2 + - 98704d357ede 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 5771902e2..c0c0c994b 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,24 +2,24 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - e821645ef8fc + - de72ba3ed6f2 + - 5f6d123679f4 - c929a006727f - a1ca9bccc7f2 - - e821645ef8fc - 29451af70c52 - - 5f6d123679f4 - - de72ba3ed6f2 - 268e91e540ee tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e49b109abc2 - 0e143b4c3987 + - 2d2cf5c1ea8a + - 5d11599b8a7d - bb1e4f63e0e6 + - 0e49b109abc2 - 12af64f93288 - - 5d11599b8a7d - - 2d2cf5c1ea8a - 7a7fd0f5f15d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -27,9 +27,9 @@ tools: owner: bgruening revisions: - 7c1beb6d6eca - - 81b1e3e1fc6c - 1d848bc4585f - dc059492a995 + - 81b1e3e1fc6c - 195e98217334 - c06951d10364 tool_panel_section_label: DeepTools @@ -37,13 +37,13 @@ tools: - name: deeptools_bigwig_compare owner: bgruening revisions: + - 71aa86af6762 + - 3d211717a775 - a67ac707496a + - 26e7304d6737 + - 07418a30ed01 - 93eb012d9eed - - 3d211717a775 - bfff7454b59a - - 71aa86af6762 - - 07418a30ed01 - - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias @@ -51,9 +51,9 @@ tools: revisions: - dd0b7398bb96 - 5be24eba848d - - 29fcfd36e90a - - 26983857c91a - b8858746dc1f + - 26983857c91a + - 29fcfd36e90a - 2bc10a9ca58b - 56d5b797ce84 tool_panel_section_label: DeepTools @@ -61,146 +61,146 @@ tools: - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 72bfafe3330b - - 9384cd033f30 - - c3e012dfe21f - e6d0bff01239 - - 7ef978dc1b8a + - c3e012dfe21f - 7e6bcd2e5128 + - 9384cd033f30 + - 7ef978dc1b8a + - 72bfafe3330b - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - 167788df3b46 - fb9cf9c97ec4 + - b73e213add0c - 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 - - e479c7ca5570 - - 5bffaa8354a1 - 86febdcc4283 - a02cfa31e9cb + - 5bffaa8354a1 - ca0616bb2cdf + - e479c7ca5570 + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 192ef85c0b0b - 004aea905d4d - 69a8621ca2f0 - 2d466b530754 - - 1fcb7adc39b8 - 01fb6a7654e6 - 78f405266706 - - 192ef85c0b0b + - 1fcb7adc39b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - db940c262830 - - 137c4beed34b - - 2f9e4843f480 - - 9ecba5e225a6 - - 459cfa861f0b - d580d6acd1df + - 9ecba5e225a6 + - 137c4beed34b - d9ce4897dbb2 + - 459cfa861f0b + - 2f9e4843f480 + - db940c262830 - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 2c66e43f1c86 - - f264afa9fa6f - bd7db9e2f2cb - - fbe773640707 - fd408d755394 - - 32e451def88c - bad3ca889618 + - 2c66e43f1c86 + - fbe773640707 + - 32e451def88c + - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 4e12ea27f788 - 9368fbc49c8b - - 56bce3c82278 - 7fda5607e777 - - 7e361d147872 - 231994413f89 - 3b9d990a0a0e - - 4e12ea27f788 + - 7e361d147872 + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - e65d16fb2724 + - ce4ce3316f74 - d9114ef1c8a5 - - 4431f39ede55 - - b1779366c8e9 - c03c3384cd81 + - e65d16fb2724 - 94ca68515826 - - ce4ce3316f74 + - 4431f39ede55 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 + - 23f7c5f1fdaf - d57251071381 - b88ebb3672a1 - f8fc4e5aff9d - - 23f7c5f1fdaf - - 4ed32329e0ed - 2da482e408b8 + - 4ed32329e0ed + - 793665fff0f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - ba6efa77fb79 + - c60570fa602f - 010e58e9d822 + - 512155688d98 + - 25d830337d31 - e4c7985d4585 - a4dfb122e52b - a7849312d328 - - c60570fa602f - - ba6efa77fb79 - - 25d830337d31 - - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - 00d869ea03a1 - - 443d9a9d6d11 - c899e0ccff8c - 4d678170d29b - - 38e3f226248b - aa200e4f3939 - 69264da0ce77 + - 38e3f226248b + - 443d9a9d6d11 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - 6662b1a8d326 - - 10301d137111 + - aac8444d6681 - a2d70c4fd406 + - 10301d137111 - 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 20cae0f1d..6f9694b7e 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -23,22 +23,22 @@ tools: - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f 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: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index c87ebd957..58b655034 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -4,7 +4,7 @@ tools: revisions: - 63dd26468588 - dba489bfcd62 - - 832c20329690 - ce385837c160 + - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index bc5ddf712..bd9cb4e06 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,10 +8,10 @@ tools: - name: bwameth owner: iuc revisions: + - 29bdbc353f20 - 62f5fab76dfb - - d82648ad25a3 - 6da3972210ee - - 29bdbc353f20 + - d82648ad25a3 - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 0b9e25709..77cdcc35f 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -9,25 +9,25 @@ tools: owner: lparsons revisions: - 660cffd8d92a - - 49370cb85f0f + - 44e2cc14f75b + - 5915ea1ec9b1 - c053d4cad713 + - 093678460093 + - c4b82dce8335 + - de6cebe3c043 - 8c0175e03cee - 5eb7e84243f2 + - 64172f1c1202 + - 135b80fb1ac2 - 288f97432497 - 8665bcc8b847 - - 4e5056fefd88 - - b1c926deaa2d - - 093678460093 - e4691e1589d3 - - 44e2cc14f75b - 48f587c13075 - - 5915ea1ec9b1 - - 64172f1c1202 + - 49370cb85f0f - c5e2e5902201 - - c4b82dce8335 + - 4e5056fefd88 + - b1c926deaa2d - fe74900d6dc7 - - 135b80fb1ac2 - - de6cebe3c043 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,8 +39,8 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - 8889eb864cef - 9db07fd39f85 + - 8889eb864cef - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -60,8 +60,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -73,16 +73,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - 8cacfcf96a52 - e626b3ff9922 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - - 859422bcb689 - 9457a20156db + - 859422bcb689 + - 516b97a23d7e 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: + - f773e98b26cf - ec0b5076173a - f81d4362b6c1 - - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -130,11 +130,11 @@ tools: - name: fastp owner: iuc revisions: + - 1d8fe9bc4cb0 - c59d48774d03 - dbf9c561ef29 - 65b93b623c77 - d60c3f704da0 - - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -146,9 +146,9 @@ tools: - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - 9115b978ce10 - b05e39b9c170 + - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -160,9 +160,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - 10b75444feae - - '144275714590' - 81a9090d6df3 + - '144275714590' + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -188,8 +188,8 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -216,9 +216,9 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: + - 03d57fea6482 - 523c2aff0376 - f3936d0632cb - - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -230,8 +230,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -244,9 +244,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: + - 09a2199cd356 - 8d958759cf2a - c885369b207b - - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -260,8 +260,8 @@ tools: revisions: - 249c8393f2d4 - e39cc71d3ed6 - - 35e38452bb3f - 397dc333436b + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -273,9 +273,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 045f0e1043f7 - 54053ea6c77e - 74db4cffab1f - - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -288,8 +288,8 @@ tools: owner: devteam revisions: - b1cea1b2fcd0 - - f86c27295151 - f0e7deab6518 + - f86c27295151 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -301,8 +301,8 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -315,16 +315,16 @@ tools: - 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: - - d5e9e83cd3d8 - 529bccd5e4a1 - 567d5b3c52b1 + - d5e9e83cd3d8 - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -337,8 +337,8 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - 0b7ec11b3c7c + - 4bedca26c133 - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -351,10 +351,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - bdf1ce174e39 - - 90858c306551 - cb1e251cac37 + - bdf1ce174e39 - 736b8f6ee456 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -366,9 +366,9 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 421f0af4ee95 - 7ce1891db6f5 - 07497255281e + - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -380,10 +380,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - f984bb114520 - - 3599f5451ee2 - 02f8a17a4ebd - b29d37ca9e41 + - 3599f5451ee2 + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -395,9 +395,9 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - - e246088b6e34 - 0c2907307ba4 + - e246088b6e34 + - 6027ef51ef91 - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -410,9 +410,9 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - 377ac2829eac - 73194cdd4f57 + - 547e8d00f11c - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -452,15 +452,15 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - 61eb4cfc7313 - fdc21382376d + - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -500,8 +500,8 @@ tools: owner: iuc revisions: - 71f649c23021 - - bf04bd405d5b - d3f58a0dc09d + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -513,11 +513,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - b557acca0b56 - 8250ea3a1501 + - 24013bf85a6f + - b557acca0b56 - 71ad4a56c40c - e654095ab143 - - 24013bf85a6f - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -537,14 +537,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 015cf18f4a15 + - 828dba98cdb4 + - 7a7e33d28f62 + - 6a675c3aa610 - 7accf7407811 + - 015cf18f4a15 - f3759eec3018 - - 9fa7803d1c51 - - 6a675c3aa610 - - 828dba98cdb4 - 27ac32a22ad2 - - 7a7e33d28f62 + - 9fa7803d1c51 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 - 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 061f598cb..64e4a7c0a 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,83 +2,83 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - e41385662e5e + - 64e9a6afdd0c - 7b4468117008 + - e41385662e5e - ce9cd02d5b88 - - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 2c64fded1286 + - ff9530579d1f - e7b2202befea - f2e8552cf1d0 + - 2c64fded1286 - 9da02be9c6cc - 3d0c7bdf12f5 - 2b0c9d9fc6ca - - ff9530579d1f - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - ad116ae3f4d9 - b6b54ba71bd8 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - - 59003d0543cd - 7306ec78632a + - 59003d0543cd + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - a72af9de6bf5 - 8880fb74ef56 - 1f296803dfa3 - - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - b2f1f75d49c4 + - 75c93c70d094 + - f7e2f1eb3a16 + - 1c2db0054039 + - 5e33b465d8d5 - bf675f34b056 - - 3d93dd18d9f8 - f7985e0479b9 + - 3d93dd18d9f8 + - b2f1f75d49c4 - 9a913cdee30e - - 1c2db0054039 - - f7e2f1eb3a16 - abfd8a6544d7 - - 75c93c70d094 - - 5e33b465d8d5 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/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index b248d7a64..9243d596c 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: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 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: - - 83a19df00eab - 141612f8c3e3 - 85ef5f5a0562 + - 83a19df00eab 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 394e068e3..c9d9399b6 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -9,16 +9,16 @@ tools: - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: + - 0c8f7322f8fc - f2f3bc622a16 - 8f53b238a360 - - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -86,30 +86,30 @@ tools: - name: gemini_load owner: iuc revisions: + - 45296e47d565 - b2c25142267e - cf61daf064fe - - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -123,8 +123,8 @@ tools: owner: iuc revisions: - 840fb4850be3 - - 666f60a9331a - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -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/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 2a6e45eeb..095be2eba 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index f82c901c7..8872e0404 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -3,9 +3,9 @@ tools: owner: galaxyp revisions: - b39347891609 - - c1b437242fee - e9df53a75f3c - 983bf725dfc2 + - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - - 1c58de56d587 - e063168e0a81 + - 1c58de56d587 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1ec814014652 - - 1790dcf3c32d + - e08a7ad4378b + - 653e89d73fc4 - 69ebb7f46e45 - - 9a776b080193 - - 734abc7ac21d - - 5e6237d58b0c - aad3885b3216 - - 83c7d564b128 - - 6ea73833cf67 - - 4317d3cb6cba - - 516a54ddf218 - - 653e89d73fc4 - - 8848455c0270 - e407b9da183a + - 7068f48d0ef9 + - 516a54ddf218 - f8054ea1c365 - ba931a59dd59 - - 7068f48d0ef9 - - f5ea3ce9b9b0 + - 83c7d564b128 - 4df8de2d0e48 - 6591f049cf7e + - 4317d3cb6cba + - 5e6237d58b0c + - 9a776b080193 + - 1ec814014652 + - 6ea73833cf67 - c441583adae5 - - e08a7ad4378b + - 1790dcf3c32d + - f5ea3ce9b9b0 + - 734abc7ac21d + - 8848455c0270 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 21a560af5913 - - 9aaa46d45472 - 75b3b3d0adbf - 34758ab8aaa4 + - 21a560af5913 + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - 054483e27a35 - - af5eccf83605 - 468c71dac78a - bfdc6a7ffd3a + - af5eccf83605 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 726ab5b04..5dd2fc5c6 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - c4bde687c846 + - 7f13dc906cb9 - a64dc31ab7f2 + - 740057a5126d - df7356989ac1 - - 7f13dc906cb9 - 4b519282a05b + - c4bde687c846 + - fd59d783248a - ae9994cf526f - 290a11559985 - - 740057a5126d - - 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: - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,22 +48,22 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - '566197475670' - 374e9062d874 - 53460afd5115 - ca7cb0eaad62 - 3b37b1b1c3a7 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 391a4cc45fea - 10515715c940 - - d3a9e32672ec - da4c086cff5b - - 391a4cc45fea - - 3d059e9c2fba + - d3a9e32672ec - 1a72f938213e + - 3d059e9c2fba tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -76,26 +76,26 @@ tools: - name: ggplot2_pca owner: iuc revisions: - - ae344ccf9d62 - b1268b7544d3 + - ae344ccf9d62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 5298e06f14f9 - - 1acf88921176 - d0fc8b746d57 - e3a675da7fd0 - 299307abd804 + - 5298e06f14f9 + - 1acf88921176 - 5fe1dc76176e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -114,8 +114,8 @@ tools: - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -134,17 +134,17 @@ tools: - name: jbrowse owner: iuc revisions: - - ca2def38369c - - 667e17248bfe + - a6e57ff585c0 - 112eb40ba6cf - - 1cfc579079a6 - - 2bb2e07a7a21 - fd5dbf0f732e + - 667e17248bfe - 17359b808b01 - - 6cd09d7b5f37 - - a6e57ff585c0 + - 2bb2e07a7a21 + - ca2def38369c - 836d1aa3e89a + - 1cfc579079a6 - 4542035c1075 + - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -163,28 +163,29 @@ tools: owner: iuc revisions: - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - 594b85e4237a - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: + - c1bed78b9ed5 - 94e0834ae4ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - f234e2e59d76 + - 85da91bbdbfb - 62e3a4e8c54c - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data @@ -205,9 +206,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 - 6c571966cfb9 - 7c9417381ad5 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -219,23 +220,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 4ac4e7083b7e - 2824d77cd8f8 - - 36b848d5f3ec - - a1abfa420d9d - 14e7c35f3d00 + - 4ac4e7083b7e + - 7dd841a32245 - 360df4999907 + - 36b848d5f3ec - 326a3db8d9d1 - - 7dd841a32245 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 2f557f6abbfb + - 44608d0193ed - 73b8cb5bddcd - 83c573f2e73c - - 44608d0193ed - - 2f557f6abbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -247,7 +248,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 0409223a9..394f38433 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -28,15 +28,15 @@ 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 owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes @@ -77,37 +77,37 @@ 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 owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 70cb0596ffef - 53ce0e336840 + - 70cb0596ffef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 28b1546857b0 - 3027cb62adbd + - 28b1546857b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -134,22 +134,22 @@ tools: - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - - d18ed15697bb - 0bab2ae44e7a + - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -176,29 +176,29 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - b2768cae00a1 - 6d4f88995e40 + - b2768cae00a1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 4428dba93375 - 0cf90e01d9f8 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - - abdb61e4afa3 - 3fb53f5e46ea + - abdb61e4afa3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - ea91cfd0444e + - 767a675b5254 - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 8402f0767..3b081fc08 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,41 +2,41 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - ed2cca6b5de4 + - 29f66c353bcb - a4c13ddcc8ee - 921a2da49a0c - - 29f66c353bcb - 9edf8894a22d + - ed2cca6b5de4 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - ec4b948dc6f0 - - 5746d61f0a91 - - 755df866ad0c - d404277cc87a - 78fb5e286609 + - 5746d61f0a91 + - 755df866ad0c + - ec4b948dc6f0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 03dd3c16ae4e - - 9e357a8b2ec3 - 11fa44ee0603 - - 977dc15add20 - 4d511437b1e5 + - 9e357a8b2ec3 + - 03dd3c16ae4e + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 0ba4f56a3613 + - 41dbf4d162a2 - 77919cc3618e - 3b5b54ed6392 - c3e5e2cf12b7 - - 41dbf4d162a2 + - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix @@ -44,8 +44,8 @@ tools: revisions: - b63363075c2e - 7babd8a46fe0 - - 9939786dd9c9 - 5308ca68ef3d + - 9939786dd9c9 - 12d51d7be66f tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 6996244bc..43ddb9639 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,20 +2,20 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 7db4fc31dbee - 0c777d708acc - - 3df9f0a4bf34 - 699a5e9146b3 - - 8bccb36e055a - - 7db4fc31dbee - 81f0cbca04a7 + - 8bccb36e055a + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - 5bc8cdc17fd0 - - 5791a7f65275 - 2436a8807ad1 + - 5791a7f65275 - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -30,9 +30,9 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: + - 77f7159d775a - b1c2c210813c - 70316d792fc9 - - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -46,34 +46,34 @@ tools: - name: bfconvert owner: imgteam revisions: - - 10eed33aa9b2 - - 85edbb7a436b - f3360fbeda64 - b07f4839ca77 - fcadded98e61 + - 10eed33aa9b2 + - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - 664232d2a3f7 - 5bf8eb50b280 - b58447a2eed2 + - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: + - eb6c08714244 - 0e4dccaafef5 - e917a2424690 - - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -126,25 +126,25 @@ tools: - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - 3245681b2f6d + - 31d195bedf6d - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - - 87d4d92d7487 - 993faa34333b + - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - ff1a86a87364 - c09dcda1143f + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -166,49 +166,49 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: + - a32c3f810ade - 91e03287f285 - 20dbb1f7ec7b - - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - - 5499dc6f8ac1 - 8536b1ae0254 + - 5499dc6f8ac1 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - d3890df07463 - - 6f4715b8540a - e972e07c7845 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 407925835dd9 - 980aed9e8fd5 + - e52c75a28c4b 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: - - b76841ee5560 - - 035a58c7f54a - 80b200ae516b + - 035a58c7f54a + - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -220,9 +220,9 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - - 8083a87d2fdf - 48102a685037 + - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images @@ -256,8 +256,8 @@ tools: - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 - f8b4eada923c 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 dc90c9b09..f888e6ad8 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: - - f362150bef41 - - 3a72fede57ce - - 3e4f434a69c6 - - e4ee04da1c19 - - e319b5b65879 + - 40737febe339 - a38934e303b9 - - d6e72da3ec35 - 1069f6db0a0e - - 40737febe339 + - 3e4f434a69c6 - 78bbd17d0703 + - e319b5b65879 + - 3a72fede57ce + - f362150bef41 + - e4ee04da1c19 + - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - 7fe36019c073 - - fcbeda41d0ac - - 9537184d421f - - 0135f1d487a0 - - 8f8df367470d - f91cfb73d369 - - c88553ec696e - - 618297d23022 + - fcbeda41d0ac - 72ddd32392cd - 2b95d5c04908 + - 618297d23022 + - 0135f1d487a0 + - 9537184d421f + - c88553ec696e + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - fafb3d685fa9 - 2cf4a1cafc16 - ad0dc9f4c9e2 - d7e79eb3bcb3 + - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 43aac8d29685 - - 5dc33613c288 - - 8d36959b000d - - ee2beb764a7b - 9eaadf03e0df - - a1c2aecd7a0d - - 3d18f8c3c0f6 - 94df24c6bc00 - - bd2a7d1316b9 + - ee2beb764a7b + - a1c2aecd7a0d + - ee29337f905c + - 43aac8d29685 + - 8c05afb547fa + - 8d36959b000d - 7f1cfa4c0e32 + - 3d18f8c3c0f6 - 28a6f1908fcc - - ee29337f905c + - bd2a7d1316b9 - 6a1515bb0687 - - 8c05afb547fa + - 5dc33613c288 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 86a20ae274fc - - a250929be21b - - c092052ed673 - - bcaa0d571ce2 - 9f978da6528a - - 5671e1d3d5ee + - e3bb03cf207a + - a250929be21b + - cb903c9dc33d + - 8858fa037a15 + - 86a20ae274fc - 5d6ed46cc101 + - db536ad45f28 + - 5671e1d3d5ee - d37ede8589b2 - - 8858fa037a15 - 364f4ffec275 - - db536ad45f28 - - e3bb03cf207a - - cb903c9dc33d + - bcaa0d571ce2 + - c092052ed673 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - e1a015876aa9 - - 3b6a16d82c1b - - abbc8041e8ec - - 49236b03e4fd - - 584beffa972b - c5c9f02b6167 - - 230b05597996 + - 49236b03e4fd - 38b91a3190cd + - 3b6a16d82c1b - ed28dd32141c - - 12d66d0d05ac + - 230b05597996 - 194e3ceee923 - f95f403841ad + - 12d66d0d05ac + - 584beffa972b + - abbc8041e8ec 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 c0e3dc15c..09781ec0b 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 + - b8a457820315 - 0f1724dd59d2 + - f198773344e4 - 17e3b698dd52 - - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - 374cb875d38a - - ac092723240d - 22c2a1ac7ae3 - ba0c40780ecf + - ac092723240d - a513e3fbb4c5 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 afa427ac5..4270ab56d 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,8 +2,8 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - 66d7efc06000 + - 522137aaa9c4 - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,40 +18,40 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: - - 2af1346e68c9 - - f1b9a42d6809 + - b6ef6d0cb6b7 - e1317b5502fa + - f1b9a42d6809 - 818f9b69d8a0 - - b6ef6d0cb6b7 + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - 1588f9076e32 - - 8334dc98c48e - - 947c2eacccb8 - - c80db5d6fd8c - 05143043ca13 + - c80db5d6fd8c + - 947c2eacccb8 + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 9991c4ddde14 - 25b46af53232 + - 1552b8cb4a94 - 29e4122c90de + - 9991c4ddde14 - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - f3dfa4bdf87e - a07ab242b0b5 - - 1a53edc4b438 - 060ca94ac049 + - 1a53edc4b438 + - f3dfa4bdf87e - 53616c8b0865 - 841a6cc5fc58 tool_panel_section_label: Machine Learning @@ -59,42 +59,42 @@ tools: - name: sklearn_generalized_linear owner: bgruening revisions: - - 927586a18553 - - d4808d5b83da + - 40f4447733b2 - dc4b5fd604a6 - - 91c4e3331208 - 2fc89dcd41c8 - - 40f4447733b2 + - 927586a18553 + - 91c4e3331208 + - d4808d5b83da 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 - e5a5ad882f1f + - 25ab6b4e376e + - 7626ea9c2e1b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - f9639b488779 - - b7c3e9a3b954 - 0630258dcf35 + - 02d2be90dedb - 80852884053f - 4ed102b922cb - - 02d2be90dedb + - f9639b488779 + - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - ec69cbe34b73 - - 61634a87efc7 + - 14180f9c831e - caeb57858702 + - 61634a87efc7 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 f30430f84..c0a867884 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: + - 3ba8d4563129 + - 03e9b2fbc005 - d5ceb9f3c25b - - 749c918495f7 + - 17062a0decb7 + - 017aba02828d - 0d4acadabb04 + - 749c918495f7 - a6d65b0c67af - - 017aba02828d - - 03e9b2fbc005 - - 3ba8d4563129 - - cd659e8cc5fa - f6877ad76b00 + - cd659e8cc5fa - 937aa69e715f - - 17062a0decb7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 3fe632431b68 - - 2477830927ec - - 64f11cf59c6e - e188dc7a68e6 - - dfd8b7f78c37 + - 64f11cf59c6e + - 2477830927ec - 53646aaaafef + - dfd8b7f78c37 + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - - 37b497aa133f - 2ff111fac1d7 - 3e1ea2facca6 + - 37b497aa133f - 60afcc2c1d05 + - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - b3eab4b67562 - - be1d967337e4 - - 11a0d50a54e6 - 037c6e54df11 - - 53c0b7a1a0c3 + - be1d967337e4 + - c0c2d0941de8 + - f54f5baedfdd - 8c6cd2650d1f - - 6b1e195506a3 - 5cc34c3f440d + - 53c0b7a1a0c3 - 3f4d6399997b - - c0c2d0941de8 - - f54f5baedfdd - - 09b53c1d4ab1 - 77b2770508f6 + - 09b53c1d4ab1 + - b3eab4b67562 + - 11a0d50a54e6 + - 6b1e195506a3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 1cd2511a396e + - 00fbfac99d39 + - 79b885ce78d7 + - b8f5f6e87f5c - 13022c3d3076 - - 9ee34ba73ebf + - 1cd2511a396e - e403d27e8f24 - ec9cbd6b9a49 - - 42ce70172b72 - - 45795f582ae9 + - 9ee34ba73ebf - 178bdbdb6d24 - 5ef7ec16b04f - - 00fbfac99d39 - - b8f5f6e87f5c - - 79b885ce78d7 + - 45795f582ae9 + - 42ce70172b72 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 26f5ded07..9a7368695 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -93,22 +93,22 @@ 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 @@ -141,8 +141,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - 1d74ae228df3 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -173,8 +173,8 @@ tools: - name: matchms_split owner: recetox revisions: - - 0cf68b536cd1 - 500f473df7e4 + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -192,8 +192,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - 90745ecc5e9f - b5467dead5b1 + - 90745ecc5e9f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -248,24 +248,24 @@ tools: - name: ramclustr owner: recetox revisions: - - 9b716db0a786 - da7722f665f4 + - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - - c53a97599181 - 79ad928a0dae + - c53a97599181 + - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - f3a18e020cdd - - 18ec7635bac6 - 149b9cc7499b + - 18ec7635bac6 + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template @@ -287,33 +287,33 @@ tools: - 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: - - 17a48d0a80f4 - - dd7bbc2b99d1 - cf061712a184 + - dd7bbc2b99d1 + - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - d7f5878a98c3 - 99d118321d5f + - d7f5878a98c3 - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ffbabefbd2e2 - ea0758b41473 - d90187b0f247 + - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 13a0bccfa..77364544a 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: - - 0094893f5001 - - 0e63d03c8790 - 18676df0cb3a + - 0e63d03c8790 + - 0094893f5001 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: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -95,11 +95,11 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - 63f86089423e - - 76d3d2b10738 - 65db807336bc + - 5b5a7af9fbb4 - 7c2100246a2f + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada @@ -108,108 +108,108 @@ tools: - 1c35dadbe76f - 84fd33a60b35 - 00f5005840fa - - 96336c6a2bb7 - 18a502a9d287 + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - 34e55239e68b - - addaf9d22850 - - e8fba04706d3 - - a9f4a217dcd6 - f732237754fc + - a9f4a217dcd6 + - e8fba04706d3 + - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 0776d824d896 - 5fe3edf19b9c + - 0776d824d896 - 04c15826a0b8 - - 75403243703a - 8c202e741d68 + - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 75c8945b0da2 - e96bbb9e24ea - - 8470de786d47 - 43c99742158b + - 8470de786d47 - 1c9b3bcd4261 + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f + - 35176674168c - 1d75bd0595e2 - - 84743da21318 - 5c865a382933 - - 35176674168c + - 306a40d4bb8f + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - 555ccac8a4c5 - - 78faebd0879c - - ac72310b038a + - 8daf4564ccda - 32c9ea835770 + - ac72310b038a + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - f947b4bb5107 - - 7b8cb2b02978 - - a58e4a43f49c - d60df8727f59 + - a58e4a43f49c + - 7b8cb2b02978 - 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 - 04144473e59e + - 7f3b59dee073 + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: + - 0a1224c4b781 - a7817705348e + - 19299bb1c6af - d943081510da - 9058d8943303 - - 19299bb1c6af - - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - 5c7ba3d85a01 - - c4db8c4de66f - - dbf1798c0dcc - 4d9445dff47b - - f8f56dd6449f - - b907a3c0434f + - dbf1798c0dcc + - 5c7ba3d85a01 - a68b985913ab - 65d52c693b8e + - f8f56dd6449f + - b907a3c0434f + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -237,24 +237,24 @@ tools: owner: iuc revisions: - e66ab198ec15 - - 6aad8ca3918b - bd7a9c6efb10 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - c6676a890f50 - - d77397f09da1 - b084117133af + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - 9704f1a3b32d - - 7f208f1eb64f - cad93abecac9 + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -279,45 +279,45 @@ tools: - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 6552df6efe6b - 60749924ad62 + - 6552df6efe6b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - - 79706f10d680 - e88b731dad59 - c409a495841f + - 31c6d107e7a5 + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 094ad9c068af - 71ea608ddfa3 - 172920f67a84 - d24841f5c3d2 - 714d5a28cc5c + - 094ad9c068af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 2bdd84912a2b - - a4d7148ccee4 + - 4137b492233e - a293a742194f + - a4d7148ccee4 - d7e9a3c41657 - 12fb63b5f63f - - 4137b492233e + - 2bdd84912a2b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -329,13 +329,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - cf87759761eb - 6fcb8ac37a3e + - cf87759761eb + - 64bc7acc22a9 - e2c71b852aba - - 75bedfb2078b - - 97f7bb0851e7 - a92c06a3afa7 - - 64bc7acc22a9 + - 97f7bb0851e7 + - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -356,19 +356,19 @@ tools: revisions: - 080ea153677c - 4033827c76b8 - - 5e5a999ffaa9 - - 2d35528d2141 - c82508e76ad1 - 4e5e73d03f0d + - 5e5a999ffaa9 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - 6b7622dda516 - - 2cd76b089570 - fc6c328c292f + - 95bf7479d53c + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -394,15 +394,15 @@ tools: - name: khmer_abundance_distribution owner: iuc revisions: - - 7624945cacd3 - e699e2747356 + - 7624945cacd3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - - 570505540a7b - b3d513c7093e + - 570505540a7b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions @@ -422,8 +422,8 @@ tools: - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 00f7064c564b - 19607c740d19 + - 00f7064c564b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median @@ -449,10 +449,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 + - 328c607150ff - cdee7158adf3 - 20e2f64aa1fe - - 328c607150ff + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -478,15 +478,15 @@ tools: - name: kraken_report owner: devteam revisions: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -498,8 +498,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -530,8 +530,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -567,14 +567,14 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 0270541aaf46 - - 327d9f4cc95f - - 7f5d7b0e9884 - - 27250f92a01a - 3cc4a60615c0 + - 327d9f4cc95f + - e073891b2afc + - 0270541aaf46 - 2cff76cf35c6 - 4fd3b5d8706b - - e073891b2afc + - 27250f92a01a + - 7f5d7b0e9884 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -648,33 +648,33 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 2131d7dca455 - 6dee4abadccb - - 289b3807e80c - - ec368db926f4 - - 1a037928504c + - 740fd2d16a28 + - 1a6cdf55390f - ef65b083bd0c + - 289b3807e80c + - 2131d7dca455 + - a92a632c4d9b - b89b0765695d - - ff8f55893e7d - a16313517e55 + - 1a037928504c + - ff8f55893e7d - fd69c607b43f - - 740fd2d16a28 - - a92a632c4d9b - - 1a6cdf55390f + - ec368db926f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -692,15 +692,15 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 2f47a294ef49 - 6034c3f3ecf0 + - 2f47a294ef49 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline @@ -720,22 +720,22 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 680fb3eb574c - 73b56418e7f4 + - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions owner: iuc revisions: - - 677f3c8db525 - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -747,8 +747,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 8e2ac1b8f70a + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -809,13 +809,13 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - aeaa20b96ef2 - - be818ae858e4 - - 4d83eccf5f81 + - 3b22de20bd4b - 4b9a8031ab74 - 141afacabcfa - - 3b22de20bd4b + - be818ae858e4 + - aeaa20b96ef2 + - 4d83eccf5f81 + - 2fd4d4c9c5c2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -845,8 +845,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - 9495df9dd6ef + - 576963db5f1b - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 383f190e9..63fd21d8b 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 9e040bb7d..b556071f4 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - cd07731e4434 - - a74dbfee5a86 + - 6ae5a7b5a0a2 - 9baa871cb1d1 - - 9eeb13a92d79 - - 94b8c6013083 + - bdfbaf0c10aa - 80f03df2e2ce - - 6ae5a7b5a0a2 - 48c13389050d - - 9422c5a87ee2 - - 8b67dd48fec1 - 2263989660f5 + - 9422c5a87ee2 + - 94b8c6013083 - 098506c54016 - - bdfbaf0c10aa + - cd07731e4434 + - a74dbfee5a86 + - 8b67dd48fec1 + - 9eeb13a92d79 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: + - 3ff17bad4006 - d7ce0ec78e51 - - be78f13134e2 - - c18157c68134 - - f14193ec1f50 - d390fe1567dc + - fc2e49f91e52 + - f0af8936ed41 + - f14193ec1f50 + - c44f824c051a - 5abf2c2249aa - - 2e093badc689 - 4a60927aaca5 + - c18157c68134 - '764845535798' - - 3ff17bad4006 + - be78f13134e2 - aaa0d6a8b808 - - fc2e49f91e52 - - f0af8936ed41 - bc3831dd65c1 - - c44f824c051a + - 2e093badc689 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,8 +46,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -67,46 +67,46 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - - bf28a8cff401 - - 8e649f27aa0d + - 15974dd17515 - c5908940967d - - 6f28e90db932 - f1a5908ea2cb - - 15974dd17515 - a65296ffb4a0 + - f0d493f8f84f + - bf28a8cff401 + - 6f28e90db932 + - 8e649f27aa0d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - - b3acbb3a6af0 - e8fdceffea4c + - b3acbb3a6af0 + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - 60698466facd - 5561a1193611 + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: + - bcd65de9725b - 48823c9635a4 - 57f042937ba7 - - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae - fb43e8887350 + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer @@ -120,8 +120,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - cf3c9489c088 - 959c1f8dae95 + - cf3c9489c088 - 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 5e968de74..c6c39a987 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -29,12 +29,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - - 72b5e9dda577 - - 0e9e7fcdd543 - cb34f00cc10f - - 79e9a869f40e + - 72b5e9dda577 - a7228a7ea146 + - fc8804320156 + - 79e9a869f40e + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -42,8 +42,8 @@ tools: revisions: - fa11aa8103b2 - 18505fe2bdb1 - - d6cddc06aeae - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -56,14 +56,14 @@ tools: owner: iuc revisions: - 0f5f4a208660 - - 222669c4afb6 - - edf6d4003fad - - 2bf63b38ee9b - - ec699520444c - 19f3b583a9b3 - - cc36773a3681 - 43815fa60f3a - eb746fa6f514 + - cc36773a3681 + - edf6d4003fad + - 2bf63b38ee9b + - ec699520444c + - 222669c4afb6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -82,45 +82,45 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - a02b8b3f5a0c + - a38bdcec9e4c - 7b379e98b9a9 - 0f1c34698076 - - a38bdcec9e4c - - edbb6c5028f5 - a3c4fe6f49ab + - 645159bcee2d + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - - 85a394edc247 - 3b6f94fc7e1d + - 85a394edc247 + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - a8d4be409446 - be95355fef8d + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - 4857d5bcce52 + - d376944466bf - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - de5b3d8f5b90 - bec636361cfd + - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop @@ -134,13 +134,14 @@ tools: - name: poretools_events owner: iuc revisions: - - daf8518d243a - 1d835c691480 + - daf8518d243a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract owner: iuc revisions: + - 7e4f1ed70187 - 08064da7b7fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -155,18 +156,21 @@ tools: owner: iuc revisions: - 5c4fa65f5733 + - a57b6350fd5d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_occupancy owner: iuc revisions: - - 0433aad600e9 + - 338d15b8d6fb - 336791b5665f + - 0433aad600e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist owner: iuc revisions: + - ae9060e764b5 - 72dfdbfab3cc tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -180,8 +184,9 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 26e6c9362b7b + - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -193,6 +198,7 @@ tools: - name: poretools_tabular owner: iuc revisions: + - 2cb2feb94f0e - 5f5f1da94d7f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -205,14 +211,15 @@ tools: - name: poretools_winner owner: iuc revisions: + - 79c1ac92f31b - 6d93709247c7 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - 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/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index dac515b80..b8787223f 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -21,15 +21,15 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 58341ad4fb42 - 96d2000977ab + - 58341ad4fb42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -59,8 +59,8 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - baceff842902 - adfd6bf710bd + - baceff842902 - 3e73c97f025d - d74850cf4e42 - 97b1b5ad1cda @@ -84,17 +84,17 @@ tools: owner: iuc revisions: - e4b4837f06f5 - - 1e34d2e3d285 - - ed1518ce2237 - edacc4bcd3cb - 2f27f3b86827 + - ed1518ce2237 + - 1e34d2e3d285 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -113,16 +113,16 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - 48a42ca61006 - 38ccd4589990 + - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -135,15 +135,15 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - b1bc53e9bbc5 - 4d3eff1bc421 + - b1bc53e9bbc5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -162,10 +162,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: + - 27a6a256cd23 + - b4b2b284230a - 172815da3d41 - 5bcf0e24f42c - - b4b2b284230a - - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -178,8 +178,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 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: - - fea85c467896 - 87febc68b45b - 19bbd19b74b3 + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -225,12 +225,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - 5fe20c915fa6 - - 2c61c30a57e7 - 9c43baa60906 - 0cb27ea69dc1 + - 4ba60cb14cb0 - d8dc037e3c13 + - 2c61c30a57e7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -243,18 +243,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - - 9d09724f2bf1 - 0db22932bc39 + - 9d09724f2bf1 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 29c738066906 - - 6e24e79d3d69 - df30a2f1db55 + - 6e24e79d3d69 - ed7a967cb11b + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -293,8 +293,8 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - d63c1442407f + - c520a52b5174 - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1067,9 +1067,9 @@ tools: - name: rdock_rbdock owner: bgruening revisions: + - c362398df83b - e4b7d1507a75 - a22969b08177 - - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1081,11 +1081,11 @@ tools: - name: salsa owner: iuc revisions: - - 9a22227bb6d0 - ab5b7f6b7198 + - 9a22227bb6d0 - 58a870ef434c - - ba7b0f11e470 - f77f7a7f3b83 + - ba7b0f11e470 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 598472f7a..b744c9216 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - d033ffc1c161 - '841557158611' - - 81e66674859e - 6a457678efcb - - a6619171428e - - 3f59ebfbfe3d - - 26de3a7b1cb9 - - f04a1264e2a2 - - b89cac5156ec - - d7c7ef3353fe + - 8834daeb9892 - 3b8b5bde0bd9 - f73435dc282b + - 26de3a7b1cb9 + - a6619171428e + - 81e66674859e - cce7b18495e4 + - 3f59ebfbfe3d + - 107d3ba7024a + - b89cac5156ec - 5a7c56a5cc08 - - 8834daeb9892 + - d033ffc1c161 + - d7c7ef3353fe - c78f3d7dd1db - - 107d3ba7024a + - f04a1264e2a2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 5fcd1ece3a6e - - 6283babe736e - - 659517798cc4 - - 6a726db04d4b + - df47d4845b62 - 88c4aa435ded + - 6a726db04d4b + - 5b777002c2de + - 6283babe736e + - 6223845127ea + - e75442c7f4da - 3b96e92e8ec3 - 4755f52427c4 - - 02b8758214b0 - - 6223845127ea + - 5fcd1ece3a6e + - a185b079b095 - 7a2092844346 + - 02b8758214b0 - b0af57c1a968 - aa8cc71438cf - - a185b079b095 - - 5b777002c2de - - e75442c7f4da - - df47d4845b62 + - 659517798cc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - - b8476e82ac20 - - 111bd54f6bc4 - 24d024316465 + - b8476e82ac20 - 524d31add34a + - 0878b7fd5260 - f97743d52b87 + - 111bd54f6bc4 + - d1c340a5664b - 70acec670c30 - - 0878b7fd5260 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd - - 9e10ba792be2 - - 4f6349228462 - daddf188c13f + - 4f6349228462 + - 9e10ba792be2 + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,33 +110,33 @@ tools: - name: pangolin owner: iuc revisions: - - ca0d8cf80567 - - b7e297c2ede6 - - 5f8727ff21e7 - - abf6dbe8c9d7 - - 3a43c3982401 - - 83a69484cb87 - - 2f1019071464 - 9d61d3fa046c - - 7bb8726be37c - - 42a174224817 - 36912871ccdc - - 437e28791761 + - 03ed9524dcd1 + - ca0d8cf80567 - a2099fb98cdb - - 14ae456b8cc5 - - 81804a978fc0 + - 83a69484cb87 + - 5f8727ff21e7 - b6abccb1f25b - - 2fa9d4f1b48f + - 3a43c3982401 + - 14ae456b8cc5 + - 437e28791761 - 8ad84c5753ea - - 03ed9524dcd1 + - 2fa9d4f1b48f + - 42a174224817 - ca337cce3888 + - abf6dbe8c9d7 + - b7e297c2ede6 + - 81804a978fc0 + - 7bb8726be37c + - 2f1019071464 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - 73a469f7dc96 - a4b71be30c3c - - ea30d3089354 - - b1e68bbe4cef - ba29b5e2a4be - 29ff6a849eac + - 73a469f7dc96 + - ea30d3089354 + - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 + - f1ccc8a6eb05 + - 15ac71df11a0 + - 9b2b122d0415 - dbe2b2204555 - 809e42326fc2 - - 9b2b122d0415 - - f1ccc8a6eb05 + - 91887494eb97 - 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 0766d34d5..37266bb4f 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: + - 1aac2a13842a + - 3f254c5ced1d - f6ced08779c4 - - b502c227b5e6 - - 881d7645d1bf - - f9242e01365a - fc288950c3b7 - - 3f254c5ced1d - 7d34178f2812 - a1f0b3f4b781 - - 1aac2a13842a + - 881d7645d1bf + - f9242e01365a + - b502c227b5e6 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 51893e5e5..2edc5fd64 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: - - a58f7eb0df2c - - 7fbec959cf2b - - 2f7702fd0a4c - - 5b85006245f3 - - eb085b3dbaf8 - - 6ab1a261520a - - 3bd420ec162d - - c0e71cb2bd1b - e4a053d67e24 - d00e15139065 + - c0e71cb2bd1b + - 6ab1a261520a + - eb085b3dbaf8 + - 2f7702fd0a4c + - 3bd420ec162d + - 7fbec959cf2b + - a58f7eb0df2c - ca90d17ff51b + - 5b85006245f3 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 a72150a4a..d1d8b5a1b 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 4c177985028a - b574b84afc4d - - 0a18ac48ac53 - - 277dc652246e - f28ad96b76dc + - 277dc652246e + - 0a18ac48ac53 - b18329a8ac14 + - 4c177985028a - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - bf06d196e23d + - e988563cc6e5 + - 525f201b86c1 - e215f71d7983 - - a9a28e46d54a - b41107d8fe89 - - 525f201b86c1 - - e988563cc6e5 + - bf06d196e23d + - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - 8da3511c9467 - bb6397b94018 + - 8da3511c9467 - 56da27be956a + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - f23d67e28cc8 - b8c79e70516d - - 528fb09022be - a8157342d9a3 - - f23d67e28cc8 - 890845926d4b + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - 25b83cbd596a + - ae304a72db7b - 59e85306eae5 - 80600735685d - a95a82eb4d50 - - 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 - 798da6bdff3d - 611d80c0e29d + - 83aac7741200 + - ed9ed1e6cca2 + - e0669b1854b1 + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: + - 5a35e3a8d013 - d426a9107a6c - 74b61bf5bc4b - - 5a35e3a8d013 - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - 91f0f5922011 - cc430977c8ff - - df2187f9013b - 82f6c2f4332d - - 91f0f5922011 + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 - - c5aa9fca18c6 - - ba92b59cd529 - 10566783d718 + - ba92b59cd529 - 1693b2126f30 + - c5aa9fca18c6 - d2483487e077 + - 043f9c91f686 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 + - ff8c9e0e8a7b - bf0728e000cd - ae4dc0c041f9 - - ff8c9e0e8a7b - - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,8 +122,8 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify @@ -137,15 +137,15 @@ tools: - name: encyclopedia_searchtolib owner: galaxyp revisions: - - fb192dd6658a - 36880dfd9fa7 + - fb192dd6658a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -158,16 +158,16 @@ 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 owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -180,16 +180,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - 4d17fcdeb8ff + - 7f432d87c82c - 97a7f34fcb6a - - 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toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c - - 06f6826d380c - c1343e3389ca + - 06f6826d380c - c7745841de24 + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - da986f83631b - - d46d64e7964d - d2eac53666f0 + - da986f83631b - b9d453dca8d3 + - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 9bf325045235 - 1199751329b0 - 8bd7734309f6 + - 9bf325045235 - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert owner: galaxyp revisions: - - 6153e8ada1ee - ab6c14374bc0 + - 6153e8ada1ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats @@ -271,24 +271,24 @@ tools: revisions: - 28434abe6c5c - 8212e342e482 - - 593839e1f2c3 - de7593c29499 + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - f4be248c3d47 - - 8960fb791701 - 01dbaf6a57e0 - 4e77b8f12cd3 + - f4be248c3d47 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -302,11 +302,11 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: + - 6ccbf9a2072c - c9eff69a7c62 - - 9cdf15d3cfc8 - - 518b1730cf2a - f7fef900f5b2 - - 6ccbf9a2072c + - 518b1730cf2a + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex @@ -321,35 +321,35 @@ tools: - name: openms_fidoadapter owner: galaxyp revisions: - - 890025d6e426 - 41859bbdc16e - 1595601708ec - 658494a2cb00 + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - 2a93a25f0599 - - 5ad0b5bf1deb - 9b7977080f6d - 6634cad7d797 + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - fe4e4587d265 - d6878d27f051 - - 05d5e1ddc985 - 0bb5056cb775 + - fe4e4587d265 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - 52ba9695e752 + - 5ad830edc021 - febd569ad26f - 4af67edd5aef tool_panel_section_label: Proteomics @@ -357,28 +357,28 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - 39e8fde08881 - b2fc8da99bcc - - 92352a475eed + - 39e8fde08881 - 27cba4c5fc42 + - 92352a475eed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - 9e26f5c770f8 - - d413dc49d650 - 0efbc235f314 + - d413dc49d650 - d3546bb9fd8e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 3720e349ba2a + - ca1740533b59 - c28f13cab67a + - 3720e349ba2a - 8a04ed1c1d1b - - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter @@ -386,8 +386,8 @@ tools: revisions: - c427a8628cbe - ca799a7246e7 - - c55dddc5844a - 382cde407f81 + - c55dddc5844a - a5d785af0ad8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -395,94 +395,94 @@ tools: owner: galaxyp revisions: - 8ddb7bab1138 - - b5d0905419da - - adca857b4884 - 39caaa778d2e + - adca857b4884 + - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - f817513840a9 - 1c5f31b8d632 - 8d4db262964c - 34e7afee141d - - f817513840a9 - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - 986e03d3201e - 111c3a00136d - 5d9f175dff81 - c69f69d7867a - - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - 476b5e296979 - be74a8cd7d66 + - 0e52c85f3b15 - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - a407b6790342 - 2b2a7551a857 - c18d8efa4474 - f5ec766d80cf + - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - 4e66c4e73909 - - d0304fb829c0 - 021fdb80f204 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - bf32e0bcf554 - 2735db4dd8d9 - ee860980edc6 - - bf32e0bcf554 - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: + - 0ced5bc9f4dd - a2a6e9551046 - 08488066d588 - - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - 2a9ff56cb279 - - de7a553552a6 - 8c01da82292c + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - 1bf940c18d93 - - c1809c05ae8c - e8f64a7dc470 + - c1809c05ae8c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator @@ -497,24 +497,24 @@ tools: owner: galaxyp revisions: - 0bddef8d144e - - d4396637b9f5 - c99d5004b74f + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 89254095cbf6 - 8b814eafce2c - 4bb198c0bd3e - - 89254095cbf6 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 @@ -536,36 +536,36 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 3d8d4ada5405 - 5ae104d0da6e - decc397c3b7e - 6b01678ec2fc + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - e039cc5c7aed + - 539a3a4dcc9e - d6aca689dd48 - 5182338d5e7c - dd173849c3d8 - - e039cc5c7aed - - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: + - d426affe977c - 16026cdb1330 - 8a45fd5a608a - - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - - dd71e020e2aa - 9c70a651a53e + - dd71e020e2aa + - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter @@ -579,25 +579,25 @@ tools: - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - - ad2ba3a95a02 - f036e8cf1a55 + - ad2ba3a95a02 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 5c2a97a234d6 + - fb52e95a370c - c8b225c69a7f - 7f6a1f27553e - - fb52e95a370c + - 5c2a97a234d6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -609,21 +609,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - cb0378d2d487 - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - da885ca16cb2 - 943a34df6047 + - 7fdd9119cc4f - 3ec27b4cee7c - - a72c48001f7c - 1beff3ddce58 - - 7fdd9119cc4f - - 3634c90301af + - da885ca16cb2 - 07ff622ec007 + - a72c48001f7c + - 3634c90301af tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - 12692567c7f9 - - 265c35540faa - 1a5690a5eedc + - 265c35540faa + - a371252a2cf6 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 002b57ee7..26e92c80c 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: - - 289b7d6b69a4 - - e345aadf914f + - 42201b90e3f4 - 110a346daf36 - 2f1d464ebfd2 + - 289b7d6b69a4 + - e345aadf914f - 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 - 0cd2df8af811 - 42d9087b4789 + - c207119ba5f6 + - fcce77c09289 + - 0345dbaaa79b + - 8501601a118d 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: - - 405a212b32ab + - 421c33b8bf17 - ad5ab22ffe24 - 04db7fd6b238 - - 89eb29319bf4 + - 405a212b32ab - 33486216eec0 - - 421c33b8bf17 + - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -54,11 +54,11 @@ tools: owner: iuc revisions: - 1d839ead7ad3 - - 7b72fde3d27e - - fa51dc5e8386 - - 7370bb65bad4 - eb784fa07f80 - f6e91108b7b1 + - 7370bb65bad4 + - fa51dc5e8386 + - 7b72fde3d27e 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: - - 1544278c272e + - 8a55d29c8fcf - 3d70c2996730 - d30e36c48c93 - a3e86cd9cac7 + - 1544278c272e - 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: - - b242deb58952 - 564c33e5c3e3 - a5969aa9347e + - e2db212d64ad - 7b881f5f5ad5 + - b242deb58952 - 887cf585cafc - - e2db212d64ad tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,9 +105,9 @@ tools: owner: iuc revisions: - b4bab607eb05 - - bd5ff77e2036 - 8cff84759bf6 - 9a171f9a450b + - bd5ff77e2036 - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,11 +120,11 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 - 4f65e343ecdf - - 6dafad990086 - 33f0793edf93 + - 887e0991eb24 - adc7a7610d4f + - 6dafad990086 - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - c5d7050e4ad7 - - c287418eb288 - - 4e280b27a831 - - 17d39bf0a63a - 97575d01f06b + - 4e280b27a831 - 43e3eeb2e0ec + - 17d39bf0a63a + - c5d7050e4ad7 + - c287418eb288 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: - - d9bf483266a1 - - a819ec3b362d + - 0b8c84a7fdb5 - 9586f08634c0 - cd034465d4a4 + - d9bf483266a1 - 09b8edb56d80 - - 0b8c84a7fdb5 + - a819ec3b362d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - a9c34a289493 - - 95351dd0fd3f - 69842dd5aa48 - bf0e43ab0416 - - 2645575d1bf2 - a4b4bd84f69e + - a9c34a289493 + - 95351dd0fd3f + - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - - 8a35a3bc6752 - - bb0475c884ff - - d1fda11e602f - cfb504394ae1 - 912f904a6e1e + - bb0475c884ff + - d1fda11e602f + - 8a35a3bc6752 + - d033e1ccb386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -236,8 +236,8 @@ tools: owner: iuc revisions: - 95286af4139b - - d504d945a655 - d1fad35bdb4a + - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 718d91020..8e79a3790 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,26 +2,26 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 31f8063eedea - - 7acb00fc980a - 2d4e3aff9dc7 + - 31f8063eedea - cf01dd6c6b1f + - 7acb00fc980a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - - 32e542c2a773 - 7a5a2d28c539 + - 32e542c2a773 + - 703a2cb3fb38 - 125d20cb23d7 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: blockclust @@ -84,9 +84,9 @@ tools: - name: cufflinks owner: devteam revisions: - - d080005cffe1 - - e04dbae2abe0 - 6926716bbfb5 + - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -98,10 +98,10 @@ tools: - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 + - 22cf48ad7b16 - cf747d1bd79a + - 86285ddd4512 - 6a6717a5f421 - - 22cf48ad7b16 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -114,8 +114,8 @@ tools: owner: devteam revisions: - 6cbfede05833 - - 9a854107dbb2 - 28b94cfbfdb9 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -127,8 +127,8 @@ tools: - name: cuffquant owner: devteam revisions: - - 679d93c99757 - 93148c05136f + - 679d93c99757 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -152,9 +152,9 @@ tools: - name: describe_samples owner: iuc revisions: + - 0693ccd171c4 - 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: - - 6a3a025714d3 - - 8fe98f7094de - - cd9874cb9019 - - 9a882d108833 + - d027d1f4984e - 0696db066a5b + - cd9874cb9019 + - 8fe98f7094de - 24a09ca67621 - - d027d1f4984e + - 9a882d108833 + - 6a3a025714d3 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: + - 2872c633f07e - 62adf13b86ea - - b47c006d90c5 - - 9a7c5b6d8f1e - df929f257179 - - 2872c633f07e + - 9a7c5b6d8f1e + - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -202,17 +202,17 @@ tools: owner: iuc revisions: - f2843df56434 - - 555659de7321 - - 5bf899c13979 - - ae2aad0a6d50 - df0c8d0a5992 - 6e53e565fc6a - - 9bdff28ae1b1 - - 3d89af8a44f0 + - 555659de7321 + - a8305cf0c951 - 334ce9b1bac5 - - 070900306913 + - 3d89af8a44f0 - 0cb907a2a810 - - a8305cf0c951 + - 070900306913 + - 5bf899c13979 + - 9bdff28ae1b1 + - ae2aad0a6d50 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: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 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: - - af814359d244 - 7db9d3ea71c9 - - a56fbe2d6ba7 - - 38b6d12edc68 - a37612abf7f9 + - f3a5f075498f - 90d16db017d7 - - ea04b737afa0 - 6f66ae7c5f7a + - af814359d244 + - a56fbe2d6ba7 - e6a2a912677a - - f3a5f075498f + - 38b6d12edc68 - f9d49f5cb597 + - ea04b737afa0 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: - - 3c97c841a443 - 0f710191a66d - 3c5e024a18cf + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -303,13 +303,13 @@ tools: - name: hisat2 owner: iuc revisions: - - d4b55e2beb12 - 6ab42baa56e9 - - f4af63aaf57a - - 26371a1df031 - - 6c19daec423d - 3fb01a8c902d - a86e80d3c09c + - f4af63aaf57a + - 6c19daec423d + - 26371a1df031 + - d4b55e2beb12 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -327,9 +327,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 4418229c501e - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a + - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -348,10 +348,10 @@ tools: owner: iuc revisions: - 01247aaf0a10 + - 5ae5c312d718 + - ce5d418183c5 - 1c75aa5de15e - 87c11c05d238 - - ce5d418183c5 - - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -364,9 +364,9 @@ tools: owner: iuc revisions: - c971db6f0fe5 - - 10c98fab6c5a - - 40985510cd98 - 4f9c4e6566e5 + - 40985510cd98 + - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -378,13 +378,13 @@ tools: - name: limma_voom owner: iuc revisions: + - 58c35179ebf0 - 0921444c832d - - d6f5fa4ee473 - - 97e06a4c7c75 + - e827f9aae031 - 708348a17fa1 - - 58c35179ebf0 - 119b069fc845 - - e827f9aae031 + - 97e06a4c7c75 + - d6f5fa4ee473 - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -403,8 +403,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -434,8 +434,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 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 - - 99b17b74a8cd - - 980d2a2e1180 + - 4df95e2d7f61 + - 4074fc1940e2 + - 7ed2edc1337f - c772497b2c32 + - 79de45b5069b - e132e7d02a3e - - b9e04854e2bb + - 0a563fd2f22e - 4014de1b6daf - - 79de45b5069b - - c7c55b694974 - - 7ed2edc1337f - - 4074fc1940e2 - - 4df95e2d7f61 - 3ea5a2a63fa2 + - 99b17b74a8cd - b0f2be869d6d + - b9e04854e2bb + - 5ec75f5dae3c + - c7c55b694974 + - 980d2a2e1180 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -491,13 +491,13 @@ tools: - name: salmon owner: bgruening revisions: - - 53e9709776a0 - - 15cd64d7c58b - - f4d5237a84f6 - - ebab418107f5 - e3d32471da11 + - ebab418107f5 - 2c0ca397d302 - 49121db48873 + - 53e9709776a0 + - 15cd64d7c58b + - f4d5237a84f6 - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -510,22 +510,22 @@ tools: - name: seurat owner: iuc revisions: - - 8c28affc7c48 - c0fd285eb553 - 56242ff81c84 + - 8c28affc7c48 - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 914cfcba0ec8 - - cef79931dda5 - - 258d696dbd7e + - dd4df992d93d - ae618321f34a - - 1ebd14235b92 - cbf488da3b2c - - dd4df992d93d + - 258d696dbd7e + - 1ebd14235b92 + - 914cfcba0ec8 + - cef79931dda5 - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -562,10 +562,10 @@ tools: - name: transdecoder owner: iuc revisions: + - c6334cb383ff - 0db979fead3a - d0d4cef4f967 - ffd1300599a1 - - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -577,10 +577,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - ba3720d7e68b - - d6a479fd4281 - 74217fbfba4d - bcc5f03f1900 + - d6a479fd4281 + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -592,10 +592,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 56162e446004 + - 478f36effca1 - c2b82a94493e - 2fb4ee002432 - - 478f36effca1 + - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -608,8 +608,8 @@ tools: owner: iuc revisions: - 3f4094b6a565 - - fab23c3b5258 - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -622,9 +622,9 @@ tools: owner: iuc revisions: - 4687ecf0eb2d - - be3f26533209 - - 34a018cbee9c - 870ac06dff8e + - 34a018cbee9c + - be3f26533209 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: - - c5fbddcac63a - - 33406f5a445c - - 5192f657f305 - 65e7dea767ea - 05ab8d5e04a2 + - 5192f657f305 + - 33406f5a445c + - c5fbddcac63a 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: + - e406ac71165d + - a35cba31d904 - 6f0fb35b799c - 1fdb25a8384d - - a35cba31d904 - - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -667,9 +667,9 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - c2c039e421af - - 964b7efe2639 - 37a1129c89d2 + - 964b7efe2639 + - c2c039e421af - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -682,9 +682,9 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - - eafea3083352 - 047c22569787 + - eafea3083352 + - 24e94d84adc9 - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -698,8 +698,8 @@ tools: owner: iuc revisions: - 1812dbc5bb7b - - 04bb8bb7c198 - 3a4ac03d1266 + - 04bb8bb7c198 - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -724,15 +724,15 @@ tools: - name: trinity owner: iuc revisions: - - 32b86cd8eb50 - - 48636f857c4b - 9fa24d5aac68 - - 8f1c3df4dd49 - - d84caa5a98ad - - cee61b3fcf78 + - d2bc35f3d1c5 + - 48636f857c4b - db1f362cca3e - c9cfec002f71 - - d2bc35f3d1c5 + - cee61b3fcf78 + - 32b86cd8eb50 + - d84caa5a98ad + - 8f1c3df4dd49 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: - - 2b093007fab9 + - 9e61bc67866f - 6fd16fad465d + - 2b093007fab9 - 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 f1dfdef45..69cd3678d 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 + - 27e16a30667a - 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 cc913921a..35117e568 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 3c661e57a88f - 10184eaa85fc - 88eedb4abea0 + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - 993b19f20c76 - - 108db6635177 - 1dfd95ee241e + - 108db6635177 + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -37,8 +37,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 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 - - 5f8e69cc4c6e + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -97,8 +97,8 @@ tools: - name: qualimap_multi_bamqc owner: iuc revisions: - - 17b35d23731f - e38af83df163 + - 17b35d23731f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -123,8 +123,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff 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 @@ -163,9 +163,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - - 6856f8a01905 - 12749212f61b + - 6856f8a01905 + - 9149ad20699a - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -179,9 +179,9 @@ tools: owner: devteam revisions: - 33208952b99d + - 06dc50b7b711 - 26b4f9f98aca - 92ec40abcdcf - - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -207,9 +207,9 @@ tools: revisions: - 720217c23995 - 66e23b11feae - - b906586a6596 - b3d99709fe1a - a8d69aee190e + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -228,11 +228,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c - - 22970df7a40e - db17d5321bad - fe34990e5ce7 + - 22970df7a40e - cc61ade70eb8 + - fefd89ab563c 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: - - 7def34e6cf4d - - 811fc2d75ad4 - - 7a6034296ae9 - 88b8c2916784 - fa5d3e61e429 + - 7def34e6cf4d + - 7a6034296ae9 + - 811fc2d75ad4 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: - - a389f74c3630 - 40fa6c240105 + - a389f74c3630 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 + - 36677f429310 + - cae2794d2deb - 740ce0a18f0d - 65a38e8c8e2a - - cae2794d2deb - - 36677f429310 + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - 9da0311ab1dd + - 329deb17a9f7 - fa7ad9b89f4a + - 583abf29fc8e - b61f5d6a7f25 - - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -307,9 +307,9 @@ tools: owner: devteam revisions: - 30388d878f81 - - bb8cfc6f6e0c - db000c6007a0 - 85e38b31e8b3 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -328,8 +328,8 @@ tools: owner: devteam revisions: - a4a10c7924d1 - - b8beef827165 - 344fc91e1bfd + - b8beef827165 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - - cab3f8d35989 - d54a4df48867 + - 6c2c1836728b - e613c1ad4c4c + - cab3f8d35989 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: - - b7f7826ef1cd - - 818030fa6bbf + - bd850490c7f1 + - 135c85f4cfaf - bcedabb53ddf + - 818030fa6bbf + - b7f7826ef1cd - 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 + - 5a08c09b9311 - 145f6d74ff5e - - 541082d03bef - 3a0efe14891f + - 541082d03bef + - 1cc79f49b8d5 - 24c5d43cb545 - - 5a08c09b9311 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: - - 2dce91e11ca7 - 32dc5f781059 - - 5826298f6a73 - - bf328cec6a42 + - c370440f901e - 0dbf49c414ae - - b72793637686 - - 350bbc5c2ffd + - 2dce91e11ca7 + - bf328cec6a42 - b01db2684fa5 + - b72793637686 - 6be888be75f9 - - c370440f901e + - 5826298f6a73 + - 350bbc5c2ffd 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 a1fe6435e..07632ead7 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: + - 5cb6146337d8 + - a62c4a11a67d + - 480d9e9d156b + - 6f6537780379 + - 59bb6d34fca6 - 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 dc29364e3..2847a5db0 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -9,31 +9,31 @@ tools: owner: bgruening revisions: - e4c01dcece8b - - e32b215b7c04 - - c9944a2600f1 - ecb9ea6269ee - f2000bc73102 + - e32b215b7c04 + - c9944a2600f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - cfaf5a405371 + - c0b037b12765 - 707023fa62fe + - cfaf5a405371 - e1c3c2f2a834 - - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 00712416fdaa - - fb9e030ffae4 - cfc3f5a57dc6 - - 93dd15e13e6a - 55e35e9203cf - - d330b3082107 + - 00712416fdaa - 32e547223c9e + - 93dd15e13e6a + - fb9e030ffae4 + - d330b3082107 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,12 +45,12 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 6f0d0c784f09 - - b9fac48532eb - - 688357ad5e61 + - ee98d611afc6 - 39e945f0b2c1 + - 688357ad5e61 - 038e32885fec - - ee98d611afc6 + - b9fac48532eb + - 6f0d0c784f09 - 0bf7fddf90c7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - b85871dd69f9 - 43cb7b5a6fe7 - ed4996a16f7f - d4af736e7b83 - - 3d748954434b - - 9bd945a03d7b + - b85871dd69f9 - 7e8c677a7b71 + - 9bd945a03d7b + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -89,37 +89,37 @@ tools: - name: baredsc_1d owner: iuc revisions: - - 769d815e4b0d - 02b1fe7aed76 - - 4fff5a293013 - 0e70b2dfe4be + - 4fff5a293013 + - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf + - aa4a6f0916b4 - 344c2af50552 - a90f8efe08b4 - - aa4a6f0916b4 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - b13d3e4c48e1 + - c32347702e12 - 5b7c81b35b89 - 050cf43887d3 - - c32347702e12 - - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: + - 239193b96d72 - 1d77986f9ddc - 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 - a9caad671439 - cdf4443d5625 - - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -195,8 +195,8 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - fb7068d30ec9 - 01c37e54e86e + - fb7068d30ec9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest @@ -237,22 +237,22 @@ tools: - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - f963c251ac77 - 9d02f1819e81 + - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -265,22 +265,22 @@ tools: - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - 8a11d70b6cd8 - c72fa6cb8817 + - 8a11d70b6cd8 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: - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat @@ -307,8 +307,8 @@ tools: - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - 0410b6aada45 - ffc33339cd3e + - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad @@ -321,15 +321,15 @@ 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 owner: bgruening revisions: - - 409396ea5cf0 - 7f7c6ead2d0d + - 409396ea5cf0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo @@ -342,29 +342,29 @@ tools: - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - c261b6b05ee3 + - 55b013e59018 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b376ef118807 - b6b8c8672756 + - b376ef118807 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -405,8 +405,8 @@ tools: - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - 36dfa2825a59 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -431,19 +431,19 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 1d201e8378b3 - 11a3385e03b5 + - 1d201e8378b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - 59be31ac9dc3 + - e98619de2776 - 4b0adaa31c95 - - 7784821452ac - eeab712b0b99 + - 7784821452ac + - 59be31ac9dc3 - 0f1aaff9b22d - - e98619de2776 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -456,8 +456,8 @@ tools: owner: bgruening revisions: - 2cfd0db49bbc - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 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: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 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: - - 0bff0ee0683a - - 7e014059a88d - - c4f39bf4a068 - a4b734cd253b + - c4f39bf4a068 - f911a64454fb + - 7e014059a88d + - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -505,10 +505,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - 7608d5faee41 - - 43c146e25a43 - d45f092caf24 - b83fbc90161e + - 43c146e25a43 + - 7608d5faee41 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -520,9 +520,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - - f3eb2291da05 - 2b0d3e2f402a + - f3eb2291da05 + - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -534,9 +534,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - a6821f856a1e - df8e4e54d367 + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -550,9 +550,9 @@ tools: revisions: - c92d0f9338c5 - 44b935f2271b - - 72979cac22b2 - - e93b008c637a - 2af7c5086a96 + - e93b008c637a + - 72979cac22b2 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: - - aaa5da8e73a9 - - 77b91b9bdf52 + - edec35114f72 - f9353ee6a0d4 - - 4d8f983cd751 - - 38db3fef7aad + - b2df381a6004 - 6f83f8fd381f + - 77b91b9bdf52 + - 4d8f983cd751 - cb43c5d3acd3 + - aaa5da8e73a9 + - 38db3fef7aad - 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 + - a03ff8633507 - fc0321c000a3 + - a97abb8cd15b + - 72a6bebab2a5 - 277313130da5 - - b409c2486353 + - 8cb783c81905 - d636ce5cde16 - 3c86f71498bc - - 8cb783c81905 - - a03ff8633507 + - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -617,17 +617,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: + - 18262103fa61 + - cc0deb593fc8 + - 5c3ebe2adc77 + - 6bd82ed14acd + - 3081ff5c84a3 - 5e9171dc8244 + - c5d3684f7c4c - f54f0f0598ad - 6c145a6868cc - 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: - - ab55fe8030b6 - - a407e7f8bdc1 - - 7b9fafe32c86 - - 146ae5d70b47 - c9cb76cf8d6c - - d844935c906c - - 94c19fb1281c - - 3bcd5445cd7a - 9f354c7c8c92 + - a407e7f8bdc1 - 56c0d4acef02 + - ab55fe8030b6 + - 3bcd5445cd7a + - d844935c906c + - 94c19fb1281c + - 7b9fafe32c86 + - 146ae5d70b47 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: - - 0185bd174ea0 + - 95777145cb92 - dbbe1ea8ecb1 - - f7446fd8d5e7 - - 1072ce66b426 + - 7647e5cd1b8b + - 40812a65a78b + - 0185bd174ea0 - 6f5349dd5c49 - - 9b0cdb8cf6be - aa0c474463c2 - - 7647e5cd1b8b - 6adf98e782f3 - - 40812a65a78b - - 95777145cb92 + - 9b0cdb8cf6be + - f7446fd8d5e7 + - 1072ce66b426 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: - - a39040ae0a38 - - 9fb627495ec2 - - d18e7a6e5cd4 - - bf2017df9837 - - fe8f16c594ec - 458e8f43a775 + - bf2017df9837 + - f2f6c703da06 - c65fce500915 - - 73ab2ac53d06 - 215733a383f2 - - f2f6c703da06 + - a39040ae0a38 + - 73ab2ac53d06 + - fe8f16c594ec + - d18e7a6e5cd4 + - 9fb627495ec2 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: - - b834074a9aff - - fd808de478b1 - 8f333f90d8d6 + - fd808de478b1 + - b834074a9aff tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -717,9 +717,9 @@ tools: - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - 652923ce664f - b7ea9f09c02f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -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 @@ -758,8 +758,8 @@ tools: owner: iuc revisions: - 46fc6751d746 - - 9e5c0bb18d08 - c99ba278dfa9 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1035,8 +1035,8 @@ 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/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index de251468d..399ef9a10 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,25 +32,25 @@ tools: - name: datamash_ops owner: iuc revisions: - - 746e8e4bf929 + - 419027d822d6 - 562f3c677828 - - 2f3c6f2dcf39 - 4c07ddedc198 - - 419027d822d6 + - 2f3c6f2dcf39 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -71,8 +71,8 @@ tools: owner: devteam revisions: - 6c29c7e347e8 - - cb1c59d69557 - 7a15159140d1 + - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,12 +120,12 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 9c3e1d3235c8 - - 840f29aad145 + - aef56d0e7a61 - 7442b94d6a1e - - 4c4ec859c31a - b1eda492f063 - - aef56d0e7a61 + - 840f29aad145 + - 9c3e1d3235c8 + - 4c4ec859c31a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes @@ -133,30 +133,30 @@ tools: revisions: - d0352e8b4c10 - 07843f917990 - - 9fda0b82f419 - 375bbd555f4a + - 9fda0b82f419 - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 8b1b2b91f8d0 - 7ae443e6217d - - cd02bf168d23 - 2c58b83c9bad - 4cc980df6265 + - 8b1b2b91f8d0 + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - 4bbaf77573ef - - e10e776f2109 - - 1dd433d2c92c - 7dd3fb35904f - bb9fc9d46ea4 + - 1dd433d2c92c - ad7e0b4291ee + - e10e776f2109 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 d55ec68b2..142ced6c8 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: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: - - 9cd341095afd - 464b9305180e - 626658afe4cb - - 6595517c2dd8 - - 02026300aa45 - - aff5135563c6 + - 13b6f0007d9e - 6e8d94597139 + - 9cd341095afd - be25c075ed54 - - 13b6f0007d9e + - 02026300aa45 + - 6595517c2dd8 + - aff5135563c6 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -79,9 +79,9 @@ tools: - name: filter_tabular owner: iuc revisions: + - 557ec8d7087d - 37cde8134c6a - 9cc411a62277 - - 557ec8d7087d - 34d29339abab - 90f657745fea tool_panel_section_label: Text Manipulation @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: - - f2aac0c5c60d - - dd40b1e9eebe - ae7843d06f8f + - dd40b1e9eebe + - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: + - 1ea4e668bf73 - 623f3eb7aa48 - - cf4397560712 + - 2e8f945f7285 + - 33d61c89fb8d - cf34c344508d + - cf4397560712 - 83069b38aa85 - 3a6b78c39dca - - 2e8f945f7285 - - 1ea4e668bf73 - - 33d61c89fb8d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 - - ae8c4b2488e7 - 503bcd6ebe4b + - ae8c4b2488e7 + - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - c4d18aa4ec4a - bce29ec10b78 - - f768f6183386 - b722161a845a - - c4d18aa4ec4a + - f768f6183386 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: - - fbf99087e067 - - d698c222f354 + - a6f147a050a2 - 74a8bef53a00 - - 9ff72e942410 - - ddf54b12c295 + - d698c222f354 + - fbf99087e067 - 86755160afbf - - 12615d397df7 + - ddf54b12c295 - 0a8c6b61f0f4 - - a6f147a050a2 + - 9ff72e942410 + - 12615d397df7 - f46f0e4f75c4 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 4e0018af0..33b4a96ba 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -35,57 +35,57 @@ tools: owner: devteam revisions: - 156b60c1530f - - 04fa42777df9 - 57def2d7c093 - - a5937157062f - ef2c525bd8cd + - a5937157062f + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 791f73caa0c8 + - e61c9ac190ad - 435b157bed6d + - 791f73caa0c8 - 09d6e4693887 - - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 4805fe3d8fda - - 074d44697036 + - 3b4b2121842f - 65432c3abf6c - dfadc322b065 - - b11e8e9c23bf - - 03627f24605f - e1461b5c52a0 - - 3b4b2121842f + - 074d44697036 + - 4805fe3d8fda + - 03627f24605f + - b11e8e9c23bf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 701d134358ad - 9cb929f21cfa - 7dfca164d2e3 + - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 971e07ca4456 - - f4473557ffc7 - c27549b9aa1f - 426d707dfc47 + - 971e07ca4456 + - f4473557ffc7 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: + - dbd9f2db9ed8 - aa35ee7f3ab2 - cdaab621d454 - - dbd9f2db9ed8 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 + - fa016f1eea1a - 5bbf9eada9c2 + - d220115f882b - c9a8ef2aa380 - - fa016f1eea1a + - 9bccc8404a3c 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 - ee4a90760848 + - 40f0591deda0 - 32f14a2723ec + - 3b1e7c170b10 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 42818629ec4c - 9793bc5d741b + - 02d81b994ef5 - 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 0a4dcec2b..e59b5dce7 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 + - ebe5fc018e72 - 265fe0f9ea64 - - 6a88248893c4 - 8a2e296c07ef - - ebe5fc018e72 - - 2c372041ed8c - - e075b1be5abb + - 6a88248893c4 - 95815a0bb307 - - b7ea370b8f5d + - e075b1be5abb 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: - - 21687e35f066 + - b03984136ce4 + - 0fba2c15b40d - 544cb432072b - - 1001172b5089 + - 21687e35f066 - 22637b1a55bf - - b03984136ce4 - c37b684e7f4e - - 0fba2c15b40d + - 1001172b5089 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: - - 8408bffd5616 - - 8627b2b383b4 - - bf1f4994f104 - 143796b504eb - - ccb83bf54de0 + - 8627b2b383b4 - 0238f68ad641 - - 01d6b7d6365e - 8ca3647c90fd + - ccb83bf54de0 + - bf1f4994f104 - 3a7084316a6e + - 8408bffd5616 + - 01d6b7d6365e 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: - - abd489215f73 - - f430a1ec7ee4 + - 03e0645395d2 - 6b6c992d3a14 - - d144af39073a + - abd489215f73 - 81426b3cf18b - - 62ca6da715bf - - 03e0645395d2 - 9b5abbf50d23 + - d144af39073a + - 62ca6da715bf + - f430a1ec7ee4 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 + - d37e313a41be - e522022137f6 - - 95c6f3f4c77f - 1171446da5db - - d37e313a41be - - 2363ef414c9b - 8aa352093d73 - d3081540d175 + - 2363ef414c9b + - 95c6f3f4c77f + - 1829900b5dcd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -101,10 +101,10 @@ tools: - 9b29129fb491 - 09f37afb3621 - 348cd212dbad - - 1137ce8efc1e - b14ff40958cb - - 012656fd329f + - 1137ce8efc1e - 92c0aff8b53e + - 012656fd329f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -117,12 +117,12 @@ tools: owner: iuc revisions: - de68c11034f6 + - cfd81f17580b - 367ba501b6eb + - 55c0e906c14c - ecc9192912b8 - - 7291189e98b4 - 1f2183a23823 - - cfd81f17580b - - 55c0e906c14c + - 7291189e98b4 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: - - 039ea3f1dea9 - - e6f4badbe6f3 - - 64a8f7dae3ad + - 6c790a091c7c - ae68ceb4cca3 - d237eaef451f + - e6f4badbe6f3 + - 64a8f7dae3ad + - 039ea3f1dea9 - 7cbf3c66d4ad - - 6c790a091c7c 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: - - cdb7b4927742 - - 5d6653c989cb - - 46fcafba49ec - - 6ea7170a016d - - 277719af4dd7 - - 33bd9301568c - 963a3635b2e1 - e7452697afd9 + - 277719af4dd7 + - 6ea7170a016d + - 46fcafba49ec + - 33bd9301568c + - cdb7b4927742 + - 5d6653c989cb 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: - - 26d97cdd5410 - - 5a321fab1fe4 - 91c1e57d5c7f + - 26d97cdd5410 + - 501bfb078342 - b7f0f59baa7e + - 5a321fab1fe4 + - a29a2f40b665 - a1213a0b7b66 - 7b4454382d39 - - a29a2f40b665 - - 501bfb078342 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: - - 709dd8291b83 + - 81e4014fa809 - 768d04526638 - - 97d19c008d15 - - 5f27e814a119 - 39bca000353d - - 81e4014fa809 + - 5f27e814a119 + - 15da1ddcfeff - c803c34361e0 + - 709dd8291b83 + - 97d19c008d15 - 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 + - 5b006286a458 + - 7ba36babba2d + - 2215287d5cc9 - b1eba148b35b - b931e65638b8 - - 7ba36babba2d - 85ee7e6c4204 - - 86296490704e - - 2215287d5cc9 - b84fda8ebef0 - - 5b006286a458 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -230,15 +230,15 @@ tools: owner: iuc revisions: - 5660b21a0dbd - - 4e1d23e5c691 - - 31ea13dfe5e6 - f506df85c652 - - 9c711df3258d + - 37757ffb4c5f - cf06b44624c7 - - 56556e1267de + - 9c711df3258d + - 31ea13dfe5e6 - ce9396ddcb2b + - 4e1d23e5c691 + - 56556e1267de - 0a5dcc9a8ec2 - - 37757ffb4c5f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 6deb4d549bc9 - - a404f786a94c - 1ca7418e46ee - - 19905c025d2a - 021693fdadaa - - 48291658fdf6 + - a404f786a94c - 271965b55437 + - 48291658fdf6 + - 19905c025d2a + - 6deb4d549bc9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -269,13 +269,13 @@ tools: owner: iuc revisions: - 5ad5d4243987 - - 69d8b7567281 - - c450406f722b - - f7879f1e77f9 - - 97e8145d7e30 - - dadbd61dc4cf - 3f6fadf8b8ff + - f7879f1e77f9 - 71c78e0eea52 + - 69d8b7567281 + - dadbd61dc4cf + - 97e8145d7e30 + - c450406f722b 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: - - 79f7a1acc2cd - - cc7f9a4e186b - - d31a2e310a52 - - 6cf13a657cf6 - 52f9e4a660e3 - - 0fe007201caf + - 6cf13a657cf6 + - cc7f9a4e186b - 2514e684f8a3 + - 0fe007201caf - 283911fe7e1a + - 79f7a1acc2cd + - d31a2e310a52 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -307,13 +307,13 @@ tools: owner: iuc revisions: - 1411bef27a75 - - 0a62420cb9cd - - 75ddd081f608 - 230e424bde67 - - 80e6e399ccd0 - 6963a6841d22 + - 80e6e399ccd0 - 026a989b7cee - a12844ca467a + - 75ddd081f608 + - 0a62420cb9cd 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: - - e493702b19eb - 450a265f92e8 - b10d1510fa84 - - 5acfca5a76af - - 5808f77b2bb6 - 444e6a756c35 - - bca7ce81688f - ba20340426fe + - 5808f77b2bb6 + - e493702b19eb + - bca7ce81688f + - 5acfca5a76af 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: - - 68fec03a63b7 - - d52b8947b269 - 157ffcdd3fa7 - - 4d236c696844 - f2482aa4862e - - dd72ff87cfd0 - - 12152af85697 + - 68fec03a63b7 - c43399f161f4 + - 4d236c696844 + - d52b8947b269 + - 12152af85697 + - dd72ff87cfd0 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: - - cbe39e530cbf - - 6f8e223f78f3 + - 75becf493cd3 - 8f2fc0ab30fb - 0e5d11004815 - - 8dbce095986c - - 75becf493cd3 - 29ba253e2e05 + - 8dbce095986c + - 6f8e223f78f3 + - cbe39e530cbf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,14 +381,14 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 8f5962c43868 - - 9708e3086f32 - - a8630d4fbaf8 - - 88bb477f45f7 - e0a856def0b0 - - 3ff5654b4e7d - a367a15c6de5 - f544f71adb73 + - 8f5962c43868 + - 88bb477f45f7 + - 3ff5654b4e7d + - a8630d4fbaf8 + - 9708e3086f32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -403,11 +403,11 @@ tools: - 6ce175385dd9 - 4ed46189d6c6 - 5c9729d54721 - - 03e30f06f15f - - 34dc0bbc7e93 - - 8b260d252ff4 - 31c096c6b156 - 96d0145c041a + - 8b260d252ff4 + - 34dc0bbc7e93 + - 03e30f06f15f 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: + - 681bdf1e22ff + - 2c4941386820 + - 09f5e45a8212 + - a730269af659 - a1aad8b559c6 - 46eb13bc2c73 - - a730269af659 - 40daf124be88 - 11af7fce71cf - - 681bdf1e22ff - - 2c4941386820 - - 09f5e45a8212 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -439,14 +439,14 @@ tools: owner: iuc revisions: - 882b2e649602 + - 12038f59c0f4 - f272b8ba0983 - 743cd1472aeb - - 12038f59c0f4 - - 8cb121b6a1d2 - - 6cbb9c47795c - b74b8cbfc1f1 - 3897eaadfbff + - 6cbb9c47795c - 0594ea1417c8 + - 8cb121b6a1d2 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: - - a9826db86d9a - - dba06328556a - adee7e8b746f + - a9826db86d9a - cced6715f926 - - 238f78e38a8b - 18cf9de1cf73 + - 238f78e38a8b + - dba06328556a - eccb508bb678 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -477,12 +477,12 @@ tools: owner: iuc revisions: - 31a1b89eab9b - - c9935c9e8a24 - - e0ad88dec40d - - f64e7ca2efd2 - e53501abf992 - - 9f36041495a3 + - f64e7ca2efd2 + - e0ad88dec40d - 3ce32adc55b2 + - c9935c9e8a24 + - 9f36041495a3 - fdec14f69010 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - d68c43202172 - - fd3539749127 - d43eb39b989e - - b7be725976b6 - - 79489d5685dd + - d68c43202172 - 2331ddcbd5aa - - 3b7b1fe7b937 - 4db0695a6fc7 + - 79489d5685dd + - b7be725976b6 + - fd3539749127 + - 3b7b1fe7b937 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: - - 1ccf0e7fb4f6 - 6a636d58dfc2 - - 78cd8b69da4c - b0d39ef600a7 - 58091e1be01b - - 1a989b4110da - 5296d26b0373 + - 1a989b4110da + - 78cd8b69da4c + - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: - - 591cc8518033 - - b641062a2587 - - bf8325a07ce7 - baa8823f8073 + - bf8325a07ce7 + - b17394940c7a + - b641062a2587 + - '388983871932' - 4d3ce9dc1525 - e8af591435d1 - - '388983871932' - - b17394940c7a + - 591cc8518033 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - 3a233c8eb814 - - 3ca3de4e5291 - - 59fa8742285e - - c2ab91a0d506 - - d1f8f55f564d - e6b5cbbf449b + - c2ab91a0d506 - 1a2ef636f48e + - 59fa8742285e - 38d75661c235 + - d1f8f55f564d + - 3ca3de4e5291 + - 3a233c8eb814 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -612,15 +612,15 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 9fd5d91eb91b - 690b1d846263 + - 9fd5d91eb91b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -633,23 +633,24 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance owner: devteam revisions: - - 48e458c721b3 - 5822b40f3037 + - 48e458c721b3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - 4bdc111b2470 - - 6b935ab36d7b - eae7c08ebb6f + - 6b935ab36d7b + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -662,29 +663,29 @@ tools: - name: vcfflatten owner: devteam revisions: - - f285aa6bdcfb - b24e368ae7b1 + - f285aa6bdcfb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -697,8 +698,8 @@ tools: - name: vcfprimers owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -711,14 +712,15 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 958b6484a7f1 - 2ba3b87f904f + - 958b6484a7f1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - ee60203e68d9 + - f0580efedada - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -749,7 +751,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 6f6bf10618d7 - 166c4f50525f + - 6f6bf10618d7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 857f6d150..4a58bd8ed 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,70 +2,70 @@ tools: - name: abricate owner: iuc revisions: + - 6e9aea89e388 - c2ef298da409 - - 78c75f134c16 - - 3f3e247c053d - 4efdca267d51 - - 6e9aea89e388 + - 3f3e247c053d + - 78c75f134c16 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval owner: iuc revisions: - - 1dd7adc21b6d - 8dc7512c9dc9 + - 1dd7adc21b6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 44018dd6b447 - - b5d8e5475247 - - a79ee60b6926 - - 4f2967b27e67 - - 1aae04680c4b - - fe3ca740a485 - f29602ae449e - - 133f36c29579 - 3e1f6f6d557e + - 133f36c29579 + - a79ee60b6926 - cd2480f35935 + - 4f2967b27e67 + - 44018dd6b447 + - b5d8e5475247 + - fe3ca740a485 + - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: + - f1e653756174 - dc027fa56d55 - - 6519ebe25019 - 7be22100e5e1 - - f1e653756174 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus @@ -73,16 +73,16 @@ tools: revisions: - bd0e53f3a891 - 28433faa6e42 - - 09855551d713 - ca6d970d931c + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - d77802fe76f7 - - da5f1924bb2e - 92eee5f31117 + - da5f1924bb2e - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,8 +90,8 @@ tools: owner: iuc revisions: - 8fd427007e93 - - fe48aa4ccd5e - 7355bbf5e05f + - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -125,8 +125,8 @@ tools: owner: galaxyp revisions: - 63662ae295d6 - - d9c3016f7283 - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -151,60 +151,60 @@ tools: owner: iuc revisions: - 9c15ca7e764e - - b6b5cd37f2a2 + - 756376aeb1ae + - 3bbe70fef6df + - 9f2455341fac - 14f588312c56 - 582fd74dc2a1 - - 9f2455341fac - - 3bbe70fef6df - - 756376aeb1ae + - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 73428a792541 - 0ffe5be70caf - - 8e1ace8f77c6 - - 989f7c061f35 - 30fb23d4c31c + - 989f7c061f35 - a230ea445788 - 1691af4a0d17 - - 73428a792541 + - 8e1ace8f77c6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 57c6718cbfcc - - e94187d661df - - 30f08d74024f - 494f0bb4a993 - - 5a5ae61da69c + - e94187d661df - 0418d28136de - 563a19373357 + - 57c6718cbfcc + - 30f08d74024f + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - d6c7106b7b2e - - 2bba2ff070d9 - 4b96ced19f75 - - 7abc5f6dd595 - 1bc5a03faf2e - f77d7b685bb3 + - 7abc5f6dd595 - f31125bb85ea + - 2bba2ff070d9 + - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - 520e30695ec3 + - b3cf4684e9c7 - 54961e026fe4 - fed64e676186 - - 52af33194019 - - b3cf4684e9c7 - - d77fdcca400e - d3af38b9c7e1 + - d77fdcca400e + - 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: - 07d7991bf205 - - 2aea122fbd25 - 79261884facd + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -230,9 +230,9 @@ tools: - name: goseq owner: iuc revisions: + - 602de62d995b - ef2ad746b589 - 43798b4caee0 - - 602de62d995b - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -264,9 +264,9 @@ tools: - name: interproscan owner: bgruening revisions: - - 98cafcbd2578 - - c55643c3d813 - 74810db257cc + - c55643c3d813 + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -284,26 +284,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: + - 3c1a01127868 - 370c210d9541 - d46d803ca6cc - - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - e95d52d295d7 + - b815ec682418 + - 624606f7c996 - c8ac28e8ac44 - 033755194fe9 - - 624606f7c996 - - b815ec682418 - - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -351,10 +351,10 @@ tools: - name: prokka owner: crs4 revisions: - - d643e3b03500 + - a17498c603ec - bf68eb663bc3 + - d643e3b03500 - 8a22554cdde2 - - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -366,15 +366,15 @@ 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: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -398,22 +398,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5b80f544c67f - 6322be79bd8e - 8f92c2b26e6d - - 68693743661e - - 5c7b70713fb5 - - cfcf33df7fc0 - 268d162b9c49 + - 5b80f544c67f - 5a29ab10dba6 + - 5c7b70713fb5 + - cfcf33df7fc0 + - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: + - 2b3e65a4252f - 09d6806c609e - 5fab4f81391d - - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -432,24 +432,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 - - e1a9d6fd258d - - ac8250086ac3 - 809dfc93d593 - - 51dd22484644 - - 37213cf56392 - - d03af1c7002c - ba6f87115e13 + - 4839e590cb26 + - ac8250086ac3 + - 37213cf56392 + - e1a9d6fd258d + - 51dd22484644 + - 45083d070fb8 - 200c378d85f3 + - d03af1c7002c - 037a11682176 - - 4839e590cb26 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 30ee18bf0..016078d17 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,79 +2,79 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - 0124fce4654a + - 890b794c997d - d6d5ccc2c581 - - 0e93176640ac + - 841084c5fc46 - a929ce596a34 - - 890b794c997d - - fa5259cc561b + - 0e93176640ac - 553bfe8bd0b5 + - fa5259cc561b - 8f1b150a2487 - - 841084c5fc46 + - 7547fcab5d19 + - 0124fce4654a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a + - ddddce450736 - 067592b6b312 - 94fe43e75ddc - b2860df42e16 + - 21e491ad532a - b9e31c5c01c7 - - ddddce450736 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - 3371c5bdc17a - - a7f16f24e9a1 - - 5258e18bbe23 - 22286dab5aa1 - faee8629b460 + - a7f16f24e9a1 + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - 8c2167481e72 + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: + - 94170eee0ad8 + - e824f5d958d0 + - e4bd1e99bacf + - cf13a1e03e5b - 46ae58b1d792 - 2babe6d5c561 - - cf13a1e03e5b - - ea8146ee148f - - 2dd755c1c6ff - 602fb8e63aa7 - 1440ae06552f - - e824f5d958d0 - - bb935709506a - - e4bd1e99bacf - - 4048d82f0c88 - - 1e62c28ba91d - 41030a6c03b7 + - 4048d82f0c88 - 0d243f458b53 - - 94170eee0ad8 + - 1e62c28ba91d + - bb935709506a + - ea8146ee148f + - 2dd755c1c6ff - 5ecdeca79a0d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 86f150c8019d - 5732f959936a + - 86f150c8019d - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,41 +87,41 @@ tools: - name: flye owner: bgruening revisions: - - e27815e82dd4 - 291923e6f276 + - e27815e82dd4 - 3ee0ef312022 - - 1ce9b1d72ec3 - - 8d4f03b5fe9d - - 3e4f8642c77e - 1f0769f0b56b - - 276f5d8712d5 - cb8dfd28c16f + - 3e4f8642c77e + - 8d4f03b5fe9d + - 276f5d8712d5 + - 1ce9b1d72ec3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - b2f674562a18 - - 460fad600dce - 01210c4e9144 - 3169a38c2656 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - 7348b69e5109 - - ba88bc5a6446 - 8b330a577046 - 06bcf65179fb + - ba88bc5a6446 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 3ef480892a9f - 3fba9c77550a - 5127a713de83 - - 3ef480892a9f - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -134,23 +134,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 60024a528cbd - - 2061fb3b81b4 - df25d4fb79b7 - - 366a11d316a7 - - f3c89da3af16 - - da9d8bf98802 - - 41cea2aa2dce - - 3f7be05a1597 - - 045c7c3d8e59 - - 5f625c63b8bc - - 9ef6920c3089 - - 6505bd37670d - 5bec28269d95 + - 045c7c3d8e59 + - 3f7be05a1597 - 284a1cb82b61 - - 0ee0c3089254 - 71740308d412 + - da9d8bf98802 - ec9e21e9c71b + - 9ef6920c3089 + - 2061fb3b81b4 + - 366a11d316a7 + - 0ee0c3089254 + - 60024a528cbd + - 6505bd37670d + - f3c89da3af16 + - 41cea2aa2dce + - 5f625c63b8bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,43 +174,43 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - 7518ee87b53d - - de387b2b2803 - a96f3ad4e0d8 + - de387b2b2803 + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b + - 09c589057ee8 - d7edbc9c3a07 - - 39edec572bae - - 9d79beb19ac3 - eb7b00ec347d - - 09c589057ee8 + - 9d79beb19ac3 + - 39edec572bae + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - eb7a370f6588 - 99ecfdafc64f - - f369ef5f210b - e731ea24e48d + - f338e9942b27 + - f369ef5f210b - 3ca2d2a9068c - - eb7a370f6588 - 606b09cc9860 - - fd128c111ab0 - 2ecf5a570907 - - f338e9942b27 + - fd128c111ab0 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: - - 8b6d0d85252b - a7b889b90140 - - 73a3846701e1 - 8dee0218ac7d + - 73a3846701e1 + - 8b6d0d85252b - 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 @@ -258,34 +258,34 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 - d256a51a656b + - 2b16ba799da9 - 79b48f02db49 + - bbe19ef04a74 + - 8fef980d48b5 - dfb8a4497339 - - 2b16ba799da9 - 02831bf9e95f - - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - 76d4cbefff85 - e9bd16ba5ebd - a315c25dc813 - - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 3061c8b029e5 - 875d0f36d66f - - 342a1d1fed7b - - 6fcbee531de6 - 72472698a2df - - 7594365c546b + - 3061c8b029e5 - 675488238c96 + - 342a1d1fed7b - 59db8ea8c845 + - 7594365c546b + - 6fcbee531de6 - ebb0dcdb621a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -293,11 +293,11 @@ tools: owner: bgruening revisions: - cd06929b224b - - d865b62f501c - a199cd7ac344 + - 39bed8de8017 + - d865b62f501c - 78c533842eeb - aa39b19ca11e - - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -309,12 +309,12 @@ tools: - name: raven owner: iuc revisions: + - 2b2a352488fa - f8564b2d7f63 - - 5c55448d0f33 - - 33b7d8481a76 - 3edba9afc9bc - - 2b2a352488fa - f11b994b7eb2 + - 5c55448d0f33 + - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -327,13 +327,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - - 1d06c8b38e77 + - ef69617ecb42 + - 5fc94b3a4704 - e122f9101584 + - 1d06c8b38e77 - 28189050e437 - 378e55aeeb25 - - 5fc94b3a4704 - - ef69617ecb42 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -345,31 +345,31 @@ tools: - name: shovill owner: iuc revisions: + - 83ead2be47b2 + - 865119fcb694 - 196a599ec43d - d9f6a00b6db7 + - ee17a294d3a3 - 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 - 5e0825476fb7 - 24e471d13fe9 - - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - c33a476f4001 + - 7490b213baa9 - 904bf932cf78 - - 051fd2db8a27 - 604782a8a53a - - 7490b213baa9 + - c33a476f4001 + - 051fd2db8a27 - 1fc82fe7ebef - 1bb12736175c tool_panel_section_label: Assembly @@ -377,91 +377,91 @@ tools: - name: spades_coronaspades owner: iuc revisions: - - d6e617c4e338 + - ad8b536d1caa - fee85957cebe + - 808b3a0a6716 + - 9678993ca5bd - 34305b013402 - 655fa188c3cc - - 9678993ca5bd - - 808b3a0a6716 - - ad8b536d1caa + - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 7e27faaad80e - - b8002c3f7141 - - 8d4b90bf9caf - 21da31ed41a1 + - e5a3b75a271f - 6b5a5842531e - 037f9927c4ff - - e5a3b75a271f + - b8002c3f7141 + - 7e27faaad80e + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 7922870efcca - 328aa71f0f3c - f1532cb33c75 + - 5b26685e5d3b - 86f66ab58e14 - 2a10645aeadd - - 5b26685e5d3b + - 7922870efcca - 9de69775f512 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: + - 6aad515a5270 + - 8cc856b935ee - 340bc17f49cf - 1708851f8804 - 85fb02c43042 - e41dcb0e913b - - 8cc856b935ee - - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - 249f6a28c751 - d159735a6a9f - - d5fb354f745d - - b65a43f70b99 - 6357b127161e - - b3490b036c5a - - 249f6a28c751 - de1260f8a300 + - b3490b036c5a + - b65a43f70b99 + - d5fb354f745d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: + - 7897763d14ec + - b7829778729f - dd7ad84f3943 - - a90db5dbaaf3 + - 33368fec3b70 - d2d1df21dfb9 - d5887ace0dd4 + - a90db5dbaaf3 - 9006e5836729 - - 33368fec3b70 - - 7897763d14ec - - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - 189e837009c9 + - 6f4c8ad6ea01 - ed2425b9fd27 - - 505a9833ab5d - ced385aa976d - 8f631679571f - - 189e837009c9 - - 6f4c8ad6ea01 + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - f31d376ce725 - 356afed970b4 + - f31d376ce725 - 9ded6109434a - e59bee4565b3 - 19bdfd1e6fe3 @@ -473,53 +473,53 @@ tools: revisions: - 4688ae3b49b5 - ebd801e712bc - - 80a17897564d - - b23249f81bc4 - af40e971a8cc + - 80a17897564d - 6dd935e4984b + - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - cb1e3db43020 - b5e35a2ca4f3 - - 59bd28f6265d - - bb11fefb23a3 - b64696992ee9 + - cb1e3db43020 + - bb11fefb23a3 + - 59bd28f6265d - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 + - 05bd7504fdb2 - 2628f6790eda - 383bb5ad32e2 - - 6bfab4a4a988 - - 05bd7504fdb2 - cb4768eeca3b + - 6bfab4a4a988 + - 6015aa0303f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - - 3e44ef016b45 - - 8f9f06995f98 - - e92675014ac9 - 9e3e80cc4ad4 + - 8f9f06995f98 + - 3e44ef016b45 + - 6e26c9afd301 - 0a3a602cd1e3 + - e92675014ac9 - e022dff952df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - - 8d09f8be269e - 920677cd220f - 08256557922f + - 5da9a0e2fb2d + - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser @@ -539,8 +539,8 @@ tools: - name: yahs owner: iuc revisions: - - ff4031bfaa22 - - 39495e107274 - 425e63adcc5d + - 39495e107274 + - ff4031bfaa22 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 26bea9656..98176a144 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,8 +2,8 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - 4768f7f8e93f + - 1ae00120dd24 - bfd290fe1588 - 392f100eebcd tool_panel_section_label: Bacterial Typing @@ -11,17 +11,17 @@ tools: - name: mlst owner: iuc revisions: - - ded48b36f3b7 - 31812e7a1315 - - 8e8dc9a1e3e5 - 1f5641a52664 + - 8e8dc9a1e3e5 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - - 24a7a95867b0 - 5c8ff92e38a9 + - 24a7a95867b0 + - 17fcac7ddf54 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 6a6f9fe38..87ef057ab 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: - - 1c427e24fb79 - - d1f62024a08b - a9c9d768b751 - 7beb76ffbc0f - 0840ba83860c - - 159b04e36791 + - 1c427e24fb79 + - d1f62024a08b - 204a131e47db + - 159b04e36791 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 e2c0e74bb..26362969c 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 0a5c785ac6db - - 07e8b80f278c - dde39ba9c031 - - 87ee588b3d45 - - a8eabd2838f6 - - b28e0cfa7ba1 + - 589e7e57fd6d - a68aa6c1204a + - b28e0cfa7ba1 + - a8eabd2838f6 - e19bebe96cd2 - - 64e2edfe7a2c - ce3c7f062223 + - 64e2edfe7a2c + - 07e8b80f278c + - 0a5c785ac6db - a1a923cd89e8 - - 589e7e57fd6d + - 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 df3ac39a5..778193e61 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 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 0e3cf9594bb7 - - d999e774072a - - e25d3acf6e68 - - cbf3f518b668 + - acf4e47b734c - 6f386c5dc4fb - 5edc472ec434 - - acf4e47b734c + - e25d3acf6e68 + - d999e774072a + - 0e3cf9594bb7 - a52d2d93e595 + - cbf3f518b668 - 2889433c7ae1 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd 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 ea8ed51e5..74fab4c9e 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 095ad4d096d1 + - 6ca543ec1bf8 - 710301bc46fa - - 27ee142314a9 - - da6bd1975a71 - f4230f116196 - c8cdde00b105 - - 6ca543ec1bf8 + - 27ee142314a9 + - 095ad4d096d1 + - da6bd1975a71 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -130,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - 88076940fa94 - - 3b8a9d5ced85 - 0fac8e2afc13 + - 79cfd9ead848 - bfb65cb551d8 + - 3b8a9d5ced85 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 715cd0e87781 - - f5d979cb4b54 - - b46d4b4d995c - eb6564a60136 - - d532b7e5f64b + - b46d4b4d995c - 55918daa5651 + - d532b7e5f64b + - f5d979cb4b54 + - 715cd0e87781 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - - fdf2cc80adb5 - - d2f955aea23a - 5579659312e6 - f26afd1b7104 + - fdf2cc80adb5 + - dae135dfd519 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - bc31d02be922 - 319a28774da9 - d1d0efda35c0 - - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: + - cac1886249a2 + - ed736e6eee39 - 2c349b027a01 - 4da9ee404eab - - cac1886249a2 - 070e3ecc3fda - - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - f197e34c33a9 - - 2e219a2d9327 - - 525ca7c8065f - c0c9a5024177 + - 525ca7c8065f + - da8753545526 + - d1f803b5943c + - 2e219a2d9327 - 73008ef1f487 - 807aa4c9293d - - d1f803b5943c - - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: + - 27ea4e1a3f95 - 1809414a9454 - c4fbab8e03c5 + - 7568ae18908a - 2c8ed1b52bf7 - - 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: - - 79e8ab8f1e81 - 730ef07b90ae - - ba83f0923369 - d7ec25187599 + - 79e8ab8f1e81 - ccfbd956a2d3 + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e2c36f62e22f - - 4242b4d68e9c - - e6011617c748 - b59c91adeac1 + - e6011617c748 + - 4242b4d68e9c + - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -350,10 +350,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 9b48456a96fe - d4c67ced6abc - - 85fad59f8168 + - 9b48456a96fe - bf99565cec1f + - 85fad59f8168 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 ae0972bad..0f3e742fe 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: - - f907216064f6 - - fa56d93f7980 - - 2605cbdaa7d8 - c97a786e8fb5 - 163688bb8f73 + - f907216064f6 + - 2605cbdaa7d8 + - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -18,16 +18,16 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 640d3af5d833 - - 424aefbd7777 - 495a4173006f + - 424aefbd7777 + - 640d3af5d833 - f5d67c722d67 - 86e2413cf3f8 tool_panel_section_label: ChiP-seq @@ -35,8 +35,8 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 02e426c53..2776d7a57 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 830961c48e42 - - 90981f86000f - - 33151a38533a - 25136a2b0cfe + - 33151a38533a + - 90981f86000f + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,8 +31,8 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd - 6cbe2f30c2d7 + - baabc30154cd - 0046692724f9 - 2dae863c8f42 tool_panel_section_label: Collection Operations diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index d1766bc1a..ebc8afbb5 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - ab9350a8ab4d + - 0b3c3ad92827 + - f3a19509108a + - a3b86937ead6 - 367b1ed91207 + - 4a6ee918c13a - 5e1240a87bcb - e3cbd2287f63 - - 3b6f97e7094c - - f3a19509108a - - a3b86937ead6 - 6ef0b5664c69 - - 0b3c3ad92827 + - 3b6f97e7094c + - ab9350a8ab4d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: + - e177a8ea0bf1 - 33c99804a32f + - 54ccb7e1f49a - 501c21cce614 - - 72ed72122deb - 584008e574b2 - - e177a8ea0bf1 - - 54ccb7e1f49a - - d4d4e9febf5c - - 091bb5922a82 + - e525f9ffb9ac - bd46669113b9 + - 091bb5922a82 + - 72ed72122deb - 1b5fc03380d4 - - e525f9ffb9ac + - d4d4e9febf5c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -65,24 +65,24 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 186b8d913e6c - 77b41c89d856 - 8979c288aefb + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 43807a65369f - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf + - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -94,9 +94,9 @@ tools: - name: gffread owner: devteam revisions: - - 154d00cbbf2d - - 4dea02886337 - 3e436657dcd0 + - 4dea02886337 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -114,8 +114,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 705821bf30d2 - f5c632894818 + - 705821bf30d2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram @@ -134,18 +134,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 78fb18899c99 - 2dcfbbf9071a + - 68f57cc8fad0 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 + - b9b385097f13 - 63769c4217a7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -158,15 +158,15 @@ 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: - - 98704d357ede - a2f83a375bf2 + - 98704d357ede tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 1b0360a8f..cf43107ca 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,146 +2,146 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - c929a006727f - a1ca9bccc7f2 + - 268e91e540ee - de72ba3ed6f2 + - e821645ef8fc - 29451af70c52 - - 268e91e540ee - 5f6d123679f4 - - e821645ef8fc - - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 5d11599b8a7d - bb1e4f63e0e6 - - 2d2cf5c1ea8a - 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tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - 7e361d147872 + - 9368fbc49c8b - 3b9d990a0a0e - 4e12ea27f788 - - 231994413f89 - - 9368fbc49c8b - - 56bce3c82278 - 7fda5607e777 + - 56bce3c82278 + - 231994413f89 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment @@ -149,58 +149,58 @@ tools: revisions: - e65d16fb2724 - c03c3384cd81 - - b1779366c8e9 - - ce4ce3316f74 - 4431f39ede55 - - d9114ef1c8a5 + - ce4ce3316f74 - 94ca68515826 + - b1779366c8e9 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 23f7c5f1fdaf - 2da482e408b8 + - 793665fff0f8 - b88ebb3672a1 - - d57251071381 - f8fc4e5aff9d - - 793665fff0f8 + - 23f7c5f1fdaf + - d57251071381 - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - e4c7985d4585 + - a4dfb122e52b - 25d830337d31 - 010e58e9d822 - - 512155688d98 + - e4c7985d4585 + - a7849312d328 - c60570fa602f - ba6efa77fb79 - - a4dfb122e52b - - a7849312d328 + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: + - 00d869ea03a1 + - 4d678170d29b + - 38e3f226248b - aa200e4f3939 - - 69264da0ce77 - c899e0ccff8c - 443d9a9d6d11 - - 00d869ea03a1 - - 38e3f226248b - - 4d678170d29b + - 69264da0ce77 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - a2d70c4fd406 - d806504e96d9 - aac8444d6681 - c361b12d207a - - 6662b1a8d326 - 10301d137111 - - a2d70c4fd406 + - 6662b1a8d326 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 69d156f58..9cebe547a 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 4cf47c504672 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index cf8b05588..f5cb27350 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 62f5fab76dfb - - cf1322aeb137 + - 29bdbc353f20 - d82648ad25a3 + - cf1322aeb137 - 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 29136720e..c534bf2ee 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -9,33 +9,33 @@ tools: owner: lparsons revisions: - 660cffd8d92a - - de6cebe3c043 - - 64172f1c1202 - - 8665bcc8b847 + - 44e2cc14f75b + - 4e5056fefd88 - 135b80fb1ac2 + - 8665bcc8b847 + - 64172f1c1202 + - c053d4cad713 + - 5eb7e84243f2 + - 5915ea1ec9b1 - 49370cb85f0f - - c4b82dce8335 - - e4691e1589d3 - 288f97432497 + - b1c926deaa2d + - e4691e1589d3 + - 48f587c13075 + - de6cebe3c043 - c5e2e5902201 - - c053d4cad713 - 8c0175e03cee - - 4e5056fefd88 - - 48f587c13075 - - 5915ea1ec9b1 - 093678460093 + - c4b82dce8335 - 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: - 8889eb864cef - - f666895cbebd - 9db07fd39f85 + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -60,9 +60,9 @@ tools: - name: fasta_formatter owner: devteam revisions: + - 9457a20156db - 859422bcb689 - 516b97a23d7e - - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -75,35 +75,35 @@ 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: - - 0dbb995c7d35 - - 56022eb50bbd - cd0874854f51 - 9c620a950d3a + - 0dbb995c7d35 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbf9c561ef29 + - 65b93b623c77 - d60c3f704da0 - - c59d48774d03 - 1d8fe9bc4cb0 - - 65b93b623c77 + - c59d48774d03 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - 9115b978ce10 + - f1dc2a761c30 - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -118,65 +118,65 @@ tools: - name: fastq_groomer owner: devteam revisions: + - 47e5dbc3e790 - 8611b80a14d6 - e9f8633db0a2 - - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - e30352e889fe - 7861f3b10c68 - 5b87038565bb + - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 4e1d64e6385f - 9dfda4e310ed + - 4e1d64e6385f - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: + - 03d57fea6482 - 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: - - 3e396e702cea - 2ccb8dcabddc - b41c2c1bcfbf + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 8d958759cf2a - 09a2199cd356 - c885369b207b + - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - - 397dc333436b - - 249c8393f2d4 - e39cc71d3ed6 + - 249c8393f2d4 + - 397dc333436b + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 045f0e1043f7 - 74db4cffab1f + - 045f0e1043f7 - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -184,16 +184,16 @@ tools: owner: devteam revisions: - f86c27295151 - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 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 @@ -206,34 +206,34 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 + - 09070cacefd8 - 567d5b3c52b1 - d5e9e83cd3d8 - - 09070cacefd8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 0b7ec11b3c7c - 4bedca26c133 + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - 90858c306551 + - 736b8f6ee456 - cb1e251cac37 - bdf1ce174e39 - - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -242,25 +242,25 @@ tools: revisions: - b29d37ca9e41 - 02f8a17a4ebd - - f984bb114520 - 3599f5451ee2 + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 177f0621c266 - 6027ef51ef91 - 0c2907307ba4 + - 177f0621c266 - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 377ac2829eac - 547e8d00f11c - 61b4cedc8934 - - 377ac2829eac - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -273,10 +273,10 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 - b4c6f054210a - - 2f804526f5fd - f69501361cec + - 037f0acc7830 + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -303,8 +303,8 @@ tools: - name: seqtk owner: iuc revisions: - - 3da72230c066 - 4b494533146a + - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -317,40 +317,40 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - - 71f649c23021 - d3f58a0dc09d + - 71f649c23021 + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f + - e654095ab143 - 71ad4a56c40c - b557acca0b56 - - a535cf1e5da4 - - e654095ab143 + - 24013bf85a6f - 8250ea3a1501 + - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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: + - 9fa7803d1c51 + - 6a675c3aa610 + - 7accf7407811 - f3759eec3018 + - 015cf18f4a15 - 27ac32a22ad2 - - 7accf7407811 - - 6a675c3aa610 - - 9fa7803d1c51 - - 7a7e33d28f62 - 828dba98cdb4 - - 015cf18f4a15 + - 7a7e33d28f62 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: - - e4e12f0b3af1 - 953b4821b183 - 4c8a1c7d3608 + - e4e12f0b3af1 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 4c9ddda74..997ff4513 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,84 +2,84 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 - 7b4468117008 - - 64e9a6afdd0c - e41385662e5e + - 64e9a6afdd0c + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 2c64fded1286 + - 2b0c9d9fc6ca - 9da02be9c6cc - - e7b2202befea + - f2e8552cf1d0 - 5ec9f6bceaee - - ff9530579d1f - - 2b0c9d9fc6ca + - e7b2202befea - 3d0c7bdf12f5 - - f2e8552cf1d0 + - ff9530579d1f + - 2c64fded1286 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - 89d299153577 - - a252d8415583 - c1a33f603da2 + - 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 - b6b54ba71bd8 + - 18a51655db17 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 + - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 8880fb74ef56 - - 1f296803dfa3 - a72af9de6bf5 + - 1f296803dfa3 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - f7e2f1eb3a16 - 75c93c70d094 - - 5e33b465d8d5 - - abfd8a6544d7 + - 1c2db0054039 - c1a4b5f3b432 - - bf675f34b056 - - 3d93dd18d9f8 - b2f1f75d49c4 + - 3d93dd18d9f8 + - f7e2f1eb3a16 + - 5e33b465d8d5 - 9a913cdee30e - - 1c2db0054039 + - bf675f34b056 + - abfd8a6544d7 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - 949f01671246 - 084bbd8ba7b8 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 1dc6b6ca8..2d183e1d1 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,15 +2,15 @@ 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 owner: peterjc revisions: - - bdaefd241921 - 7c40a1fbc82e + - bdaefd241921 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index e4f053657..cbf35a4aa 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,23 +2,23 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: + - 0c8f7322f8fc - 8f53b238a360 - f2f3bc622a16 - - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -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 @@ -86,8 +86,8 @@ tools: - name: gemini_load owner: iuc revisions: - - cf61daf064fe - b2c25142267e + - cf61daf064fe - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -101,8 +101,8 @@ tools: - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: - - 840fb4850be3 - da74170c55c7 - 666f60a9331a + - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,15 +137,15 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -158,8 +158,8 @@ 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 diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 9844ff03b..2b81e95ea 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,8 +9,8 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -23,8 +23,8 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 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 a8b11c03f..4e9065821 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,9 +3,9 @@ tools: owner: galaxyp revisions: - 983bf725dfc2 - - e9df53a75f3c - b39347891609 - c1b437242fee + - e9df53a75f3c 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: + - e063168e0a81 - 1c58de56d587 - 28587613264f - - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1790dcf3c32d - - 516a54ddf218 - - 69ebb7f46e45 - - 4df8de2d0e48 - - f5ea3ce9b9b0 - - 653e89d73fc4 - - 6591f049cf7e + - c441583adae5 + - 83c7d564b128 + - 7068f48d0ef9 - aad3885b3216 - - 1ec814014652 + - 8848455c0270 - 9a776b080193 + - f8054ea1c365 - 734abc7ac21d - - e407b9da183a + - f5ea3ce9b9b0 - 6ea73833cf67 - - 83c7d564b128 - - 7068f48d0ef9 - - 5e6237d58b0c - - f8054ea1c365 - - c441583adae5 - - 8848455c0270 - ba931a59dd59 - - e08a7ad4378b + - 653e89d73fc4 + - 1790dcf3c32d + - 1ec814014652 - 4317d3cb6cba + - 5e6237d58b0c + - e08a7ad4378b + - 6591f049cf7e + - e407b9da183a + - 69ebb7f46e45 + - 4df8de2d0e48 + - 516a54ddf218 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 21a560af5913 + - 34758ab8aaa4 - 75b3b3d0adbf - 9aaa46d45472 - - 34758ab8aaa4 - - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a - - af5eccf83605 - 95fb5712344f - 468c71dac78a - 054483e27a35 + - bfdc6a7ffd3a + - af5eccf83605 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 ff1324d5d..9d823f79e 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,14 +2,14 @@ tools: - name: circos owner: iuc revisions: - - 4b519282a05b - df7356989ac1 - - a64dc31ab7f2 - - ae9994cf526f + - 4b519282a05b - 740057a5126d - - fd59d783248a + - ae9994cf526f - 7f13dc906cb9 + - a64dc31ab7f2 - c4bde687c846 + - fd59d783248a - 290a11559985 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,35 +54,35 @@ tools: revisions: - 10515715c940 - 391a4cc45fea + - 3d059e9c2fba - da4c086cff5b - 1a72f938213e - - 3d059e9c2fba - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - 6fc8bab811da - b0d96516e6a5 + - 6fc8bab811da tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - 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: + - 299307abd804 - 5298e06f14f9 - d0fc8b746d57 - - 1acf88921176 - - 5fe1dc76176e - - 299307abd804 - e3a675da7fd0 + - 5fe1dc76176e + - 1acf88921176 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -101,15 +101,15 @@ 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: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f 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: + - 836d1aa3e89a - 112eb40ba6cf - 1cfc579079a6 - - 6cd09d7b5f37 - - fd5dbf0f732e - - 836d1aa3e89a - - 17359b808b01 - 2bb2e07a7a21 - - 667e17248bfe - ca2def38369c - a6e57ff585c0 + - 667e17248bfe - 4542035c1075 + - 17359b808b01 + - 6cd09d7b5f37 + - fd5dbf0f732e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -155,24 +155,24 @@ tools: - name: pathview owner: iuc revisions: - - 03c13085aecc - f1691de443a7 + - 03c13085aecc - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - bd1416eea1f0 - 594b85e4237a + - bd1416eea1f0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - - 62e3a4e8c54c - 1c5dcef5ce0f + - 62e3a4e8c54c + - 85da91bbdbfb - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -193,8 +193,8 @@ tools: owner: iuc revisions: - 44c66e8d21e6 - - 6c571966cfb9 - 7c9417381ad5 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -207,22 +207,22 @@ tools: owner: iuc revisions: - 360df4999907 - - a1abfa420d9d + - 2824d77cd8f8 + - 4ac4e7083b7e - 14e7c35f3d00 - 36b848d5f3ec - - 7dd841a32245 - - 2824d77cd8f8 + - a1abfa420d9d - 326a3db8d9d1 - - 4ac4e7083b7e + - 7dd841a32245 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c + - 44608d0193ed - 73b8cb5bddcd - 2f557f6abbfb - - 44608d0193ed - - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 0f8d4aa06..c9a2e63a0 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: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,29 +21,29 @@ 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 owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - - 23d838d1569d - cc64914b0cf4 + - 23d838d1569d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster @@ -63,8 +63,8 @@ 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 @@ -91,9 +91,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 94697510d55f - ff6decc0f432 - 9a2f72d7dbd2 - - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -106,29 +106,29 @@ tools: - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - 0387a2179f88 + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 7d5c97823f8b - 1be0fc4d8654 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -141,8 +141,8 @@ 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 @@ -155,15 +155,15 @@ tools: - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt owner: ebi-gxa revisions: - - 03921aa8b29c - 12f67b0c1a94 + - 03921aa8b29c tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_fdg @@ -176,8 +176,8 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - 6d4f88995e40 - b2768cae00a1 + - 6d4f88995e40 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca @@ -190,8 +190,8 @@ tools: - name: scanpy_run_tsne owner: ebi-gxa revisions: - - abdb61e4afa3 - 3fb53f5e46ea + - abdb61e4afa3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap @@ -205,7 +205,7 @@ tools: - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 2a8edcea3..b3d8981b7 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -3,19 +3,19 @@ tools: owner: bgruening revisions: - ed2cca6b5de4 - - 29f66c353bcb - 921a2da49a0c - a4c13ddcc8ee - 9edf8894a22d + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 755df866ad0c + - 78fb5e286609 - d404277cc87a - ec4b948dc6f0 - - 78fb5e286609 - - 755df866ad0c - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,9 +23,9 @@ tools: owner: bgruening revisions: - 9e357a8b2ec3 + - 03dd3c16ae4e - 11fa44ee0603 - 977dc15add20 - - 03dd3c16ae4e - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu @@ -33,8 +33,8 @@ tools: owner: bgruening revisions: - c3e5e2cf12b7 - - 3b5b54ed6392 - 77919cc3618e + - 3b5b54ed6392 - 41dbf4d162a2 - 0ba4f56a3613 tool_panel_section_label: HiCExplorer @@ -42,11 +42,11 @@ tools: - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - - 12d51d7be66f + - b63363075c2e - 7babd8a46fe0 - 5308ca68ef3d - - b63363075c2e + - 12d51d7be66f + - 9939786dd9c9 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 949718097..749674c14 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: - - 0c777d708acc - 3df9f0a4bf34 - - 8bccb36e055a - - 7db4fc31dbee - 81f0cbca04a7 - 699a5e9146b3 + - 8bccb36e055a + - 0c777d708acc + - 7db4fc31dbee tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5bc8cdc17fd0 - - 0a53256b48c6 - 5791a7f65275 + - 0a53256b48c6 - 2436a8807ad1 + - 5bc8cdc17fd0 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 9d47aabda459 - 6ad1d3cfdea1 + - 9d47aabda459 - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: + - 77f7159d775a - 70316d792fc9 - b1c2c210813c - - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - dba87c4b32d3 - - f70b215d155c - d51310ab328a + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_split_binaryimage_by_watershed @@ -52,10 +52,10 @@ tools: - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - fcadded98e61 - b07f4839ca77 - 10eed33aa9b2 + - f3360fbeda64 - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -69,80 +69,80 @@ tools: - name: count_objects owner: imgteam revisions: + - 5bf8eb50b280 - b58447a2eed2 - 664232d2a3f7 - - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - 6070780813d9 - - 670975e92458 - e7273daa5ae2 + - 670975e92458 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - - cdf8e3c57dae - ef4aed1d34c4 + - cdf8e3c57dae + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 5d28ac336861 - - 6a7da2e5f696 - 2484086dee41 + - 6a7da2e5f696 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 - ad271f78a87a - 31d195bedf6d + - 3245681b2f6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - - 87d4d92d7487 - 993faa34333b + - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -180,17 +180,17 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - 8536b1ae0254 + - b64af54c5c09 - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: + - 6f4715b8540a - e972e07c7845 - d3890df07463 - - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -205,16 +205,16 @@ tools: owner: bgruening revisions: - 79e10d12d90a - - acf3aa487283 - d85f11570109 + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -227,17 +227,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 8083a87d2fdf - 48102a685037 + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 27edbb90ab2b - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -263,9 +263,9 @@ tools: - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - - 7b6d9412c7f8 - f8b4eada923c + - 7b6d9412c7f8 + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index fae443492..28bdd3297 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - d6e72da3ec35 - - 40737febe339 - - 3a72fede57ce - - 1069f6db0a0e - - 78bbd17d0703 - a38934e303b9 - - e4ee04da1c19 - - f362150bef41 - 3e4f434a69c6 + - 78bbd17d0703 + - 1069f6db0a0e + - f362150bef41 + - e4ee04da1c19 + - 40737febe339 - e319b5b65879 + - 3a72fede57ce + - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - f91cfb73d369 + - 2b95d5c04908 - 7fe36019c073 - 0135f1d487a0 - 618297d23022 - - 8f8df367470d - fcbeda41d0ac - - 72ddd32392cd - 9537184d421f - - 2b95d5c04908 + - 72ddd32392cd - c88553ec696e - - f91cfb73d369 + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 - - fafb3d685fa9 - ad0dc9f4c9e2 - 2cf4a1cafc16 + - fafb3d685fa9 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 7f1cfa4c0e32 - - 6a1515bb0687 - - 3d18f8c3c0f6 - - bd2a7d1316b9 - - ee2beb764a7b - 9eaadf03e0df - - a1c2aecd7a0d - - 5dc33613c288 - - 28a6f1908fcc - - 94df24c6bc00 - - 43aac8d29685 - 8d36959b000d + - bd2a7d1316b9 + - 28a6f1908fcc - 8c05afb547fa + - 3d18f8c3c0f6 + - a1c2aecd7a0d + - 94df24c6bc00 + - 6a1515bb0687 - ee29337f905c + - 7f1cfa4c0e32 + - 5dc33613c288 + - ee2beb764a7b + - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - 9f978da6528a + - cb903c9dc33d + - 86a20ae274fc + - 8858fa037a15 + - 5d6ed46cc101 + - c092052ed673 - a250929be21b - - 5671e1d3d5ee - db536ad45f28 - - 86a20ae274fc - d37ede8589b2 - - bcaa0d571ce2 - - c092052ed673 - - 364f4ffec275 - - cb903c9dc33d - e3bb03cf207a - - 9f978da6528a - - 8858fa037a15 - - 5d6ed46cc101 + - 364f4ffec275 + - bcaa0d571ce2 + - 5671e1d3d5ee 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 + - ed28dd32141c - 49236b03e4fd - c5c9f02b6167 + - 3b6a16d82c1b + - e1a015876aa9 + - 194e3ceee923 + - f95f403841ad - abbc8041e8ec - - ed28dd32141c + - 584beffa972b - 38b91a3190cd + - 230b05597996 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 61e1d35d7..17fa87f3c 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: - - 17e3b698dd52 - - f198773344e4 - - b8a457820315 - 0f1724dd59d2 + - b8a457820315 + - f198773344e4 + - 17e3b698dd52 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 + - 374cb875d38a + - a513e3fbb4c5 + - 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 302787147..399b483ab 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -3,98 +3,98 @@ tools: owner: bgruening revisions: - 522137aaa9c4 - - 772e0e89fc68 - 66d7efc06000 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - 8a794e6d3388 - - 4d81e3e2fb63 - f22a9297440f + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - f1b9a42d6809 - - 2af1346e68c9 - - b6ef6d0cb6b7 - 818f9b69d8a0 + - b6ef6d0cb6b7 + - 2af1346e68c9 - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 1588f9076e32 - 8334dc98c48e - - 947c2eacccb8 - c80db5d6fd8c - 05143043ca13 + - 1588f9076e32 + - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 83228baae3c5 - - 9991c4ddde14 + - 1552b8cb4a94 - 29e4122c90de - 25b46af53232 - - 1552b8cb4a94 + - 9991c4ddde14 + - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - a07ab242b0b5 - - f3dfa4bdf87e - - 1a53edc4b438 - 841a6cc5fc58 + - 1a53edc4b438 - 53616c8b0865 - 060ca94ac049 + - f3dfa4bdf87e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - 91c4e3331208 - d4808d5b83da - 40f4447733b2 - - dc4b5fd604a6 + - 2fc89dcd41c8 - 927586a18553 + - 91c4e3331208 + - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 36e8d6d5d01b - - 25ab6b4e376e - 301e07345c93 - c6ae57f774c6 - 7626ea9c2e1b - e5a5ad882f1f + - 36e8d6d5d01b + - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 + - b7c3e9a3b954 - 02d2be90dedb - f9639b488779 - - 80852884053f - - b7c3e9a3b954 - 4ed102b922cb + - 80852884053f + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - ec69cbe34b73 - - 61634a87efc7 - 14180f9c831e - caeb57858702 + - 61634a87efc7 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 9405789b0..e1ef3de4b 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -3,16 +3,16 @@ tools: owner: devteam revisions: - 937aa69e715f - - 749c918495f7 - - 3ba8d4563129 - 017aba02828d - cd659e8cc5fa - - 03e9b2fbc005 - f6877ad76b00 - - d5ceb9f3c25b - 17062a0decb7 - - a6d65b0c67af - 0d4acadabb04 + - 03e9b2fbc005 + - 3ba8d4563129 + - a6d65b0c67af + - 749c918495f7 + - d5ceb9f3c25b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -32,11 +32,11 @@ tools: owner: devteam revisions: - 64f11cf59c6e - - e188dc7a68e6 - - dfd8b7f78c37 - 2477830927ec - - 53646aaaafef - 3fe632431b68 + - e188dc7a68e6 + - 53646aaaafef + - dfd8b7f78c37 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: - - 3e1ea2facca6 - 37b497aa133f - 60afcc2c1d05 - - 2ff111fac1d7 - e7f19d6a9af8 + - 3e1ea2facca6 + - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - f54f5baedfdd - - 11a0d50a54e6 - - 6b1e195506a3 - - 3f4d6399997b - - 5cc34c3f440d - - 09b53c1d4ab1 - 77b2770508f6 - - b3eab4b67562 - - 53c0b7a1a0c3 - be1d967337e4 - 037c6e54df11 - - 8c6cd2650d1f + - b3eab4b67562 + - 6b1e195506a3 + - 5cc34c3f440d + - 11a0d50a54e6 - c0c2d0941de8 + - 3f4d6399997b + - f54f5baedfdd + - 53c0b7a1a0c3 + - 09b53c1d4ab1 + - 8c6cd2650d1f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - ec9cbd6b9a49 - - 42ce70172b72 + - 13022c3d3076 - 178bdbdb6d24 - 1cd2511a396e - - e403d27e8f24 - - 00fbfac99d39 + - 42ce70172b72 - b8f5f6e87f5c - 9ee34ba73ebf + - 79b885ce78d7 + - e403d27e8f24 - 45795f582ae9 - - 13022c3d3076 + - 00fbfac99d39 - 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 710532e67..8b9ef42ee 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -82,8 +82,8 @@ tools: - 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 @@ -103,15 +103,15 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - b576ed720711 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -148,8 +148,8 @@ 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 @@ -224,16 +224,16 @@ tools: - name: ramclustr owner: recetox revisions: - - 9b716db0a786 - da7722f665f4 + - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - - c53a97599181 - 79ad928a0dae + - c53a97599181 + - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters @@ -256,40 +256,40 @@ tools: 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 - - b3413f335327 - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - 17a48d0a80f4 - cf061712a184 + - 17a48d0a80f4 - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - 99d118321d5f - 24278c6b6d1c - d7f5878a98c3 + - 99d118321d5f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - ffbabefbd2e2 - - d90187b0f247 - ea0758b41473 + - d90187b0f247 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -301,8 +301,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 2c6fa447f6a0 - 6b5dec818827 + - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -320,8 +320,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 5a6bb93ec656 - 0b28816c1c2c + - 5a6bb93ec656 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index ecc37c47a..d336dbe15 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -10,15 +10,15 @@ tools: owner: iuc revisions: - 0e63d03c8790 - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -90,128 +90,128 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc - 7c2100246a2f - - 5b5a7af9fbb4 - - 76d3d2b10738 - 63f86089423e + - 65db807336bc + - 76d3d2b10738 + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - - 18a502a9d287 - 1c35dadbe76f - - 96336c6a2bb7 - 00f5005840fa + - 18a502a9d287 + - 96336c6a2bb7 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - f732237754fc - - 34e55239e68b - e8fba04706d3 - - addaf9d22850 - a9f4a217dcd6 + - addaf9d22850 + - f732237754fc + - 34e55239e68b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 75403243703a - 0776d824d896 - - 5fe3edf19b9c + - 75403243703a - 8c202e741d68 + - 5fe3edf19b9c - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 8470de786d47 - - e96bbb9e24ea + - 1c9b3bcd4261 - 75c8945b0da2 - 43c99742158b - - 1c9b3bcd4261 + - 8470de786d47 + - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - 1d75bd0595e2 - - 35176674168c - 306a40d4bb8f - - 84743da21318 - 5c865a382933 + - 35176674168c + - 84743da21318 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - 8daf4564ccda - 555ccac8a4c5 - - ac72310b038a - 78faebd0879c - - 8daf4564ccda - 32c9ea835770 + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - 7b8cb2b02978 - - d60df8727f59 - a58e4a43f49c - cae017b76acb + - d60df8727f59 + - 7b8cb2b02978 - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7136e9ab70db + - 04144473e59e - 073608a50ac3 - - 1bc3657cd694 - 7f3b59dee073 - - 04144473e59e + - 7136e9ab70db + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - - 9058d8943303 - d943081510da - 0a1224c4b781 - a7817705348e + - 9058d8943303 + - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - 65d52c693b8e - - f8f56dd6449f - a68b985913ab - b907a3c0434f - - c4db8c4de66f - - dbf1798c0dcc - - 4d9445dff47b - 5c7ba3d85a01 + - 4d9445dff47b + - f8f56dd6449f + - dbf1798c0dcc + - c4db8c4de66f 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 @@ -231,17 +231,17 @@ 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 - - c6676a890f50 - d77397f09da1 + - c6676a890f50 + - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -281,37 +281,37 @@ tools: - name: humann_reduce_table owner: iuc revisions: - - 6552df6efe6b - 60749924ad62 + - 6552df6efe6b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - 79706f10d680 + - c409a495841f - 31c6d107e7a5 - e88b731dad59 - - c409a495841f + - 79706f10d680 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 - 714d5a28cc5c - - 71ea608ddfa3 + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - 2bdd84912a2b - a4d7148ccee4 + - a293a742194f - 4137b492233e - d7e9a3c41657 - - 2bdd84912a2b - - a293a742194f - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -324,13 +324,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 75bedfb2078b + - 64bc7acc22a9 - 6fcb8ac37a3e - - cf87759761eb + - 75bedfb2078b - a92c06a3afa7 + - cf87759761eb - 97f7bb0851e7 - e2c71b852aba - - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -349,21 +349,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - - c82508e76ad1 - - 5e5a999ffaa9 - 4033827c76b8 - - 4e5e73d03f0d + - 5e5a999ffaa9 + - c82508e76ad1 - 2d35528d2141 + - 4e5e73d03f0d + - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - fc6c328c292f - 2cd76b089570 - - 6b7622dda516 + - fc6c328c292f - 95bf7479d53c + - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -397,8 +397,8 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - 1061711538c6 - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -411,8 +411,8 @@ tools: - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 00f7064c564b - 19607c740d19 + - 00f7064c564b 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: - - 5a0fa29951ae - 8388fe31d604 + - 5a0fa29951ae 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 - 4a9da2b6c2e3 + - 20e2f64aa1fe + - cdee7158adf3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - f03c7ba8d8bc - 50bd98b3ae5a + - f03c7ba8d8bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -460,15 +460,15 @@ 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: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -506,8 +506,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 4960abe31b4d - 073c867c5244 + - 4960abe31b4d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -519,8 +519,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -556,21 +556,21 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 3cc4a60615c0 - - 327d9f4cc95f - e073891b2afc - - 4fd3b5d8706b - - 27250f92a01a - 0270541aaf46 - - 2cff76cf35c6 - 7f5d7b0e9884 + - 2cff76cf35c6 + - 327d9f4cc95f + - 3cc4a60615c0 + - 4fd3b5d8706b + - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - eb50e7eca3dc - 708abf08a626 + - eb50e7eca3dc - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -644,19 +644,19 @@ tools: - name: metaphlan owner: iuc revisions: - - 1a037928504c - - a16313517e55 - - ec368db926f4 - - 1a6cdf55390f - - a92a632c4d9b - - 6dee4abadccb - - b89b0765695d - - fd69c607b43f - - ff8f55893e7d - - ef65b083bd0c - 2131d7dca455 + - b89b0765695d - 289b3807e80c + - ec368db926f4 + - ef65b083bd0c - 740fd2d16a28 + - a16313517e55 + - ff8f55893e7d + - 1a037928504c + - a92a632c4d9b + - fd69c607b43f + - 1a6cdf55390f + - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -701,22 +701,22 @@ tools: - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 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: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs @@ -761,8 +761,8 @@ 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 @@ -792,20 +792,20 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - 4d83eccf5f81 - 3b22de20bd4b - - aeaa20b96ef2 + - 4b9a8031ab74 - be818ae858e4 + - aeaa20b96ef2 + - 4d83eccf5f81 + - 2fd4d4c9c5c2 - 141afacabcfa - - 4b9a8031ab74 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 9495df9dd6ef - 576963db5f1b - b3c7199d8786 + - 9495df9dd6ef 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 aeb746c63..76bc50eb9 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -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: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 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 c70964317..4138dde55 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,38 +2,38 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - a74dbfee5a86 - - 2263989660f5 - - bdfbaf0c10aa + - 80f03df2e2ce - 94b8c6013083 + - 9422c5a87ee2 + - 2263989660f5 + - 8b67dd48fec1 - 9baa871cb1d1 - - cd07731e4434 + - a74dbfee5a86 + - bdfbaf0c10aa - 9eeb13a92d79 - - 48c13389050d - - 80f03df2e2ce - - 8b67dd48fec1 - - 9422c5a87ee2 - - 6ae5a7b5a0a2 - 098506c54016 + - 6ae5a7b5a0a2 + - cd07731e4434 + - 48c13389050d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c44f824c051a + - 2e093badc689 + - f14193ec1f50 - 5abf2c2249aa - - aaa0d6a8b808 - - '764845535798' - d7ce0ec78e51 - - bc3831dd65c1 - - 4a60927aaca5 + - c44f824c051a + - d390fe1567dc + - '764845535798' - 3ff17bad4006 + - be78f13134e2 - f0af8936ed41 - - 2e093badc689 - - d390fe1567dc + - 4a60927aaca5 - c18157c68134 - - f14193ec1f50 - - be78f13134e2 + - aaa0d6a8b808 + - bc3831dd65c1 - fc2e49f91e52 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,27 +53,27 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 1de657a3198d - 5efbd15675ca + - 1de657a3198d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - bf28a8cff401 - - f1a5908ea2cb - 8e649f27aa0d - - 6f28e90db932 - - 15974dd17515 - f0d493f8f84f + - bf28a8cff401 + - 6f28e90db932 - c5908940967d + - f1a5908ea2cb + - 15974dd17515 - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -89,39 +89,39 @@ tools: owner: iuc revisions: - 60698466facd - - 5561a1193611 - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - - 57f042937ba7 - 48823c9635a4 + - 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 - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - e18267f90096 + - 7cd7a55a678d - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: + - cf3c9489c088 - 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 db4bf8ccc..719c3b548 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: + - 7c47b3c9e493 - 18a8d140ec6f - 28928576e1ea - - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: - - 99c9427219d3 - fc5b6491cf78 - 63d8ecfcfab1 + - 99c9427219d3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - 79e9a869f40e + - cb34f00cc10f - 72b5e9dda577 - - fc8804320156 - - a7228a7ea146 - 0e9e7fcdd543 + - a7228a7ea146 + - fc8804320156 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - 18505fe2bdb1 - - fa11aa8103b2 - db25ec99c3ea - d6cddc06aeae + - fa11aa8103b2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -51,14 +51,14 @@ tools: owner: iuc revisions: - cc36773a3681 - - 43815fa60f3a - - edf6d4003fad - 2bf63b38ee9b - 0f5f4a208660 - - eb746fa6f514 - - 222669c4afb6 + - edf6d4003fad - ec699520444c + - 43815fa60f3a + - 222669c4afb6 - 19f3b583a9b3 + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -77,13 +77,13 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - 645159bcee2d - 7b379e98b9a9 - - a02b8b3f5a0c - a38bdcec9e4c - 0f1c34698076 + - a02b8b3f5a0c - edbb6c5028f5 + - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -97,40 +97,40 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - a8d4be409446 + - 90a922f32523 - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - 449e9aeded2d - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - a3afc5f0a96c + - bec636361cfd - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 93d623d9979c - 5f76b20953e5 - 543cbeef3949 + - 93d623d9979c 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 @@ -142,8 +142,8 @@ 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 @@ -175,8 +175,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 26e6c9362b7b + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index d49b79582..a4b29f7c6 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -27,18 +27,18 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 3e73c97f025d - 97b1b5ad1cda - baceff842902 - - adfd6bf710bd - d74850cf4e42 + - 3e73c97f025d + - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 9dd107db92c2 + - 1586b111d2a3 - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,12 +51,12 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 + - 1e34d2e3d285 + - 19b6a2f0dbe2 - e4b4837f06f5 + - 2f27f3b86827 - ed1518ce2237 - 13851aefa67a - - 1e34d2e3d285 - - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -75,8 +75,8 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 74af283d8ebd - 472dabcb03bf + - 74af283d8ebd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 @@ -90,8 +90,8 @@ tools: - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -131,10 +131,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 172815da3d41 - b4b2b284230a - - 52b6a4d98009 - 27a6a256cd23 + - 172815da3d41 + - 52b6a4d98009 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: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 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 - - 87febc68b45b - fea85c467896 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -174,8 +174,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -193,35 +193,35 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 2c61c30a57e7 + - d8dc037e3c13 + - 4ba60cb14cb0 - 5fe20c915fa6 - 9c43baa60906 - - 4ba60cb14cb0 - - d8dc037e3c13 - 0cb27ea69dc1 + - 2c61c30a57e7 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: - - 0db22932bc39 - aec831b54a5b - 9d09724f2bf1 + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - - 6e24e79d3d69 - df30a2f1db55 + - 6e24e79d3d69 + - ed7a967cb11b - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -240,9 +240,9 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - ad90c2da4f38 - 1865e693d8b2 - 3e4d45aca422 - - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -767,6 +767,12 @@ tools: - b19e21af9c52 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu +- name: plot_ragtag_paf + owner: galaxy-australia + revisions: + - c1bed78b9ed5 + tool_panel_section_label: None + tool_shed_url: toolshed.g2.bx.psu.edu - name: proteomics_datatypes owner: iracooke revisions: @@ -782,8 +788,8 @@ 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: rsem_datatypes @@ -795,11 +801,11 @@ tools: - name: salsa owner: iuc revisions: - - ba7b0f11e470 - 9a22227bb6d0 - - f77f7a7f3b83 - - ab5b7f6b7198 - 58a870ef434c + - ab5b7f6b7198 + - ba7b0f11e470 + - f77f7a7f3b83 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 75456a5f0..c4f03f75f 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - d033ffc1c161 + - d7c7ef3353fe - b89cac5156ec - - f73435dc282b - - a6619171428e - 6a457678efcb - - 5a7c56a5cc08 - - d033ffc1c161 - - 8834daeb9892 - '841557158611' - - cce7b18495e4 - 3f59ebfbfe3d - - 3b8b5bde0bd9 + - a6619171428e + - 81e66674859e - c78f3d7dd1db + - 3b8b5bde0bd9 - 26de3a7b1cb9 + - 8834daeb9892 + - 5a7c56a5cc08 - f04a1264e2a2 + - cce7b18495e4 + - f73435dc282b - 107d3ba7024a - - d7c7ef3353fe - - 81e66674859e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 659517798cc4 - - aa8cc71438cf - 6283babe736e - - 4755f52427c4 - - 6223845127ea - 7a2092844346 - - 3b96e92e8ec3 - - 6a726db04d4b - - 5b777002c2de - - b0af57c1a968 - - 5fcd1ece3a6e - - 88c4aa435ded - e75442c7f4da + - aa8cc71438cf + - 5fcd1ece3a6e + - 02b8758214b0 + - 6223845127ea + - b0af57c1a968 + - 659517798cc4 - a185b079b095 + - 4755f52427c4 + - 5b777002c2de + - 88c4aa435ded + - 6a726db04d4b + - 3b96e92e8ec3 - df47d4845b62 - - 02b8758214b0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 0878b7fd5260 - 111bd54f6bc4 - c1d53e95327f - - d1c340a5664b - - b8476e82ac20 - f97743d52b87 - 24d024316465 + - d1c340a5664b + - b8476e82ac20 - 70acec670c30 + - 0878b7fd5260 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd - daddf188c13f - 9e10ba792be2 - 4f6349228462 + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -104,33 +104,33 @@ tools: - name: pangolin owner: iuc revisions: - - 8ad84c5753ea - - 14ae456b8cc5 + - b6abccb1f25b - ca0d8cf80567 - - ca337cce3888 - - 7bb8726be37c - - abf6dbe8c9d7 - - 9d61d3fa046c - - 3a43c3982401 - - 5f8727ff21e7 - - b7e297c2ede6 - - 42a174224817 - - 2f1019071464 - - 36912871ccdc - - a2099fb98cdb - - 2fa9d4f1b48f - 83a69484cb87 + - 42a174224817 + - b7e297c2ede6 + - 8ad84c5753ea + - 5f8727ff21e7 + - 7bb8726be37c - 81804a978fc0 + - ca337cce3888 - 437e28791761 - - b6abccb1f25b + - 36912871ccdc + - 3a43c3982401 + - 9d61d3fa046c - 03ed9524dcd1 + - 2f1019071464 + - 14ae456b8cc5 + - abf6dbe8c9d7 + - 2fa9d4f1b48f + - a2099fb98cdb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -145,20 +145,20 @@ tools: - ea30d3089354 - b1e68bbe4cef - ba29b5e2a4be + - 29ff6a849eac - a4b71be30c3c - 73a469f7dc96 - - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - f1ccc8a6eb05 - - e88a7de55d6e + - 809e42326fc2 - 91887494eb97 + - e88a7de55d6e - 9b2b122d0415 - - 15ac71df11a0 - - 809e42326fc2 - dbe2b2204555 + - 15ac71df11a0 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 7bcec9799..57d154963 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: + - 1aac2a13842a - 881d7645d1bf - - f9242e01365a - f6ced08779c4 - - 1aac2a13842a - - 7d34178f2812 + - 3f254c5ced1d - b502c227b5e6 - a1f0b3f4b781 + - 7d34178f2812 - fc288950c3b7 - - 3f254c5ced1d + - f9242e01365a 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 b7d478b7e..19b20f795 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: - - ca90d17ff51b + - a58f7eb0df2c - eb085b3dbaf8 - - 7fbec959cf2b + - 6ab1a261520a - e4a053d67e24 - - d00e15139065 + - 7fbec959cf2b - 2f7702fd0a4c - c0e71cb2bd1b + - ca90d17ff51b - 3bd420ec162d - - a58f7eb0df2c - - 6ab1a261520a + - d00e15139065 - 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 767f3091a..52e4ba20c 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,43 +2,43 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 4c177985028a - - b18329a8ac14 + - ece627528a78 - 0a18ac48ac53 - - f28ad96b76dc + - b18329a8ac14 - 277dc652246e - - ece627528a78 + - f28ad96b76dc + - 4c177985028a - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - a9a28e46d54a - - e215f71d7983 - - bf06d196e23d + - e988563cc6e5 - 525f201b86c1 + - bf06d196e23d + - a9a28e46d54a - b41107d8fe89 - - e988563cc6e5 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - bb6397b94018 - 56da27be956a - 8da3511c9467 + - bb6397b94018 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - a8157342d9a3 - - 890845926d4b - - b8c79e70516d - - f23d67e28cc8 - 528fb09022be + - f23d67e28cc8 + - b8c79e70516d + - 890845926d4b + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images @@ -46,50 +46,50 @@ tools: revisions: - ae304a72db7b - a69865da6f80 - - 25b83cbd596a - - 80600735685d - - a95a82eb4d50 - 59e85306eae5 + - a95a82eb4d50 + - 80600735685d + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - f1897eb07081 + - ed9ed1e6cca2 - 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: - - 5a35e3a8d013 - - 74b61bf5bc4b - - d426a9107a6c - a7fb9b395ddf + - d426a9107a6c + - 74b61bf5bc4b + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - 91f0f5922011 + - cc430977c8ff - 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 + - c5aa9fca18c6 - 043f9c91f686 - d2483487e077 + - 1693b2126f30 - ba92b59cd529 - 10566783d718 - - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -108,8 +108,8 @@ tools: owner: galaxyp revisions: - ae4dc0c041f9 - - bf0728e000cd - ff8c9e0e8a7b + - bf0728e000cd - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -130,24 +130,24 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 4081e4faa4ab - 0fa397f4f40b + - 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 @@ -159,8 +159,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - d286ff4600dd + - e66f552a3c47 - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,23 +174,23 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - f522c08e900c - - 1f39c833f65f - - 2133b0be850a - - 4d17fcdeb8ff - - e42225f8a659 + - 9c52362ae7bb - 837224ad1694 - - 97a7f34fcb6a + - 4d17fcdeb8ff - 37d669de2828 + - 2133b0be850a + - f522c08e900c + - 1f39c833f65f - 7f432d87c82c - - 9c52362ae7bb + - 97a7f34fcb6a + - e42225f8a659 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -211,18 +211,18 @@ tools: - name: metaquantome_expand owner: galaxyp revisions: - - 352b37c66d97 - - 767c1d761aaf - 1974224d63c2 + - 352b37c66d97 - 990b4560ead7 + - 767c1d761aaf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 99450519d727 - deaf035bbe9f - 35cc7ca0bdc7 + - 99450519d727 - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -230,16 +230,16 @@ tools: owner: galaxyp revisions: - e79958768a2c - - c7745841de24 - 06f6826d380c + - c7745841de24 - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - da986f83631b + - b9d453dca8d3 - d2eac53666f0 - d46d64e7964d tool_panel_section_label: Proteomics @@ -247,33 +247,33 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: + - 1199751329b0 - 944b43462104 - - 9bf325045235 - 8bd7734309f6 - - 1199751329b0 + - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 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: - - 593839e1f2c3 - 8212e342e482 - 28434abe6c5c - de7593c29499 + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -287,155 +287,155 @@ tools: owner: galaxyp revisions: - f4be248c3d47 + - 8960fb791701 - 4e77b8f12cd3 - 01dbaf6a57e0 - - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 25529df60a81 - 06cca574e337 - 370141bc0da3 + - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 518b1730cf2a - - 6ccbf9a2072c - - 9cdf15d3cfc8 - c9eff69a7c62 + - 9cdf15d3cfc8 + - 518b1730cf2a - f7fef900f5b2 + - 6ccbf9a2072c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 9876bda3ec53 - - 5e948629bc73 - - ca88bd28f116 - dff6c756eee5 + - ca88bd28f116 + - 5e948629bc73 + - 9876bda3ec53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 890025d6e426 - - 1595601708ec - 658494a2cb00 + - 1595601708ec + - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 9b7977080f6d - 2a93a25f0599 - 5ad0b5bf1deb - 6634cad7d797 - - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp 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+ - 3720e349ba2a + - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - ca799a7246e7 + - c427a8628cbe - c55dddc5844a - 382cde407f81 - a5d785af0ad8 - - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 39caaa778d2e - 8ddb7bab1138 - - b5d0905419da + - 39caaa778d2e - adca857b4884 + - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c - - 1c5f31b8d632 - - 34e7afee141d - f817513840a9 - 18f93351f8b6 + - 34e7afee141d + - 1c5f31b8d632 + - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - c69f69d7867a - 986e03d3201e - 5d9f175dff81 - 111c3a00136d - - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - be74a8cd7d66 + - 4204882495f2 - 476b5e296979 - 0e52c85f3b15 - - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - c18d8efa4474 - - f5ec766d80cf - 2b2a7551a857 - a407b6790342 + - f5ec766d80cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -449,10 +449,10 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - 2735db4dd8d9 - - bf32e0bcf554 - 8098330f6d91 + - ee860980edc6 + - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -467,64 +467,64 @@ tools: owner: galaxyp revisions: - 2a9ff56cb279 - - 8c01da82292c - de7a553552a6 + - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - c1809c05ae8c - - 1bf940c18d93 - e8f64a7dc470 + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - - f861ec9fbe59 - 496cf619e311 + - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - c99d5004b74f - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 89254095cbf6 - - 4bb198c0bd3e - 8b814eafce2c + - 4bb198c0bd3e + - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - f82b320ceb90 - - 05ec9fb05ed1 - f9ed7e074900 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - 18826fb8e5db + - 6e8cc5ed2a9b - d31426ef20f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: + - 4a7b96835140 - 2aebe58de46e - bc63b4d12779 - - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires @@ -532,25 +532,25 @@ tools: revisions: - 6b01678ec2fc - 3d8d4ada5405 - - 5ae104d0da6e - decc397c3b7e + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - 539a3a4dcc9e - - dd173849c3d8 - e039cc5c7aed - - 5182338d5e7c + - dd173849c3d8 - d6aca689dd48 + - 5182338d5e7c + - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - d426affe977c - 8a45fd5a608a + - d426affe977c - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -558,32 +558,32 @@ tools: owner: galaxyp revisions: - 9c70a651a53e - - dd71e020e2aa - 43b9ed22e8ce + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 1b03536aa3c9 - 9020199dba0a - d063e2fe4ba4 - - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - f036e8cf1a55 - 78c080d36945 - ad2ba3a95a02 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 5c2a97a234d6 - - 7f6a1f27553e - c8b225c69a7f + - 7f6a1f27553e + - 5c2a97a234d6 - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -603,21 +603,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 7fdd9119cc4f - - 3634c90301af - - a72c48001f7c - 07ff622ec007 - - da885ca16cb2 - - 1beff3ddce58 - 943a34df6047 + - da885ca16cb2 + - a72c48001f7c + - 7fdd9119cc4f - 3ec27b4cee7c + - 3634c90301af + - 1beff3ddce58 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: - - a371252a2cf6 - - 265c35540faa - 1a5690a5eedc - 12692567c7f9 + - a371252a2cf6 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index a1e1ae682..5b78b8a8c 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,22 +2,22 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - cd5f98911089 + - 42201b90e3f4 - 110a346daf36 - - 289b7d6b69a4 + - cd5f98911089 - 2f1d464ebfd2 - - 42201b90e3f4 + - 289b7d6b69a4 - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: + - fcce77c09289 + - 0345dbaaa79b - 8501601a118d - 0cd2df8af811 - 42d9087b4789 - - fcce77c09289 - - 0345dbaaa79b - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,21 +25,21 @@ tools: owner: iuc revisions: - 405a212b32ab - - 04db7fd6b238 - 421c33b8bf17 - - ad5ab22ffe24 - 33486216eec0 + - 04db7fd6b238 - 89eb29319bf4 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - 7370bb65bad4 - - eb784fa07f80 + - 7b72fde3d27e - f6e91108b7b1 - fa51dc5e8386 - - 7b72fde3d27e + - eb784fa07f80 - 1d839ead7ad3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,62 +48,62 @@ tools: revisions: - a3e86cd9cac7 - 3d70c2996730 + - d30e36c48c93 - 1544278c272e - 8a55d29c8fcf - - d30e36c48c93 - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 564c33e5c3e3 + - a5969aa9347e - 887cf585cafc - e2db212d64ad - b242deb58952 - - a5969aa9347e + - 564c33e5c3e3 - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 9a171f9a450b - 8cff84759bf6 - - e897c74a48bb - b4bab607eb05 + - 9a171f9a450b - bd5ff77e2036 + - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 33f0793edf93 - - 4f65e343ecdf - - 887e0991eb24 - - adc7a7610d4f - 5e10f396979e - 6dafad990086 + - adc7a7610d4f + - 33f0793edf93 + - 887e0991eb24 + - 4f65e343ecdf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 43e3eeb2e0ec - c287418eb288 - - 17d39bf0a63a - - 4e280b27a831 - - c5d7050e4ad7 - 97575d01f06b + - c5d7050e4ad7 + - 4e280b27a831 + - 43e3eeb2e0ec + - 17d39bf0a63a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - - cd034465d4a4 - d9bf483266a1 + - cd034465d4a4 - 0b8c84a7fdb5 + - 9586f08634c0 - a819ec3b362d - 09b8edb56d80 tool_panel_section_label: RAD-seq @@ -111,22 +111,22 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - a4b4bd84f69e + - a9c34a289493 - 69842dd5aa48 - 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: - - bb0475c884ff + - d033e1ccb386 + - d1fda11e602f - cfb504394ae1 - 912f904a6e1e - - d1fda11e602f - - d033e1ccb386 + - bb0475c884ff - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -163,8 +163,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - 95286af4139b - d504d945a655 + - 95286af4139b - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 22a50fd15..bbef2d304 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,18 +2,18 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 7acb00fc980a - 2d4e3aff9dc7 - - 31f8063eedea - cf01dd6c6b1f + - 7acb00fc980a + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 7a5a2d28c539 - - 125d20cb23d7 - 703a2cb3fb38 + - 125d20cb23d7 + - 7a5a2d28c539 - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -33,8 +33,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: chira_collapse @@ -82,24 +82,24 @@ tools: - name: cuffcompare owner: devteam revisions: - - ad5d061fbdf2 - f648e5180e40 + - ad5d061fbdf2 - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: + - e04dbae2abe0 - d080005cffe1 - 6926716bbfb5 - - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 22cf48ad7b16 - 6a6717a5f421 + - 22cf48ad7b16 - 86285ddd4512 - cf747d1bd79a tool_panel_section_label: RNA-seq @@ -107,9 +107,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 28b94cfbfdb9 - 9a854107dbb2 - 6cbfede05833 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -135,29 +135,29 @@ tools: owner: iuc revisions: - 3b36efd62b3e - - 8f0181aacb7a - 0693ccd171c4 - e3b16fd7dd08 + - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 8fe98f7094de - 0696db066a5b - - d027d1f4984e - - 9a882d108833 - 24a09ca67621 - 6a3a025714d3 - cd9874cb9019 + - d027d1f4984e + - 8fe98f7094de + - 9a882d108833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 2872c633f07e - 62adf13b86ea - b47c006d90c5 + - 2872c633f07e - df929f257179 - 9a7c5b6d8f1e tool_panel_section_label: RNA-seq @@ -165,18 +165,18 @@ tools: - name: edger owner: iuc revisions: - - df0c8d0a5992 - - f2843df56434 - - 3d89af8a44f0 - - 0cb907a2a810 - - 5bf899c13979 + - 9bdff28ae1b1 + - 334ce9b1bac5 - 070900306913 + - df0c8d0a5992 - ae2aad0a6d50 - 555659de7321 - a8305cf0c951 - - 9bdff28ae1b1 + - 3d89af8a44f0 + - f2843df56434 + - 0cb907a2a810 - 6e53e565fc6a - - 334ce9b1bac5 + - 5bf899c13979 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -195,17 +195,17 @@ tools: - name: featurecounts owner: iuc revisions: - - af814359d244 - - a56fbe2d6ba7 + - 38b6d12edc68 + - f9d49f5cb597 + - a37612abf7f9 + - 90d16db017d7 - e6a2a912677a - - f3a5f075498f + - a56fbe2d6ba7 - ea04b737afa0 - - 90d16db017d7 - - a37612abf7f9 - - 7db9d3ea71c9 - - 38b6d12edc68 + - f3a5f075498f + - af814359d244 - 6f66ae7c5f7a - - f9d49f5cb597 + - 7db9d3ea71c9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -229,9 +229,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - - 0f710191a66d - 3c5e024a18cf + - 0f710191a66d + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -243,20 +243,20 @@ tools: - name: hisat2 owner: iuc revisions: - - 3fb01a8c902d - f4af63aaf57a - - 6c19daec423d - - 26371a1df031 + - 6ab42baa56e9 - a86e80d3c09c - d4b55e2beb12 - - 6ab42baa56e9 + - 6c19daec423d + - 26371a1df031 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 4418229c501e - 67b0b160903a + - 4418229c501e - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -269,33 +269,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 1c75aa5de15e - - 01247aaf0a10 - ce5d418183c5 - - 5ae5c312d718 + - 01247aaf0a10 - 87c11c05d238 + - 1c75aa5de15e + - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 + - c971db6f0fe5 - 4f9c4e6566e5 + - 40985510cd98 - 10c98fab6c5a - - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - e827f9aae031 - - 0921444c832d - 708348a17fa1 - - d6f5fa4ee473 - - 32511f586472 - 58c35179ebf0 - 119b069fc845 + - d6f5fa4ee473 + - 0921444c832d - 97e06a4c7c75 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -307,8 +307,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -351,21 +351,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4014de1b6daf + - c772497b2c32 + - e132e7d02a3e - 0a563fd2f22e - - 980d2a2e1180 - - 4074fc1940e2 - - 5ec75f5dae3c - - b0f2be869d6d - - 4df95e2d7f61 - 79de45b5069b + - 5ec75f5dae3c - 3ea5a2a63fa2 + - 980d2a2e1180 + - b0f2be869d6d - c7c55b694974 - - e132e7d02a3e - - b9e04854e2bb - - 99b17b74a8cd + - 4074fc1940e2 - 7ed2edc1337f - - c772497b2c32 + - 4df95e2d7f61 + - 99b17b74a8cd + - b9e04854e2bb + - 4014de1b6daf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -378,12 +378,12 @@ tools: owner: bgruening revisions: - e3d32471da11 - - 15cd64d7c58b - - 53e9709776a0 - cc05793bb896 - ebab418107f5 - - f4d5237a84f6 - 49121db48873 + - f4d5237a84f6 + - 53e9709776a0 + - 15cd64d7c58b - 2c0ca397d302 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -391,21 +391,21 @@ tools: owner: iuc revisions: - 8c28affc7c48 + - fab6ff46e019 - 56242ff81c84 - c0fd285eb553 - - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - 258d696dbd7e - - ae618321f34a - - cef79931dda5 - - 1ebd14235b92 - dd4df992d93d - cbf488da3b2c + - ae618321f34a + - 1ebd14235b92 - 76d290331481 + - cef79931dda5 - 914cfcba0ec8 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -436,91 +436,91 @@ tools: - name: transdecoder owner: iuc revisions: - - ffd1300599a1 - 0db979fead3a - - c6334cb383ff - d0d4cef4f967 + - ffd1300599a1 + - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - ba3720d7e68b - - bcc5f03f1900 - - d6a479fd4281 - 74217fbfba4d + - d6a479fd4281 + - bcc5f03f1900 + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 + - 56162e446004 - 2fb4ee002432 - c2b82a94493e - - 56162e446004 + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - - 9ff3765e7172 - 3f4094b6a565 + - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - - 34a018cbee9c - - 4687ecf0eb2d - be3f26533209 + - 4687ecf0eb2d + - 34a018cbee9c + - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 05ab8d5e04a2 - - 5192f657f305 + - c5fbddcac63a - 33406f5a445c + - 5192f657f305 - 65e7dea767ea - - c5fbddcac63a + - 05ab8d5e04a2 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 - c2c039e421af - 7c7fbf13aadd + - 964b7efe2639 - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 - - eafea3083352 - 1d689e4e1caf - 047c22569787 + - eafea3083352 + - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: + - 9871104ea630 - 04bb8bb7c198 - 3a4ac03d1266 - 1812dbc5bb7b - - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -538,15 +538,15 @@ tools: - name: trinity owner: iuc revisions: - - d84caa5a98ad - - d2bc35f3d1c5 + - c9cfec002f71 - 48636f857c4b - - 9fa24d5aac68 - - cee61b3fcf78 - 8f1c3df4dd49 - db1f362cca3e - - c9cfec002f71 + - cee61b3fcf78 + - d84caa5a98ad + - d2bc35f3d1c5 - 32b86cd8eb50 + - 9fa24d5aac68 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 233430f7b..ce45ca84c 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 27e16a30667a - - 080fd5739bb4 - 473382134e56 + - 080fd5739bb4 - 1a052c827e88 + - 27e16a30667a 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 b88aaf9ce..9c5409dfc 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -3,17 +3,17 @@ tools: owner: devteam revisions: - 10184eaa85fc - - 3c661e57a88f - 88eedb4abea0 + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - 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: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools @@ -76,8 +76,8 @@ tools: owner: iuc revisions: - 19ece8afbaab - - 30a201c9c310 - e7fd6754d093 + - 30a201c9c310 - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -103,15 +103,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -123,26 +123,26 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 + - 9149ad20699a - 6856f8a01905 - 12749212f61b - - 9149ad20699a + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 33208952b99d - - 06dc50b7b711 - 92ec40abcdcf - 26b4f9f98aca + - 33208952b99d + - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,11 +160,11 @@ tools: - name: samtools_fastx owner: iuc revisions: + - a8d69aee190e + - 720217c23995 - b3d99709fe1a - - 66e23b11feae - b906586a6596 - - 720217c23995 - - a8d69aee190e + - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate @@ -177,21 +177,21 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - db17d5321bad - - fefd89ab563c - - cc61ade70eb8 - 22970df7a40e - fe34990e5ce7 + - cc61ade70eb8 + - fefd89ab563c + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 + - 7a6034296ae9 - fa5d3e61e429 - - 7def34e6cf4d - 88b8c2916784 - - 7a6034296ae9 + - 7def34e6cf4d + - 811fc2d75ad4 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -205,36 +205,36 @@ tools: owner: iuc revisions: - 65a38e8c8e2a - - 740ce0a18f0d - - cae2794d2deb - 36677f429310 + - 740ce0a18f0d - b40e2d865d52 + - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - b61f5d6a7f25 - - 9da0311ab1dd + - 329deb17a9f7 - 8da515fbc1bf - 583abf29fc8e + - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - 85e38b31e8b3 - - 30388d878f81 - bb8cfc6f6e0c - db000c6007a0 + - 30388d878f81 + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -246,27 +246,27 @@ 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: - - 6c2c1836728b - - cab3f8d35989 - e613c1ad4c4c + - cab3f8d35989 + - 6c2c1836728b - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - - bd850490c7f1 - bcedabb53ddf + - bd850490c7f1 - 5d9ae78f34d3 + - b7f7826ef1cd - 818030fa6bbf - 135c85f4cfaf tool_panel_section_label: SAM/BAM @@ -276,24 +276,24 @@ tools: revisions: - 24c5d43cb545 - 5a08c09b9311 - - 145f6d74ff5e - 3a0efe14891f - 541082d03bef + - 145f6d74ff5e - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 350bbc5c2ffd - - b01db2684fa5 - - 2dce91e11ca7 - - 6be888be75f9 - 0dbf49c414ae - - c370440f901e + - b72793637686 + - b01db2684fa5 - 5826298f6a73 + - c370440f901e - bf328cec6a42 + - 6be888be75f9 - 32dc5f781059 - - b72793637686 + - 350bbc5c2ffd + - 2dce91e11ca7 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 4cea33b64..cb7f2e713 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: + - d147d6455873 + - a62c4a11a67d + - 5cb6146337d8 + - 59bb6d34fca6 + - 480d9e9d156b - 4aab5ae907b6 - 6f6537780379 - - 480d9e9d156b - ea5e944f447d - - 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 a27d277a3..3bb147ebb 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -10,98 +10,98 @@ tools: revisions: - e32b215b7c04 - f2000bc73102 - - c9944a2600f1 - ecb9ea6269ee - e4c01dcece8b + - c9944a2600f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - e1c3c2f2a834 - - c0b037b12765 - cfaf5a405371 - 707023fa62fe + - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - d330b3082107 - 32e547223c9e - cfc3f5a57dc6 - - 93dd15e13e6a - - 55e35e9203cf - fb9e030ffae4 + - 55e35e9203cf + - d330b3082107 + - 93dd15e13e6a - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 39e945f0b2c1 + - b9fac48532eb - 0bf7fddf90c7 - 6f0d0c784f09 - 688357ad5e61 - - ee98d611afc6 - 038e32885fec - - 39e945f0b2c1 - - b9fac48532eb + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - ed4996a16f7f - 3d748954434b - - d4af736e7b83 - 43cb7b5a6fe7 - - ed4996a16f7f - - 9bd945a03d7b - 7e8c677a7b71 + - d4af736e7b83 + - 9bd945a03d7b - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - fe75d2414dc0 - - a4774b7b2e85 - 2e8022f1923c + - a4774b7b2e85 + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 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: - - a90f8efe08b4 + - 344c2af50552 - aa4a6f0916b4 + - a90f8efe08b4 - c29e7bb492bf - - 344c2af50552 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - 5b7c81b35b89 + - b13d3e4c48e1 - 050cf43887d3 - c32347702e12 - - b13d3e4c48e1 - - 5b7c81b35b89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 02fc39c8610d - - 1d77986f9ddc - 239193b96d72 + - 02fc39c8610d - ae969fdb8442 + - 1d77986f9ddc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -171,36 +171,36 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - fb7068d30ec9 - 01c37e54e86e + - fb7068d30ec9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 57aeaf6b237d - 9d42a6133690 + - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 163fd744e235 - 23b8d6b8960c + - 163fd744e235 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 013e53ccc7ac - f47ac4a0b337 + - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -220,15 +220,15 @@ tools: - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - 40fee49bc6c3 - f881c94fb3b3 + - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -248,36 +248,36 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - 2ba6cee8e4db + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - ea19190ce5e0 - 62b720dceb56 + - ea19190ce5e0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -304,22 +304,22 @@ tools: - 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 owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - c261b6b05ee3 + - 55b013e59018 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains @@ -339,15 +339,15 @@ 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 owner: bgruening revisions: - - ea5d67ec94ab - dd9988943f53 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -407,19 +407,19 @@ 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 - - eeab712b0b99 + - 7784821452ac + - 59be31ac9dc3 - e98619de2776 - 0f1aaff9b22d - - 7784821452ac + - eeab712b0b99 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -431,9 +431,9 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 7ffaa0968da3 - 282819d09a4f - 2cfd0db49bbc - - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -446,8 +446,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -467,42 +467,42 @@ tools: revisions: - f911a64454fb - 0bff0ee0683a - - a4b734cd253b - - c4f39bf4a068 - 7e014059a88d + - c4f39bf4a068 + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - - b83fbc90161e - - 43c146e25a43 - 7608d5faee41 + - 43c146e25a43 + - b83fbc90161e + - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - f3eb2291da05 + - 37a47c4fd84d - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - - a6821f856a1e - - 69018f285aa3 - df8e4e54d367 + - 69018f285aa3 + - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - 72979cac22b2 - - e93b008c637a - 2af7c5086a96 + - e93b008c637a + - 72979cac22b2 - 44b935f2271b - c92d0f9338c5 tool_panel_section_label: Single-cell @@ -522,106 +522,106 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - 6acb08931836 - - aaa5da8e73a9 - f9353ee6a0d4 + - aaa5da8e73a9 - cb43c5d3acd3 - - 6f83f8fd381f + - 4d8f983cd751 - 38db3fef7aad + - b2df381a6004 + - 6f83f8fd381f - 77b91b9bdf52 - - 4d8f983cd751 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - a03ff8633507 - b409c2486353 - - fc0321c000a3 - - d636ce5cde16 - - 277313130da5 - a97abb8cd15b - - 8cb783c81905 - 3c86f71498bc - 72a6bebab2a5 + - 277313130da5 + - d636ce5cde16 + - fc0321c000a3 + - a03ff8633507 + - 8cb783c81905 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - f54f0f0598ad + - 5e9171dc8244 - 3081ff5c84a3 + - c5d3684f7c4c + - 6bd82ed14acd - c0a80a16560f - 6c145a6868cc - - 5e9171dc8244 + - 5c3ebe2adc77 - 18262103fa61 - - 6bd82ed14acd - 4338bf96809e - - c5d3684f7c4c - - 5c3ebe2adc77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 146ae5d70b47 + - 7b9fafe32c86 + - d844935c906c + - ab55fe8030b6 - 94c19fb1281c - a407e7f8bdc1 - - 7b9fafe32c86 + - 146ae5d70b47 - 9f354c7c8c92 + - 3bcd5445cd7a - 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: - - 9b0cdb8cf6be + - f7446fd8d5e7 + - 1072ce66b426 - 7647e5cd1b8b - - 95777145cb92 - - aa0c474463c2 + - 6f5349dd5c49 - 6adf98e782f3 - 0185bd174ea0 - - 1072ce66b426 - - f7446fd8d5e7 - - dbbe1ea8ecb1 + - 9b0cdb8cf6be + - aa0c474463c2 - 40812a65a78b - - 6f5349dd5c49 + - dbbe1ea8ecb1 + - 95777145cb92 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - c65fce500915 + - 458e8f43a775 + - 9fb627495ec2 - fe8f16c594ec - f2f6c703da06 - - a39040ae0a38 - - 215733a383f2 - bf2017df9837 - - c65fce500915 - - 9fb627495ec2 - - 73ab2ac53d06 - - 458e8f43a775 - d18e7a6e5cd4 + - 215733a383f2 + - 73ab2ac53d06 + - a39040ae0a38 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - b834074a9aff - fd808de478b1 + - b834074a9aff - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: + - b7ea9f09c02f - 652923ce664f - 7a365ec81b52 - - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -634,8 +634,8 @@ tools: owner: iuc revisions: - ef4c80837bc5 - - 81e5bdff4853 - 2e41b35b5bdd + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -647,8 +647,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - c99ba278dfa9 + - 9e5c0bb18d08 - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -925,8 +925,8 @@ 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/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index dcd70136a..b2b53e12e 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,47 +32,47 @@ tools: - name: datamash_ops owner: iuc revisions: + - 2f3c6f2dcf39 - 562f3c677828 + - 4c07ddedc198 - 746e8e4bf929 - 419027d822d6 - - 4c07ddedc198 - - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - cb1c59d69557 - - 6c29c7e347e8 - 7a15159140d1 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 9c3e1d3235c8 - - 4c4ec859c31a - aef56d0e7a61 - - 840f29aad145 - b1eda492f063 + - 4c4ec859c31a + - 840f29aad145 - 7442b94d6a1e + - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - - 30d21a6041f6 + - 07843f917990 - 375bbd555f4a - 9fda0b82f419 - - 07843f917990 + - 30d21a6041f6 + - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - 8b1b2b91f8d0 - - 4cc980df6265 - cd02bf168d23 - 2c58b83c9bad - 7ae443e6217d + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - 1dd433d2c92c + - e10e776f2109 - ad7e0b4291ee - 4bbaf77573ef - - bb9fc9d46ea4 - - e10e776f2109 - 7dd3fb35904f + - bb9fc9d46ea4 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 cc2e4f7fc..c4e9a6c98 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -27,21 +27,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 9cd341095afd - 13b6f0007d9e - - 6595517c2dd8 + - be25c075ed54 + - aff5135563c6 - 02026300aa45 - - 6e8d94597139 - 464b9305180e - - aff5135563c6 - - be25c075ed54 + - 9cd341095afd + - 6595517c2dd8 + - 6e8d94597139 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: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - - 90f657745fea - 557ec8d7087d - - 34d29339abab - 37cde8134c6a + - 90f657745fea + - 34d29339abab + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -113,21 +113,21 @@ tools: - name: query_tabular owner: iuc revisions: - - 623f3eb7aa48 - 1ea4e668bf73 - - cf4397560712 + - 83069b38aa85 - 2e8f945f7285 + - cf4397560712 - 3a6b78c39dca - - cf34c344508d + - 623f3eb7aa48 - 33d61c89fb8d - - 83069b38aa85 + - cf34c344508d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 - ae8c4b2488e7 + - 399da6b5ec21 - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,28 +142,28 @@ tools: revisions: - c4d18aa4ec4a - b722161a845a - - bce29ec10b78 - f768f6183386 + - bce29ec10b78 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: - - 74a8bef53a00 - - 12615d397df7 - - fbf99087e067 - - ddf54b12c295 - - d698c222f354 + - 9ff72e942410 - f46f0e4f75c4 - a6f147a050a2 + - 12615d397df7 + - d698c222f354 + - ddf54b12c295 + - 74a8bef53a00 + - fbf99087e067 - 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 7f02efb36..95aa22e1f 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,8 +14,8 @@ tools: - name: breseq owner: iuc revisions: - - 85c57cc9b558 - 82fb5e3bb93e + - 85c57cc9b558 - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,18 +34,18 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 - - ef2c525bd8cd - 57def2d7c093 - 156b60c1530f - a5937157062f + - ef2c525bd8cd + - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - e61c9ac190ad - 09d6e4693887 + - e61c9ac190ad - 435b157bed6d - 791f73caa0c8 tool_panel_section_label: Variant Calling @@ -53,13 +53,13 @@ tools: - name: lofreq_call owner: iuc revisions: - - b11e8e9c23bf - - dfadc322b065 + - e1461b5c52a0 - 3b4b2121842f + - 4805fe3d8fda + - b11e8e9c23bf - 65432c3abf6c - - e1461b5c52a0 + - dfadc322b065 - 03627f24605f - - 4805fe3d8fda - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -76,16 +76,16 @@ tools: revisions: - 426d707dfc47 - c27549b9aa1f - - 971e07ca4456 - f4473557ffc7 + - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - aa35ee7f3ab2 - - dbd9f2db9ed8 - cdaab621d454 + - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -142,20 +142,20 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 40f0591deda0 - e7aff4a85df5 - - 3b1e7c170b10 - ee4a90760848 + - 3b1e7c170b10 - 32f14a2723ec - - 40f0591deda0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - - 42818629ec4c - 02d81b994ef5 + - adc0645b945c - 9793bc5d741b + - 42818629ec4c - 4934c0ac6197 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index 1547afafc..65bd11289 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,327 +2,327 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - 2c372041ed8c + - 8a2e296c07ef - 95815a0bb307 - b7ea370b8f5d - - e075b1be5abb - 6a88248893c4 - - ebe5fc018e72 + - e075b1be5abb - 265fe0f9ea64 - - 8a2e296c07ef - - 2c372041ed8c + - ebe5fc018e72 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call owner: iuc revisions: - - 21687e35f066 + - 22637b1a55bf - 07396b423218 - - c37b684e7f4e - 544cb432072b - 1001172b5089 + - c37b684e7f4e + - 21687e35f066 - b03984136ce4 - - 22637b1a55bf - 0fba2c15b40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv owner: iuc revisions: - - 01d6b7d6365e - - 143796b504eb - - 8627b2b383b4 - bf1f4994f104 - 3a7084316a6e - - 0238f68ad641 - ccb83bf54de0 - 8ca3647c90fd + - 8627b2b383b4 + - 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