From 09368d49fa6954e279f4f1fdfdb133ebdb7a5e18 Mon Sep 17 00:00:00 2001 From: admin Date: Tue, 8 Oct 2024 03:04:29 +0000 Subject: [PATCH] Jenkins install build 1649. --- automated_tool_installation_log.tsv | 2 + requests/gtn_20241004.yml | 9 - staging.gvl.org.au/annotation.yml | 126 ++++---- staging.gvl.org.au/assembly.yml | 266 ++++++++--------- staging.gvl.org.au/bacterial_typing.yml | 4 +- staging.gvl.org.au/bb_tools.yml | 8 +- staging.gvl.org.au/bed.yml | 16 +- staging.gvl.org.au/blast.yml | 10 +- staging.gvl.org.au/chemicaltoolbox.yml | 58 ++-- staging.gvl.org.au/chip_seq.yml | 10 +- staging.gvl.org.au/collection_operations.yml | 6 +- staging.gvl.org.au/convert_formats.yml | 40 +-- staging.gvl.org.au/deeptools.yml | 124 ++++---- staging.gvl.org.au/dna_metabarcoding.yml | 6 +- staging.gvl.org.au/emboss.yml | 2 +- staging.gvl.org.au/epigenetics.yml | 6 +- staging.gvl.org.au/fastafastq.yml | 104 +++---- staging.gvl.org.au/fastq_quality_control.yml | 30 +- .../fetch_alignmentssequences.yml | 2 +- staging.gvl.org.au/filter_and_sort.yml | 4 +- staging.gvl.org.au/gemini_tools.yml | 28 +- staging.gvl.org.au/genome_editing.yml | 8 +- staging.gvl.org.au/get_data.yml | 44 +-- staging.gvl.org.au/graphdisplay_data.yml | 74 ++--- staging.gvl.org.au/hca_single_cell.yml | 32 +- staging.gvl.org.au/hicexplorer.yml | 26 +- staging.gvl.org.au/imaging.yml | 68 ++--- staging.gvl.org.au/ivar.yml | 72 ++--- .../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 | 20 +- staging.gvl.org.au/metagenomic_analysis.yml | 144 ++++----- staging.gvl.org.au/mothur.yml | 8 +- staging.gvl.org.au/multiple_alignments.yml | 56 ++-- staging.gvl.org.au/nanopore.yml | 62 ++-- staging.gvl.org.au/none.yml | 56 ++-- staging.gvl.org.au/phylogenetics.yml | 96 +++--- staging.gvl.org.au/picard.yml | 12 +- staging.gvl.org.au/proteomic_ai.yml | 14 +- staging.gvl.org.au/proteomics.yml | 204 ++++++------- staging.gvl.org.au/rad_seq.yml | 68 ++--- staging.gvl.org.au/rna_seq.yml | 166 +++++------ staging.gvl.org.au/rseqc.yml | 4 +- staging.gvl.org.au/sambam.yml | 74 ++--- staging.gvl.org.au/send_data.yml | 8 +- staging.gvl.org.au/single_cell.yml | 184 ++++++------ staging.gvl.org.au/statistics.yml | 28 +- staging.gvl.org.au/text_manipulation.yml | 40 +-- staging.gvl.org.au/variant_calling.yml | 38 +-- staging.gvl.org.au/vcfbcf.yml | 276 +++++++++--------- staging.gvl.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 116 ++++---- usegalaxy.org.au/assembly.yml | 234 +++++++-------- 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 | 10 +- usegalaxy.org.au/chemicaltoolbox.yml | 62 ++-- usegalaxy.org.au/chip_seq.yml | 12 +- usegalaxy.org.au/collection_operations.yml | 10 +- usegalaxy.org.au/convert_formats.yml | 42 +-- usegalaxy.org.au/deeptools.yml | 112 +++---- usegalaxy.org.au/dna_metabarcoding.yml | 12 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 6 +- usegalaxy.org.au/fastafastq.yml | 94 +++--- usegalaxy.org.au/fastq_quality_control.yml | 28 +- usegalaxy.org.au/filter_and_sort.yml | 4 +- usegalaxy.org.au/gemini_tools.yml | 26 +- usegalaxy.org.au/genome_editing.yml | 2 +- usegalaxy.org.au/get_data.yml | 48 +-- usegalaxy.org.au/graphdisplay_data.yml | 66 ++--- usegalaxy.org.au/hca_single_cell.yml | 16 +- usegalaxy.org.au/hicexplorer.yml | 20 +- usegalaxy.org.au/imaging.yml | 62 ++-- usegalaxy.org.au/ivar.yml | 74 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 2 +- usegalaxy.org.au/machine_learning.yml | 44 +-- usegalaxy.org.au/mapping.yml | 52 ++-- usegalaxy.org.au/metabolomics.yml | 30 +- usegalaxy.org.au/metagenomic_analysis.yml | 170 +++++------ usegalaxy.org.au/mothur.yml | 8 +- usegalaxy.org.au/multiple_alignments.yml | 54 ++-- usegalaxy.org.au/nanopore.yml | 40 +-- usegalaxy.org.au/none.yml | 54 ++-- usegalaxy.org.au/phylogenetics.yml | 94 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 10 +- usegalaxy.org.au/proteomics.yml | 196 ++++++------- usegalaxy.org.au/qiime_2.yml | 2 +- usegalaxy.org.au/rad_seq.yml | 54 ++-- usegalaxy.org.au/rna_seq.yml | 166 +++++------ usegalaxy.org.au/rseqc.yml | 6 +- usegalaxy.org.au/sambam.yml | 86 +++--- usegalaxy.org.au/send_data.yml | 8 +- usegalaxy.org.au/single_cell.yml | 168 +++++------ usegalaxy.org.au/statistics.yml | 28 +- usegalaxy.org.au/text_manipulation.yml | 40 +-- usegalaxy.org.au/variant_calling.yml | 38 +-- usegalaxy.org.au/vcfbcf.yml | 270 ++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 102 files changed, 2789 insertions(+), 2784 deletions(-) delete mode 100644 requests/gtn_20241004.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 9a68dfb7e..d1361fc81 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7884,3 +7884,5 @@ Update 212 02/10/24 18:00:28 use_theoretical_mz_annotations False Installed rece Update 212 02/10/24 18:01:05 vcffilter False Installed devteam 4bdc111b2470 4bdc111b2470 VCF/BCF toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_212/install_log.txt Update 212 02/10/24 18:01:43 vcfsort False Installed devteam ee60203e68d9 ee60203e68d9 VCF/BCF toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_212/install_log.txt Install 1645 03/10/24 15:00:53 kmc True Installed galaxy-australia 87ddc8ca7859 87ddc8ca7859 11/11 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1645/install_log.txt +Install 1649 08/10/24 12:32:57 ctb_im_conformers True Installed bgruening a4b1474efada latest 1/1 ChemicalToolBox toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1649/install_log.txt +Install 1649 08/10/24 13:04:04 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_1649/install_log.txt diff --git a/requests/gtn_20241004.yml b/requests/gtn_20241004.yml deleted file mode 100644 index 0641b1b39..000000000 --- a/requests/gtn_20241004.yml +++ /dev/null @@ -1,9 +0,0 @@ -tools: -- name: gprofiler_gost - owner: iuc - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ctb_im_conformers - owner: bgruening - tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index ec2914c28..50b9d25a1 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - c2ef298da409 - - 3f3e247c053d + - 6e9aea89e388 - 78c75f134c16 + - 3f3e247c053d + - c2ef298da409 - 4efdca267d51 - - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -33,30 +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: - 133f36c29579 - - 4f2967b27e67 - - 1aae04680c4b + - 3e1f6f6d557e + - a79ee60b6926 - 44018dd6b447 - cd2480f35935 - f29602ae449e - - fe3ca740a485 - - 3e1f6f6d557e - - a79ee60b6926 - b5d8e5475247 + - 4f2967b27e67 + - fe3ca740a485 + - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -70,26 +70,26 @@ tools: - name: augustus owner: bgruening revisions: - - ca6d970d931c - 09855551d713 + - ca6d970d931c - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - 92eee5f31117 - 728dacaf08a9 - - d77802fe76f7 - da5f1924bb2e + - d77802fe76f7 + - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - 8fd427007e93 - 7355bbf5e05f - fe48aa4ccd5e - - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -115,16 +115,16 @@ tools: owner: bgruening revisions: - 8e9e228c54c4 - - 1ac12c0cc7a0 - 7ccc6234b54e + - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: + - 63662ae295d6 - 9d1fbff733cf - d9c3016f7283 - - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -148,61 +148,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 14f588312c56 - - 3bbe70fef6df - - 582fd74dc2a1 - - 9c15ca7e764e - b6b5cd37f2a2 - - 9f2455341fac - 756376aeb1ae + - 9f2455341fac + - 14f588312c56 + - 9c15ca7e764e + - 582fd74dc2a1 + - 3bbe70fef6df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - a230ea445788 - 1691af4a0d17 + - 8e1ace8f77c6 + - 0ffe5be70caf - 73428a792541 - - 989f7c061f35 - 30fb23d4c31c - - 0ffe5be70caf - - a230ea445788 - - 8e1ace8f77c6 + - 989f7c061f35 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: + - 5a5ae61da69c + - 494f0bb4a993 + - 563a19373357 - 0418d28136de - 30f08d74024f - - e94187d661df - - 494f0bb4a993 - 57c6718cbfcc - - 5a5ae61da69c - - 563a19373357 + - e94187d661df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: + - 4b96ced19f75 - 2bba2ff070d9 - - 7abc5f6dd595 - - 1bc5a03faf2e - - f77d7b685bb3 - f31125bb85ea - d6c7106b7b2e - - 4b96ced19f75 + - f77d7b685bb3 + - 1bc5a03faf2e + - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 52af33194019 + - d3af38b9c7e1 - b3cf4684e9c7 - 520e30695ec3 - - d3af38b9c7e1 - 54961e026fe4 - d77fdcca400e - fed64e676186 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -215,8 +215,8 @@ tools: owner: iuc revisions: - 79261884facd - - 07d7991bf205 - 2aea122fbd25 + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -228,10 +228,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - - 602de62d995b - 43798b4caee0 + - 602de62d995b - 8b3e3657034e + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -255,16 +255,16 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: + - c55643c3d813 - 74810db257cc - 98cafcbd2578 - - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -282,15 +282,15 @@ 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: - - d46d803ca6cc - 3c1a01127868 + - d46d803ca6cc - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -298,10 +298,10 @@ tools: owner: iuc revisions: - 624606f7c996 + - 033755194fe9 + - e95d52d295d7 - b815ec682418 - c8ac28e8ac44 - - e95d52d295d7 - - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -343,9 +343,9 @@ tools: - name: prokka owner: crs4 revisions: + - a17498c603ec - d643e3b03500 - bf68eb663bc3 - - a17498c603ec - eaee459f3d69 - 8a22554cdde2 tool_panel_section_label: Annotation @@ -366,8 +366,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -391,22 +391,22 @@ tools: - name: snpeff owner: iuc revisions: - - 268d162b9c49 - - 5b80f544c67f - - 5c7b70713fb5 - - 6322be79bd8e + - 8f92c2b26e6d - 5a29ab10dba6 - 68693743661e + - 6322be79bd8e - cfcf33df7fc0 - - 8f92c2b26e6d + - 268d162b9c49 + - 5b80f544c67f + - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - - 2b3e65a4252f - 5fab4f81391d + - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -418,8 +418,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -431,24 +431,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - e1a9d6fd258d - - ba6f87115e13 - - 51dd22484644 - - 45083d070fb8 - - 200c378d85f3 + - d03af1c7002c - 37213cf56392 + - e1a9d6fd258d + - ac8250086ac3 - 037a11682176 - - d03af1c7002c + - 51dd22484644 + - ba6f87115e13 - 4839e590cb26 - - ac8250086ac3 - 809dfc93d593 + - 45083d070fb8 + - 200c378d85f3 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 758018e3c..0f732512c 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: - - 553bfe8bd0b5 + - 8f1b150a2487 - 841084c5fc46 - - 0e93176640ac - - d6d5ccc2c581 - - 0124fce4654a - - a929ce596a34 - 890b794c997d + - 0e93176640ac - fa5259cc561b + - 553bfe8bd0b5 + - 0124fce4654a + - d6d5ccc2c581 - 7547fcab5d19 - - 8f1b150a2487 + - a929ce596a34 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - ddddce450736 + - b9e31c5c01c7 - 067592b6b312 - - b2860df42e16 - - 94fe43e75ddc - 21e491ad532a - - b9e31c5c01c7 + - 94fe43e75ddc + - ddddce450736 + - b2860df42e16 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -35,40 +35,40 @@ tools: - name: bionano_scaffold owner: bgruening revisions: + - 22286dab5aa1 - 3371c5bdc17a - a7f16f24e9a1 - faee8629b460 - - 22286dab5aa1 - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 8c2167481e72 - 53dd00a4ab68 + - 8c2167481e72 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - cf13a1e03e5b - - 94170eee0ad8 + - bb935709506a + - 0d243f458b53 + - 4048d82f0c88 + - e824f5d958d0 + - 1e62c28ba91d + - 5ecdeca79a0d + - 41030a6c03b7 - 46ae58b1d792 + - 2babe6d5c561 + - 94170eee0ad8 - e4bd1e99bacf - - 1e62c28ba91d + - 2dd755c1c6ff + - cf13a1e03e5b - 1440ae06552f - - 5ecdeca79a0d - f18f0b887c31 - - 2dd755c1c6ff - - 2babe6d5c561 - - bb935709506a - - 0d243f458b53 - - 41030a6c03b7 - - 602fb8e63aa7 - - 4048d82f0c88 - ea8146ee148f - - e824f5d958d0 + - 602fb8e63aa7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu @@ -88,42 +88,42 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 - - 8d4f03b5fe9d - - e27815e82dd4 - - cb8dfd28c16f - 3e4f8642c77e - - 1f0769f0b56b - 1ce9b1d72ec3 - - 3ee0ef312022 + - e27815e82dd4 + - 1f0769f0b56b + - 8d4f03b5fe9d + - 276f5d8712d5 - 291923e6f276 + - cb8dfd28c16f + - 3ee0ef312022 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 3169a38c2656 - 01210c4e9144 - b2f674562a18 - 460fad600dce - - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - ba88bc5a6446 - - 8b330a577046 + - 06bcf65179fb - 7348b69e5109 + - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3ef480892a9f - - 5127a713de83 - 3fba9c77550a + - 5127a713de83 - 690c2caa367e + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -135,23 +135,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 0ee0c3089254 + - 5bec28269d95 + - da9d8bf98802 + - 284a1cb82b61 + - 60024a528cbd - ec9e21e9c71b - 5f625c63b8bc - - 9ef6920c3089 + - 366a11d316a7 - f3c89da3af16 - df25d4fb79b7 - - 3f7be05a1597 - - 284a1cb82b61 - - da9d8bf98802 - - 2061fb3b81b4 - - 6505bd37670d - - 5bec28269d95 - - 045c7c3d8e59 - - 366a11d316a7 + - 0ee0c3089254 - 71740308d412 - - 60024a528cbd + - 2061fb3b81b4 + - 3f7be05a1597 - 41cea2aa2dce + - 045c7c3d8e59 + - 9ef6920c3089 + - 6505bd37670d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -169,43 +169,43 @@ tools: - name: megahit owner: iuc revisions: + - a96f3ad4e0d8 - 7518ee87b53d - 14ddfc8ffb93 - de387b2b2803 - - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - - f8113c25bc6b - 9d79beb19ac3 - - d7edbc9c3a07 - 09c589057ee8 + - f8113c25bc6b + - d7edbc9c3a07 + - 39edec572bae - eb7b00ec347d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - eadfd71dde37 - 29dabd8db6f2 - 51c2360aa807 - - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - fd128c111ab0 - - f369ef5f210b - - e731ea24e48d - - f338e9942b27 - 2ecf5a570907 - - 99ecfdafc64f - - 606b09cc9860 - eb7a370f6588 + - f338e9942b27 - 3ca2d2a9068c + - 99ecfdafc64f + - 606b09cc9860 + - e731ea24e48d + - f369ef5f210b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -217,11 +217,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8b6d0d85252b - - 8dee0218ac7d - - a7b889b90140 - 73a3846701e1 - b799a615995d + - a7b889b90140 + - 8b6d0d85252b + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -239,8 +239,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 7c2f5268d01c + - 64a1c751d99b - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -253,46 +253,46 @@ tools: - name: pretext_map owner: iuc revisions: + - 79b48f02db49 - dfb8a4497339 - - 2b16ba799da9 - - bbe19ef04a74 - 8fef980d48b5 - - 79b48f02db49 - - 02831bf9e95f + - bbe19ef04a74 + - 2b16ba799da9 - d256a51a656b + - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - - 76d4cbefff85 - a315c25dc813 + - 76d4cbefff85 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 3061c8b029e5 + - 7594365c546b + - 72472698a2df + - 342a1d1fed7b - 59db8ea8c845 - 6fcbee531de6 + - 875d0f36d66f + - 3061c8b029e5 - 675488238c96 - - 72472698a2df - - 7594365c546b - ebb0dcdb621a - - 342a1d1fed7b - - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 + - cd06929b224b + - 78c533842eeb + - 39bed8de8017 - d865b62f501c - aa39b19ca11e - - 39bed8de8017 - - 78c533842eeb - - cd06929b224b + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -310,12 +310,12 @@ tools: - name: raven owner: iuc revisions: + - 5c55448d0f33 - 2b2a352488fa - - 33b7d8481a76 - - 3edba9afc9bc - f8564b2d7f63 + - 33b7d8481a76 - f11b994b7eb2 - - 5c55448d0f33 + - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -328,13 +328,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - - 1d06c8b38e77 - - 5fc94b3a4704 - - 378e55aeeb25 - ef69617ecb42 - e122f9101584 + - 1d06c8b38e77 + - 378e55aeeb25 + - 53c2bc8c2ae3 - 28189050e437 + - 5fc94b3a4704 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,20 +346,20 @@ tools: - name: shovill owner: iuc revisions: - - ad80238462c1 - - ee17a294d3a3 + - d9f6a00b6db7 + - 865119fcb694 - 83ead2be47b2 + - ad80238462c1 - 196a599ec43d + - ee17a294d3a3 - f698c7604b3b - - 865119fcb694 - - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - 015283de3004 + - 24e471d13fe9 - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -367,138 +367,138 @@ tools: owner: iuc revisions: - 604782a8a53a - - c33a476f4001 + - 1fc82fe7ebef - 1bb12736175c - - 7490b213baa9 - 051fd2db8a27 - - 1fc82fe7ebef + - 7490b213baa9 - 904bf932cf78 + - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - d6e617c4e338 + - 655fa188c3cc - ad8b536d1caa - - fee85957cebe - - 34305b013402 - 808b3a0a6716 - 9678993ca5bd - - 655fa188c3cc + - d6e617c4e338 + - 34305b013402 + - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 6b5a5842531e - 7e27faaad80e - - e5a3b75a271f - - 037f9927c4ff - b8002c3f7141 - - 8d4b90bf9caf + - 037f9927c4ff + - e5a3b75a271f - 21da31ed41a1 + - 6b5a5842531e + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 328aa71f0f3c - - 2a10645aeadd - - 5b26685e5d3b + - 86f66ab58e14 - 7922870efcca + - 2a10645aeadd - f1532cb33c75 + - 5b26685e5d3b - 9de69775f512 - - 86f66ab58e14 + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 8cc856b935ee + - e41dcb0e913b - 340bc17f49cf - - 85fb02c43042 - - 1708851f8804 - 6aad515a5270 - - e41dcb0e913b + - 1708851f8804 + - 85fb02c43042 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - b3490b036c5a - d159735a6a9f + - 249f6a28c751 - d5fb354f745d - 6357b127161e - - de1260f8a300 - - 249f6a28c751 - b65a43f70b99 - - b3490b036c5a + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: + - b7829778729f - a90db5dbaaf3 + - dd7ad84f3943 - 7897763d14ec - 33368fec3b70 - - 9006e5836729 - - b7829778729f - d2d1df21dfb9 - - dd7ad84f3943 - d5887ace0dd4 + - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - 505a9833ab5d + - 8f631679571f - ced385aa976d - 189e837009c9 - - 8f631679571f - - 6f4c8ad6ea01 - - 505a9833ab5d - ed2425b9fd27 + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: + - f31d376ce725 - 9ded6109434a - - 356afed970b4 - - 19bdfd1e6fe3 - d40ed4eb0c0e - - f31d376ce725 + - 356afed970b4 - e59bee4565b3 + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - ebd801e712bc - - af40e971a8cc - 4688ae3b49b5 - - b23249f81bc4 + - ebd801e712bc - 80a17897564d - 6dd935e4984b + - b23249f81bc4 + - af40e971a8cc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - b5e35a2ca4f3 + - b64696992ee9 - bb11fefb23a3 - 59bd28f6265d - - b64696992ee9 - cb1e3db43020 - - b5e35a2ca4f3 - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 2628f6790eda - 6015aa0303f2 - - cb4768eeca3b - - 6bfab4a4a988 - 05bd7504fdb2 - - 2628f6790eda + - 6bfab4a4a988 + - cb4768eeca3b - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -507,30 +507,30 @@ tools: revisions: - 0a3a602cd1e3 - 9e3e80cc4ad4 - - 3e44ef016b45 + - 6e26c9afd301 - 8f9f06995f98 - e92675014ac9 + - 3e44ef016b45 - e022dff952df - - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 920677cd220f - - 8d09f8be269e - 5da9a0e2fb2d + - 8d09f8be269e + - 920677cd220f + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 0e2b4e3f9ca1 - d81360ea69d8 - - 4a53b89fa703 - - 82398ba86ba7 - 37d88f41c810 + - 0e2b4e3f9ca1 + - 82398ba86ba7 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 7804ad643..ca41eb5b1 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: - - bfd290fe1588 - 4768f7f8e93f - 1ae00120dd24 - 392f100eebcd + - bfd290fe1588 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -18,8 +18,8 @@ tools: owner: iuc revisions: - 8e8dc9a1e3e5 - - ded48b36f3b7 - 1f5641a52664 + - ded48b36f3b7 - 31812e7a1315 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 83e935453..9ce523402 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 1c427e24fb79 - - 204a131e47db - 7beb76ffbc0f - - a9c9d768b751 - - 0840ba83860c + - 204a131e47db - d1f62024a08b + - 1c427e24fb79 - 159b04e36791 + - a9c9d768b751 + - 0840ba83860c tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index ae8d77957..1db0144ee 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: - - dde39ba9c031 - - b28e0cfa7ba1 - - 87ee588b3d45 - - a68aa6c1204a - - 64e2edfe7a2c - - 589e7e57fd6d - 0a5c785ac6db + - a1a923cd89e8 + - 87ee588b3d45 - e19bebe96cd2 - a8eabd2838f6 - - ce3c7f062223 - - a1a923cd89e8 + - b28e0cfa7ba1 - 07e8b80f278c + - 589e7e57fd6d + - dde39ba9c031 + - a68aa6c1204a + - 64e2edfe7a2c + - ce3c7f062223 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 60273f651..2cd83209d 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,8 +9,8 @@ tools: owner: bgruening revisions: - 62c9df8382c2 - - 54f751e413f4 - e8ac2b53f262 + - 54f751e413f4 - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 5edc472ec434 - cbf3f518b668 + - 5edc472ec434 + - 2889433c7ae1 - d999e774072a - - acf4e47b734c + - 6f386c5dc4fb - e25d3acf6e68 - - 2889433c7ae1 - 0e3cf9594bb7 + - acf4e47b734c - a52d2d93e595 - - 6f386c5dc4fb 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 97b22a652..9992cc575 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - c8cdde00b105 - - f4230f116196 - 710301bc46fa - 6ca543ec1bf8 - - 095ad4d096d1 - - da6bd1975a71 - 27ee142314a9 + - da6bd1975a71 + - f4230f116196 + - 095ad4d096d1 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -96,6 +96,12 @@ tools: - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu +- name: ctb_im_conformers + owner: bgruening + revisions: + - a4b1474efada + tool_panel_section_label: ChemicalToolBox + tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_rxn_maker owner: bgruening revisions: @@ -124,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 - 79cfd9ead848 - - 88076940fa94 - bfb65cb551d8 + - 88076940fa94 + - 3b8a9d5ced85 - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - b46d4b4d995c - - 55918daa5651 + - eb6564a60136 - 715cd0e87781 + - b46d4b4d995c - d532b7e5f64b - - eb6564a60136 - f5d979cb4b54 + - 55918daa5651 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 5579659312e6 - fdf2cc80adb5 - 97872d87ba80 - d2f955aea23a - f26afd1b7104 + - 5579659312e6 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 - - 2c349b027a01 - ed736e6eee39 + - 2c349b027a01 - 070e3ecc3fda + - cac1886249a2 - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 - - c0c9a5024177 - - f197e34c33a9 - - d1f803b5943c - 525ca7c8065f - - 2e219a2d9327 + - d1f803b5943c - 73008ef1f487 + - 2e219a2d9327 + - da8753545526 - 807aa4c9293d + - f197e34c33a9 + - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 2c8ed1b52bf7 + - 1809414a9454 + - 61094e01eff9 - 27ea4e1a3f95 - c4fbab8e03c5 + - 2c8ed1b52bf7 - 7568ae18908a - - 61094e01eff9 - - 1809414a9454 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -205,9 +211,9 @@ tools: revisions: - 79e8ab8f1e81 - ba83f0923369 + - ccfbd956a2d3 - d7ec25187599 - 730ef07b90ae - - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -262,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - e6011617c748 + - b59c91adeac1 - 4242b4d68e9c - 1400d1977e7b - - b59c91adeac1 - - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -277,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 7672039a0bb0 - 75ee9c410951 + - 7672039a0bb0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -333,9 +339,9 @@ tools: owner: bgruening revisions: - 9b48456a96fe + - bf99565cec1f - d4c67ced6abc - 85fad59f8168 - - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index b0b1024f2..83fe043ac 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 - - c97a786e8fb5 - fa56d93f7980 + - c97a786e8fb5 - 163688bb8f73 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -30,10 +30,10 @@ tools: - name: macs2 owner: iuc revisions: - - 424aefbd7777 - - 495a4173006f - 640d3af5d833 - 86e2413cf3f8 + - 495a4173006f + - 424aefbd7777 - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,8 +53,8 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 - 4a14714649b4 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 8b53bde6d..da39336a4 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -10,9 +10,9 @@ tools: owner: nml revisions: - 25136a2b0cfe - - 33151a38533a - 90981f86000f - 830961c48e42 + - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -32,9 +32,9 @@ tools: owner: bgruening revisions: - 6cbe2f30c2d7 - - 0046692724f9 - - baabc30154cd - 2dae863c8f42 + - baabc30154cd + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 62a91c012..300c44608 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: - - e7449b2c14bf - abba05ead5d7 + - e7449b2c14bf 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: - - f3a19509108a - - 3b6f97e7094c - - 0b3c3ad92827 + - e3cbd2287f63 - 5e1240a87bcb - - a3b86937ead6 + - 3b6f97e7094c - 6ef0b5664c69 - - e3cbd2287f63 + - 0b3c3ad92827 + - ab9350a8ab4d + - f3a19509108a - 367b1ed91207 + - a3b86937ead6 - 4a6ee918c13a - - ab9350a8ab4d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - 091bb5922a82 - - 501c21cce614 - - 584008e574b2 - - d4d4e9febf5c - - e525f9ffb9ac - bd46669113b9 - 72ed72122deb + - 33c99804a32f + - d4d4e9febf5c - e177a8ea0bf1 + - 584008e574b2 + - e525f9ffb9ac - 1b5fc03380d4 - 54ccb7e1f49a - - 33c99804a32f + - 501c21cce614 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,16 +59,16 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 186b8d913e6c - - 77b41c89d856 - 8979c288aefb + - 77b41c89d856 + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -100,9 +100,9 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - 154d00cbbf2d - 4dea02886337 + - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -120,8 +120,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 705821bf30d2 + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram @@ -141,18 +141,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - 19e45916daf9 - - 63769c4217a7 + - b9b385097f13 - 92ac8e086317 - 26c6706bfb07 - - b9b385097f13 + - 63769c4217a7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 46328a680..77423a5a0 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,85 +2,85 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - 268e91e540ee + - 29451af70c52 - 5f6d123679f4 - de72ba3ed6f2 - a1ca9bccc7f2 - - c929a006727f - e821645ef8fc - - 268e91e540ee - - 29451af70c52 + - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e143b4c3987 - - bb1e4f63e0e6 - 12af64f93288 - - 5d11599b8a7d + - bb1e4f63e0e6 + - 7a7fd0f5f15d + - 0e143b4c3987 - 0e49b109abc2 + - 5d11599b8a7d - 2d2cf5c1ea8a - - 7a7fd0f5f15d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - dc059492a995 + - 7c1beb6d6eca - 195e98217334 - 81b1e3e1fc6c - - 7c1beb6d6eca - - c06951d10364 + - dc059492a995 - 1d848bc4585f + - c06951d10364 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 71aa86af6762 - - 26e7304d6737 + - 3d211717a775 - 93eb012d9eed + - 07418a30ed01 - a67ac707496a - bfff7454b59a - - 07418a30ed01 - - 3d211717a775 + - 26e7304d6737 + - 71aa86af6762 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - 56d5b797ce84 - - b8858746dc1f - - 26983857c91a - - 29fcfd36e90a - 2bc10a9ca58b - - dd0b7398bb96 - 5be24eba848d + - 29fcfd36e90a + - b8858746dc1f + - dd0b7398bb96 + - 26983857c91a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - e6d0bff01239 - - c3e012dfe21f - 7ef978dc1b8a - 9384cd033f30 - - 72bfafe3330b - - ee3a1b0f45f1 + - e6d0bff01239 - 7e6bcd2e5128 + - ee3a1b0f45f1 + - 72bfafe3330b + - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 167788df3b46 - - 9470f29702f8 - - b73e213add0c - a60c359ec43c + - 9470f29702f8 + - d9a637e83828 - fd1275e01605 - - 514fa53b5efb - fb9cf9c97ec4 - - d9a637e83828 + - b73e213add0c + - 514fa53b5efb + - 167788df3b46 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias @@ -90,117 +90,117 @@ tools: - e479c7ca5570 - ca0616bb2cdf - 2c37ce318bc3 - - 5bffaa8354a1 - - c34d11ea4ba6 - a02cfa31e9cb + - c34d11ea4ba6 + - 5bffaa8354a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - 2d466b530754 - - 69a8621ca2f0 - 192ef85c0b0b - - 01fb6a7654e6 + - 004aea905d4d - 78f405266706 + - 01fb6a7654e6 + - 69a8621ca2f0 - 1fcb7adc39b8 - - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 - - d580d6acd1df - 137c4beed34b - - d9ce4897dbb2 - 3c9f0c486cca + - d580d6acd1df - 2f9e4843f480 - - 459cfa861f0b - db940c262830 + - d9ce4897dbb2 + - 9ecba5e225a6 + - 459cfa861f0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 2c66e43f1c86 - - fbe773640707 - - bad3ca889618 - f264afa9fa6f - - fd408d755394 - bd7db9e2f2cb + - bad3ca889618 + - fd408d755394 + - fbe773640707 - 32e451def88c + - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7fda5607e777 - - 4e12ea27f788 - - 9368fbc49c8b - - 7e361d147872 - 56bce3c82278 + - 7e361d147872 - 231994413f89 + - 9368fbc49c8b + - 7fda5607e777 - 3b9d990a0a0e + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 94ca68515826 - - d9114ef1c8a5 - - e65d16fb2724 - c03c3384cd81 + - e65d16fb2724 - 4431f39ede55 - - b1779366c8e9 - ce4ce3316f74 + - b1779366c8e9 + - 94ca68515826 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 2da482e408b8 + - d57251071381 + - b88ebb3672a1 - 4ed32329e0ed - - 793665fff0f8 - f8fc4e5aff9d + - 793665fff0f8 + - 2da482e408b8 - 23f7c5f1fdaf - - d57251071381 - - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - c60570fa602f + - ba6efa77fb79 - 25d830337d31 - - 512155688d98 - e4c7985d4585 - - a7849312d328 + - c60570fa602f - a4dfb122e52b - - ba6efa77fb79 - 010e58e9d822 + - a7849312d328 + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 443d9a9d6d11 + - 00d869ea03a1 + - 69264da0ce77 + - 38e3f226248b - aa200e4f3939 + - 443d9a9d6d11 - c899e0ccff8c - 4d678170d29b - - 38e3f226248b - - 69264da0ce77 - - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - c361b12d207a - - a2d70c4fd406 - 10301d137111 - 6662b1a8d326 - d806504e96d9 + - a2d70c4fd406 + - aac8444d6681 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 f4312a7d1..ee87345b5 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -16,8 +16,8 @@ tools: - name: obi_convert owner: iuc revisions: - - e328ced6cf0a - 4d705e3443a7 + - e328ced6cf0a tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -30,15 +30,15 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index aaf7a1b11..08bf8c016 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -4,7 +4,7 @@ tools: revisions: - dba489bfcd62 - 63dd26468588 - - ce385837c160 - 832c20329690 + - ce385837c160 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 f5cb27350..da8dc7575 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 62f5fab76dfb - - 29bdbc353f20 - d82648ad25a3 - - cf1322aeb137 + - 29bdbc353f20 - 6da3972210ee + - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 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 71b9e563d..371ffd65a 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5eb7e84243f2 - - 49370cb85f0f + - 48f587c13075 - b1c926deaa2d + - c5e2e5902201 + - 44e2cc14f75b + - 093678460093 + - fe74900d6dc7 - 4e5056fefd88 - - c053d4cad713 - de6cebe3c043 - - 44e2cc14f75b - - 8c0175e03cee - - 48f587c13075 - - 660cffd8d92a - - c4b82dce8335 - - e4691e1589d3 - 64172f1c1202 - 135b80fb1ac2 - - 8665bcc8b847 - - fe74900d6dc7 - 288f97432497 + - 5eb7e84243f2 + - 8c0175e03cee + - 8665bcc8b847 + - c053d4cad713 + - 660cffd8d92a - 5915ea1ec9b1 - - c5e2e5902201 - - 093678460093 + - c4b82dce8335 + - e4691e1589d3 + - 49370cb85f0f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,9 +39,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - 9db07fd39f85 - - 8889eb864cef - f666895cbebd + - 8889eb864cef + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -53,8 +53,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - de2db1bdfbf8 - 7d37cfda8e00 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -73,16 +73,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - 8cacfcf96a52 - e626b3ff9922 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - - 859422bcb689 - 516b97a23d7e + - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -101,9 +101,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - ec0b5076173a - f81d4362b6c1 + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -117,8 +117,8 @@ tools: revisions: - cd0874854f51 - 0dbb995c7d35 - - 9c620a950d3a - 56022eb50bbd + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -131,10 +131,10 @@ tools: owner: iuc revisions: - d60c3f704da0 - - c59d48774d03 - - 1d8fe9bc4cb0 - 65b93b623c77 + - 1d8fe9bc4cb0 - dbf9c561ef29 + - c59d48774d03 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -167,15 +167,15 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -202,8 +202,8 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - 35e38452bb3f + - 249c8393f2d4 - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -216,9 +216,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 54053ea6c77e - 045f0e1043f7 - 74db4cffab1f - - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -250,9 +250,9 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 09070cacefd8 - - d5e9e83cd3d8 - 567d5b3c52b1 + - d5e9e83cd3d8 + - 09070cacefd8 - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -265,9 +265,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -279,10 +279,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 736b8f6ee456 - - bdf1ce174e39 - cb1e251cac37 - 90858c306551 + - 736b8f6ee456 + - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -294,9 +294,9 @@ tools: - name: fastx_collapser owner: devteam revisions: + - 7ce1891db6f5 - 07497255281e - 421f0af4ee95 - - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -308,10 +308,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - 02f8a17a4ebd - - b29d37ca9e41 + - 3599f5451ee2 - f984bb114520 + - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -323,9 +323,9 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: + - e246088b6e34 - 0c2907307ba4 - 6027ef51ef91 - - e246088b6e34 - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -338,10 +338,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - 61b4cedc8934 - 377ac2829eac - 73194cdd4f57 + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -365,10 +365,10 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 + - b4c6f054210a - f69501361cec + - 037f0acc7830 - 2f804526f5fd - - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -380,8 +380,8 @@ 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 @@ -401,8 +401,8 @@ tools: - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -420,16 +420,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - - bf04bd405d5b - 71f649c23021 + - bf04bd405d5b + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -441,11 +441,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - e654095ab143 - - a535cf1e5da4 - - 8250ea3a1501 - b557acca0b56 + - 8250ea3a1501 + - 24013bf85a6f + - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -464,12 +464,12 @@ tools: owner: iuc revisions: - 015cf18f4a15 + - 828dba98cdb4 - 7accf7407811 + - f3759eec3018 - 9fa7803d1c51 - - 27ac32a22ad2 - 6a675c3aa610 - - f3759eec3018 - - 828dba98cdb4 + - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -487,7 +487,7 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 953b4821b183 - 4c8a1c7d3608 + - 953b4821b183 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 ecb94587c..ba5bf222a 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,75 +2,75 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 - - 64e9a6afdd0c - e41385662e5e - 7b4468117008 + - 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: - - e7b2202befea - 9da02be9c6cc - - 2b0c9d9fc6ca + - ff9530579d1f - f2e8552cf1d0 + - e7b2202befea - 5ec9f6bceaee - 3d0c7bdf12f5 + - 2b0c9d9fc6ca - 2c64fded1286 - - ff9530579d1f tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - ad116ae3f4d9 + - 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 - cc0fd298cc17 - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - a72af9de6bf5 - - 1f296803dfa3 - 8880fb74ef56 + - 1f296803dfa3 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 9a913cdee30e + - 75c93c70d094 - f7985e0479b9 + - 9a913cdee30e + - 1c2db0054039 + - b2f1f75d49c4 + - abfd8a6544d7 - 3d93dd18d9f8 - f7e2f1eb3a16 - - b2f1f75d49c4 - - 1c2db0054039 - - 75c93c70d094 - 5e33b465d8d5 - - abfd8a6544d7 - bf675f34b056 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 0dfc5355c..c01999d90 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: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 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 85c239a05..b248d7a64 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -16,7 +16,7 @@ tools: owner: peterjc revisions: - 83a19df00eab - - 85ef5f5a0562 - 141612f8c3e3 + - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 12c3f5809..0e067e78f 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -9,15 +9,15 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,45 +86,45 @@ tools: - name: gemini_load owner: iuc revisions: - - b2c25142267e - 45296e47d565 + - b2c25142267e - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c 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 owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - da74170c55c7 - 840fb4850be3 - 666f60a9331a + - da74170c55c7 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: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -158,14 +158,14 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 659e8a5eb..28aa17fae 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,29 +2,29 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 077116581..2b3817d19 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - e9df53a75f3c - - c1b437242fee - 983bf725dfc2 - b39347891609 + - e9df53a75f3c + - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,52 +17,52 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 1c58de56d587 + - e063168e0a81 - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1790dcf3c32d - - 4317d3cb6cba - - 653e89d73fc4 - - f8054ea1c365 - - aad3885b3216 - - 6591f049cf7e - - 8848455c0270 - - e407b9da183a + - 1ec814014652 - c441583adae5 - - 734abc7ac21d - - ba931a59dd59 - - 83c7d564b128 - - 7068f48d0ef9 + - e407b9da183a + - 653e89d73fc4 - 516a54ddf218 - 4df8de2d0e48 - - e08a7ad4378b - - 5e6237d58b0c - - 6ea73833cf67 - 9a776b080193 + - ba931a59dd59 - 69ebb7f46e45 - - 1ec814014652 + - f8054ea1c365 + - 7068f48d0ef9 + - 8848455c0270 + - 83c7d564b128 + - 734abc7ac21d + - 6ea73833cf67 + - 4317d3cb6cba + - 1790dcf3c32d + - 6591f049cf7e + - aad3885b3216 - f5ea3ce9b9b0 + - 5e6237d58b0c + - e08a7ad4378b tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - 9aaa46d45472 - - 21a560af5913 - 34758ab8aaa4 + - 75b3b3d0adbf + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a - af5eccf83605 + - bfdc6a7ffd3a - 468c71dac78a - 054483e27a35 tool_panel_section_label: Get Data diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 009447977..eaedea8b2 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: - - a64dc31ab7f2 - - c4bde687c846 - - 740057a5126d - - fd59d783248a - 4b519282a05b + - fd59d783248a + - c4bde687c846 + - 7f13dc906cb9 + - a64dc31ab7f2 - 290a11559985 - - ae9994cf526f + - 740057a5126d - df7356989ac1 - - 7f13dc906cb9 + - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,54 +48,54 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 + - 374e9062d874 - 3b37b1b1c3a7 + - 53460afd5115 - ca7cb0eaad62 - - 374e9062d874 - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 3d059e9c2fba + - 391a4cc45fea - 1a72f938213e + - 10515715c940 - da4c086cff5b - d3a9e32672ec - - 3d059e9c2fba - - 10515715c940 - - 391a4cc45fea 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: - - ae344ccf9d62 - b1268b7544d3 + - ae344ccf9d62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - 5fe1dc76176e - - e3a675da7fd0 - - 1acf88921176 - d0fc8b746d57 + - 1acf88921176 - 5298e06f14f9 + - 299307abd804 + - e3a675da7fd0 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 - - 2bb2e07a7a21 + - 17359b808b01 + - 1cfc579079a6 + - 836d1aa3e89a + - 112eb40ba6cf - fd5dbf0f732e - - 6cd09d7b5f37 - 4542035c1075 - - 667e17248bfe - - 1cfc579079a6 - - 17359b808b01 - a6e57ff585c0 - - 112eb40ba6cf - - 836d1aa3e89a + - 2bb2e07a7a21 + - ca2def38369c + - 667e17248bfe + - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -176,17 +176,17 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c - - f234e2e59d76 + - 85da91bbdbfb - 1c5dcef5ce0f + - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -198,9 +198,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 6c571966cfb9 - 7c9417381ad5 - 44c66e8d21e6 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -212,23 +212,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 2824d77cd8f8 - 326a3db8d9d1 + - 14e7c35f3d00 - 36b848d5f3ec + - 2824d77cd8f8 + - a1abfa420d9d - 4ac4e7083b7e - 7dd841a32245 - - 14e7c35f3d00 - - a1abfa420d9d - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd - - 83c573f2e73c - 44608d0193ed + - 73b8cb5bddcd - 2f557f6abbfb + - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index ed3faedf5..e9f6c47c0 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,50 +21,50 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells 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: - - cc64914b0cf4 - 23d838d1569d + - cc64914b0cf4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - 36735850e461 - fc4b3b46dc9d + - 36735850e461 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - d8f5224005bb - 0a8e527d1517 + - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes 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 @@ -84,16 +84,16 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - 9a2f72d7dbd2 - - ff6decc0f432 - 94697510d55f + - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -106,15 +106,15 @@ tools: - 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 owner: ebi-gxa revisions: - - 73d43034c860 - d4c9061c8fef + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -148,8 +148,8 @@ tools: - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - d18ed15697bb + - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -183,29 +183,29 @@ tools: - 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 - 0f98603d0116 + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 7782e4dea..e6c75aac2 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -3,49 +3,49 @@ tools: owner: bgruening revisions: - ed2cca6b5de4 - - 29f66c353bcb - 921a2da49a0c - - 9edf8894a22d - a4c13ddcc8ee + - 29f66c353bcb + - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 5746d61f0a91 - - d404277cc87a - - 78fb5e286609 - 755df866ad0c + - d404277cc87a - ec4b948dc6f0 + - 5746d61f0a91 + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 03dd3c16ae4e - - 977dc15add20 - - 4d511437b1e5 - 11fa44ee0603 - 9e357a8b2ec3 + - 4d511437b1e5 + - 977dc15add20 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 77919cc3618e - - 41dbf4d162a2 - 3b5b54ed6392 - - 0ba4f56a3613 + - 77919cc3618e - c3e5e2cf12b7 + - 0ba4f56a3613 + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e - 12d51d7be66f - - 7babd8a46fe0 - 5308ca68ef3d + - b63363075c2e + - 7babd8a46fe0 - 9939786dd9c9 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 d69252e34..94115c1d6 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,45 +2,45 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 0c777d708acc - 8bccb36e055a - - 81f0cbca04a7 - 699a5e9146b3 - - 3df9f0a4bf34 + - 81f0cbca04a7 - 7db4fc31dbee - - 0c777d708acc + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 2436a8807ad1 - - 5bc8cdc17fd0 - 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: - - 6ad1d3cfdea1 - - 9d47aabda459 - e576b73a2e2f + - 9d47aabda459 + - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: + - b1c2c210813c - 70316d792fc9 - 77f7159d775a - - b1c2c210813c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - - dba87c4b32d3 - d51310ab328a + - dba87c4b32d3 + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert @@ -48,8 +48,8 @@ tools: revisions: - f3360fbeda64 - 85edbb7a436b - - fcadded98e61 - 10eed33aa9b2 + - fcadded98e61 - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,39 +63,39 @@ tools: - name: count_objects owner: imgteam revisions: - - 664232d2a3f7 - b58447a2eed2 + - 664232d2a3f7 - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: + - e917a2424690 - 0e4dccaafef5 - eb6c08714244 - - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - 670975e92458 - 6070780813d9 - e7273daa5ae2 + - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -110,33 +110,33 @@ tools: - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - f2ed92b011a9 + - bace5a93a97c - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - d0178bdcd00e - f8fa0f6718a3 + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - - ad271f78a87a - 3245681b2f6d + - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -151,48 +151,48 @@ tools: owner: bgruening revisions: - 667a513e67e4 - - b178453ea8d1 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - a1a961c46d4b - 2564f461de62 + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: + - 20dbb1f7ec7b - 91e03287f285 - a32c3f810ade - - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - e972e07c7845 - 6f4715b8540a + - d3890df07463 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 @@ -206,9 +206,9 @@ tools: - 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 @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 48102a685037 + - 3a3033222f61 - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 33f4fa1413fb - 4ecf93628f97 - 27edbb90ab2b - - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,8 +242,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -255,9 +255,9 @@ 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/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index b9621bb89..9834aff8d 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: - - 3a72fede57ce - - 78bbd17d0703 + - 3e4f434a69c6 + - 40737febe339 - a38934e303b9 + - 3a72fede57ce - e4ee04da1c19 - - d6e72da3ec35 - - 3e4f434a69c6 - e319b5b65879 - f362150bef41 - - 40737febe339 - 1069f6db0a0e + - 78bbd17d0703 + - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 7fe36019c073 - - 8f8df367470d - - 0135f1d487a0 - - 9537184d421f - fcbeda41d0ac - - 618297d23022 + - 9537184d421f - f91cfb73d369 + - 7fe36019c073 + - 2b95d5c04908 - c88553ec696e + - 618297d23022 - 72ddd32392cd - - 2b95d5c04908 + - 0135f1d487a0 + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 - - ad0dc9f4c9e2 - 2cf4a1cafc16 - fafb3d685fa9 + - ad0dc9f4c9e2 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - a1c2aecd7a0d - 8d36959b000d - - 43aac8d29685 - - 94df24c6bc00 - - 3d18f8c3c0f6 - - 9eaadf03e0df - - ee29337f905c - - 5dc33613c288 - bd2a7d1316b9 - - 8c05afb547fa + - 5dc33613c288 - 7f1cfa4c0e32 + - 3d18f8c3c0f6 + - 9eaadf03e0df + - 94df24c6bc00 - 28a6f1908fcc - - ee2beb764a7b - 6a1515bb0687 + - a1c2aecd7a0d + - 43aac8d29685 + - ee2beb764a7b + - 8c05afb547fa + - ee29337f905c tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - a250929be21b - - c092052ed673 + - cb903c9dc33d - 5d6ed46cc101 + - a250929be21b + - bcaa0d571ce2 - 9f978da6528a - - cb903c9dc33d + - 8858fa037a15 - 5671e1d3d5ee - 364f4ffec275 - - bcaa0d571ce2 - - db536ad45f28 - - e3bb03cf207a - d37ede8589b2 + - db536ad45f28 + - c092052ed673 - 86a20ae274fc - - 8858fa037a15 + - e3bb03cf207a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - ed28dd32141c - - 584beffa972b + - f95f403841ad + - 194e3ceee923 - c5c9f02b6167 - - 230b05597996 - - 12d66d0d05ac + - e1a015876aa9 - abbc8041e8ec - - 194e3ceee923 - 49236b03e4fd - - e1a015876aa9 - 3b6a16d82c1b - - f95f403841ad + - ed28dd32141c + - 584beffa972b + - 230b05597996 + - 12d66d0d05ac - 38b91a3190cd 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 2897d7922..29fb32c4e 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - 17e3b698dd52 - - f198773344e4 - 0f1724dd59d2 + - f198773344e4 - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu @@ -12,9 +12,9 @@ tools: owner: iuc revisions: - 374cb875d38a - - 22c2a1ac7ae3 + - ac092723240d - ba0c40780ecf + - 22c2a1ac7ae3 - a513e3fbb4c5 - - ac092723240d 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 f9a0457f6..16722bb8a 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,37 +2,37 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 522137aaa9c4 + - 66d7efc06000 - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: + - 8a794e6d3388 - f22a9297440f - 4d81e3e2fb63 - - 8a794e6d3388 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - 818f9b69d8a0 + - e1317b5502fa - 2af1346e68c9 - - b6ef6d0cb6b7 - f1b9a42d6809 - - e1317b5502fa + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - - 947c2eacccb8 - - 1588f9076e32 - 05143043ca13 + - 947c2eacccb8 - 8334dc98c48e + - 1588f9076e32 + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction @@ -40,18 +40,18 @@ tools: revisions: - 1552b8cb4a94 - 9991c4ddde14 - - 29e4122c90de - 83228baae3c5 - 25b46af53232 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 1a53edc4b438 - - 060ca94ac049 - f3dfa4bdf87e + - 1a53edc4b438 - a07ab242b0b5 + - 060ca94ac049 - 53616c8b0865 - 841a6cc5fc58 tool_panel_section_label: Machine Learning @@ -60,41 +60,41 @@ tools: owner: bgruening revisions: - 2fc89dcd41c8 + - 927586a18553 + - dc4b5fd604a6 - d4808d5b83da - - 91c4e3331208 - 40f4447733b2 - - dc4b5fd604a6 - - 927586a18553 + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 25ab6b4e376e - 7626ea9c2e1b + - c6ae57f774c6 + - 25ab6b4e376e + - 301e07345c93 - 36e8d6d5d01b - e5a5ad882f1f - - 301e07345c93 - - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 - - 02d2be90dedb + - 4ed102b922cb + - 0630258dcf35 - 80852884053f - f9639b488779 - - 0630258dcf35 - - 4ed102b922cb + - b7c3e9a3b954 + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 61634a87efc7 + - ec69cbe34b73 - caeb57858702 + - 61634a87efc7 - 14180f9c831e - - ec69cbe34b73 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 c47982fc8..1a9e5ff1d 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: - - 749c918495f7 - d5ceb9f3c25b - - 03e9b2fbc005 + - 017aba02828d + - 937aa69e715f + - a6d65b0c67af - 3ba8d4563129 + - f6877ad76b00 - 0d4acadabb04 - - a6d65b0c67af - cd659e8cc5fa - - f6877ad76b00 - - 017aba02828d + - 03e9b2fbc005 + - 749c918495f7 - 17062a0decb7 - - 937aa69e715f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - 3fe632431b68 - 53646aaaafef - - 2477830927ec - dfd8b7f78c37 - - 64f11cf59c6e + - 3fe632431b68 - e188dc7a68e6 + - 2477830927ec + - 64f11cf59c6e 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 + - 60afcc2c1d05 - 37b497aa133f - 3e1ea2facca6 - 2ff111fac1d7 - - 60afcc2c1d05 + - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 09b53c1d4ab1 + - be1d967337e4 + - 11a0d50a54e6 - f54f5baedfdd - - 8c6cd2650d1f - 53c0b7a1a0c3 - - 5cc34c3f440d - - 6b1e195506a3 - - be1d967337e4 + - 037c6e54df11 + - 09b53c1d4ab1 + - 8c6cd2650d1f - b3eab4b67562 - 3f4d6399997b - - 77b2770508f6 - - 11a0d50a54e6 - c0c2d0941de8 - - 037c6e54df11 + - 5cc34c3f440d + - 6b1e195506a3 + - 77b2770508f6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 42ce70172b72 - - 79b885ce78d7 - - 5ef7ec16b04f - - e403d27e8f24 - 45795f582ae9 - - b8f5f6e87f5c - - ec9cbd6b9a49 - - 13022c3d3076 - - 178bdbdb6d24 - - 1cd2511a396e - 9ee34ba73ebf + - 5ef7ec16b04f + - 1cd2511a396e + - 79b885ce78d7 + - ec9cbd6b9a49 - 00fbfac99d39 + - 178bdbdb6d24 + - b8f5f6e87f5c + - e403d27e8f24 + - 13022c3d3076 + - 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 f830f120e..f2b80eb76 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -128,8 +128,8 @@ tools: - name: matchms_metadata_match owner: recetox revisions: - - 1d443ed476a1 - 03bc9b7f40f6 + - 1d443ed476a1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -241,8 +241,8 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - 5f2b58dadb39 - f2c1d0bbb074 + - 5f2b58dadb39 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr @@ -256,32 +256,32 @@ tools: owner: recetox revisions: - 79ad928a0dae - - 7b42ee54d757 - c53a97599181 + - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: + - 149b9cc7499b - 18ec7635bac6 - f3a18e020cdd - - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - dfebc82ba1f0 - - 481d769e2f7a - 134be5abb208 + - 481d769e2f7a + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 02c772a49998 - 51332c2520c7 - 9064aecc78a7 + - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table @@ -295,9 +295,9 @@ tools: - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - dd7bbc2b99d1 - cf061712a184 - 17a48d0a80f4 - - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals @@ -312,8 +312,8 @@ tools: owner: recetox revisions: - d90187b0f247 - - ea0758b41473 - ffbabefbd2e2 + - ea0758b41473 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -344,8 +344,8 @@ 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/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index c96f611bc..f41ba92a3 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,8 +8,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 0e63d03c8790 - 18676df0cb3a + - 0e63d03c8790 - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -96,29 +96,29 @@ tools: owner: iuc revisions: - 63f86089423e - - 65db807336bc - 7c2100246a2f - - 76d3d2b10738 - 5b5a7af9fbb4 + - 76d3d2b10738 + - 65db807336bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 18a502a9d287 - 96336c6a2bb7 - 1c35dadbe76f - - 84fd33a60b35 - 00f5005840fa - - 18a502a9d287 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - a9f4a217dcd6 - e8fba04706d3 - - f732237754fc - 34e55239e68b + - f732237754fc + - a9f4a217dcd6 - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -127,69 +127,69 @@ tools: revisions: - 5fe3edf19b9c - 8c202e741d68 + - 04c15826a0b8 - 75403243703a - 0776d824d896 - - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - e96bbb9e24ea - - 75c8945b0da2 + - 8470de786d47 - 1c9b3bcd4261 - 43c99742158b - - 8470de786d47 + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - - 84743da21318 - 306a40d4bb8f - 35176674168c + - 84743da21318 + - 1d75bd0595e2 - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 78faebd0879c - - ac72310b038a + - 8daf4564ccda - 32c9ea835770 - 555ccac8a4c5 - - 8daf4564ccda + - 78faebd0879c + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - cae017b76acb - a58e4a43f49c + - 7b8cb2b02978 - f947b4bb5107 + - cae017b76acb - d60df8727f59 - - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7f3b59dee073 - 073608a50ac3 - - 04144473e59e - - 1bc3657cd694 - 7136e9ab70db + - 1bc3657cd694 + - 7f3b59dee073 + - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - d943081510da - - 9058d8943303 - 0a1224c4b781 + - 19299bb1c6af - a7817705348e + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -202,14 +202,14 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - f8f56dd6449f - - 65d52c693b8e + - b907a3c0434f - 4d9445dff47b + - 65d52c693b8e - 5c7ba3d85a01 - - b907a3c0434f + - dbf1798c0dcc - a68b985913ab - c4db8c4de66f - - dbf1798c0dcc + - f8f56dd6449f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -222,9 +222,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6c84982ee6f7 - 6d364c65c946 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -237,23 +237,23 @@ tools: owner: iuc revisions: - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - - d77397f09da1 - b084117133af + - d77397f09da1 + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 9704f1a3b32d + - cad93abecac9 - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -286,38 +286,38 @@ 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: - - e88b731dad59 - c409a495841f - - 79706f10d680 + - e88b731dad59 - 31c6d107e7a5 + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c - - 172920f67a84 - 71ea608ddfa3 - - 094ad9c068af + - 172920f67a84 - d24841f5c3d2 + - 094ad9c068af + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - a293a742194f - - 12fb63b5f63f - - 2bdd84912a2b - 4137b492233e - a4d7148ccee4 + - 12fb63b5f63f + - a293a742194f + - 2bdd84912a2b + - d7e9a3c41657 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: - - e2c71b852aba - - a92c06a3afa7 - 6fcb8ac37a3e - - 64bc7acc22a9 - cf87759761eb - - 97f7bb0851e7 + - a92c06a3afa7 - 75bedfb2078b + - 64bc7acc22a9 + - e2c71b852aba + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -354,20 +354,20 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 080ea153677c - c82508e76ad1 - 5e5a999ffaa9 - - 080ea153677c - - 4033827c76b8 - 2d35528d2141 + - 4033827c76b8 - 4e5e73d03f0d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - fc6c328c292f - 6b7622dda516 - 2cd76b089570 + - fc6c328c292f - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -441,17 +441,17 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 - 4a9da2b6c2e3 - 20e2f64aa1fe - 328c607150ff + - 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 @@ -509,8 +509,8 @@ 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 @@ -522,8 +522,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -560,21 +560,21 @@ tools: owner: iuc revisions: - 3cc4a60615c0 - - e073891b2afc - 2cff76cf35c6 + - 27250f92a01a - 7f5d7b0e9884 - - 0270541aaf46 - 327d9f4cc95f + - e073891b2afc - 4fd3b5d8706b - - 27250f92a01a + - 0270541aaf46 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - eb50e7eca3dc - 76bc4efa1aeb - 708abf08a626 - - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -647,19 +647,19 @@ tools: - name: metaphlan owner: iuc revisions: - - fd69c607b43f - - 2131d7dca455 - - ff8f55893e7d - - 6dee4abadccb + - 1a037928504c + - ec368db926f4 - 1a6cdf55390f - - b89b0765695d + - a92a632c4d9b + - 2131d7dca455 + - fd69c607b43f - a16313517e55 - 289b3807e80c + - b89b0765695d - ef65b083bd0c - - ec368db926f4 - - a92a632c4d9b + - 6dee4abadccb + - ff8f55893e7d - 740fd2d16a28 - - 1a037928504c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -712,22 +712,22 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions owner: iuc revisions: - - 677f3c8db525 - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -739,8 +739,8 @@ 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 @@ -801,13 +801,13 @@ tools: - name: staramr owner: nml revisions: + - 4d83eccf5f81 + - be818ae858e4 - 4b9a8031ab74 - 141afacabcfa - - aeaa20b96ef2 - 2fd4d4c9c5c2 - - 4d83eccf5f81 - 3b22de20bd4b - - be818ae858e4 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -837,8 +837,8 @@ tools: - name: vsearch owner: iuc revisions: + - 9495df9dd6ef - b3c7199d8786 - 576963db5f1b - - 9495df9dd6ef 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 f3b33a02e..d64c813ba 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 7238968f58f7 - ab12df91b47f + - 7238968f58f7 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -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/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 153f25796..a54c8c4bb 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: - - bdfbaf0c10aa - - 9422c5a87ee2 - - 098506c54016 - - 8b67dd48fec1 - 9baa871cb1d1 - 48c13389050d - 80f03df2e2ce + - 8b67dd48fec1 - 94b8c6013083 - - a74dbfee5a86 - - 6ae5a7b5a0a2 - - cd07731e4434 + - bdfbaf0c10aa - 2263989660f5 - 9eeb13a92d79 + - cd07731e4434 + - 6ae5a7b5a0a2 + - 098506c54016 + - a74dbfee5a86 + - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 3ff17bad4006 - - c18157c68134 - f14193ec1f50 - - aaa0d6a8b808 - 2e093badc689 - - f0af8936ed41 - fc2e49f91e52 - - be78f13134e2 - - 4a60927aaca5 - - d390fe1567dc - '764845535798' - - d7ce0ec78e51 + - 4a60927aaca5 + - aaa0d6a8b808 - bc3831dd65c1 + - d390fe1567dc + - f0af8936ed41 + - be78f13134e2 + - 3ff17bad4006 - 5abf2c2249aa + - d7ce0ec78e51 - c44f824c051a + - c18157c68134 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,15 +46,15 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -66,61 +66,61 @@ tools: - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - f1a5908ea2cb - f0d493f8f84f - - bf28a8cff401 - - 15974dd17515 + - c5908940967d - 8e649f27aa0d + - f1a5908ea2cb + - 15974dd17515 - 6f28e90db932 - - c5908940967d + - bf28a8cff401 + - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - b3acbb3a6af0 - fbca557a4847 - e8fdceffea4c - - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - 60698466facd - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - bcd65de9725b - - 48823c9635a4 - 57f042937ba7 + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - fb43e8887350 - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: + - 7cd7a55a678d - e18267f90096 - 636b049e6141 - - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - 959c1f8dae95 - - cf3c9489c088 - b4124df98b26 + - cf3c9489c088 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 8af9ed226..454d16183 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,16 +8,16 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 28928576e1ea - 7c47b3c9e493 - 18a8d140ec6f + - 28928576e1ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado owner: galaxy-australia revisions: - - 63d8ecfcfab1 - fc5b6491cf78 + - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -29,21 +29,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - - 72b5e9dda577 - 79e9a869f40e - - 0e9e7fcdd543 - a7228a7ea146 + - 0e9e7fcdd543 + - 72b5e9dda577 + - fc8804320156 - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae + - fa11aa8103b2 - 18505fe2bdb1 + - d6cddc06aeae - db25ec99c3ea - - fa11aa8103b2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -55,22 +55,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - ec699520444c - - 2bf63b38ee9b - - 19f3b583a9b3 - edf6d4003fad - - 0f5f4a208660 - - eb746fa6f514 - 222669c4afb6 - - cc36773a3681 + - eb746fa6f514 - 43815fa60f3a + - 19f3b583a9b3 + - 2bf63b38ee9b + - cc36773a3681 + - ec699520444c + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -82,21 +82,21 @@ tools: - name: nanoplot owner: iuc revisions: + - a38bdcec9e4c - edbb6c5028f5 + - a02b8b3f5a0c - a3c4fe6f49ab - - 7b379e98b9a9 - - a38bdcec9e4c - 645159bcee2d - - a02b8b3f5a0c + - 7b379e98b9a9 - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: + - 3b6f94fc7e1d - 85a394edc247 - d219b6d8158a - - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation @@ -111,15 +111,15 @@ tools: owner: bgruening revisions: - d376944466bf - - 4857d5bcce52 - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - de5b3d8f5b90 + - bec636361cfd - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -127,22 +127,22 @@ tools: owner: iuc revisions: - 5f76b20953e5 - - 543cbeef3949 - 93d623d9979c + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - daf8518d243a + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract owner: iuc revisions: - - 08064da7b7fb - 7e4f1ed70187 + - 08064da7b7fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_hist @@ -155,16 +155,16 @@ tools: - name: poretools_nucdist owner: iuc revisions: - - 5c4fa65f5733 - a57b6350fd5d + - 5c4fa65f5733 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - - 338d15b8d6fb - 0433aad600e9 + - 338d15b8d6fb + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -177,16 +177,16 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 626b6c2be5c2 - 2e22ebec211a + - 626b6c2be5c2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - - ce8af9373061 - 26e6c9362b7b + - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -198,8 +198,8 @@ tools: - name: poretools_tabular owner: iuc revisions: - - 2cb2feb94f0e - 5f5f1da94d7f + - 2cb2feb94f0e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_times @@ -218,8 +218,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 5be71e221..9fea002f1 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -28,8 +28,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 96d2000977ab - 58341ad4fb42 + - 96d2000977ab tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -59,18 +59,18 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - baceff842902 - - d74850cf4e42 - - adfd6bf710bd - 3e73c97f025d + - adfd6bf710bd + - baceff842902 - 97b1b5ad1cda + - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - 9dd107db92c2 + - 83da94c0e4a6 - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -83,11 +83,11 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - ed1518ce2237 - 2f27f3b86827 - e4b4837f06f5 - - ed1518ce2237 - - 1e34d2e3d285 - edacc4bcd3cb + - 1e34d2e3d285 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -113,9 +113,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 38ccd4589990 - 48a42ca61006 - 5711fc06a63e - - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -128,8 +128,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -155,31 +155,31 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - b4b2b284230a - - 27a6a256cd23 - 5bcf0e24f42c - 172815da3d41 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - df84aaed4769 - 10232d2b5062 + - df84aaed4769 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -192,8 +192,8 @@ tools: owner: iuc revisions: - 19bbd19b74b3 - - fea85c467896 - 87febc68b45b + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -206,8 +206,8 @@ 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 @@ -225,36 +225,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 + - 0cb27ea69dc1 - d8dc037e3c13 + - 5fe20c915fa6 + - 9c43baa60906 - 4ba60cb14cb0 - 2c61c30a57e7 - - 0cb27ea69dc1 - - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 9d09724f2bf1 - - aec831b54a5b - 0db22932bc39 + - aec831b54a5b + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: + - df30a2f1db55 - 6e24e79d3d69 - ed7a967cb11b - 29c738066906 - - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -273,8 +273,8 @@ tools: owner: devteam revisions: - ad90c2da4f38 - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -293,17 +293,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - 64deddb6a8ec - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 625fd9476402 - 94a50db37d1a - 9946bc39c834 - - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1053,8 +1053,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbcavity @@ -1081,10 +1081,10 @@ tools: - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - 58a870ef434c - - 9a22227bb6d0 - ba7b0f11e470 + - 9a22227bb6d0 + - ab5b7f6b7198 - f77f7a7f3b83 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 6501ecf88..d70d63285 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - cce7b18495e4 + - d7c7ef3353fe - 3f59ebfbfe3d - - a6619171428e - - 6a457678efcb + - d033ffc1c161 - 8834daeb9892 - - d7c7ef3353fe - - 107d3ba7024a + - 3b8b5bde0bd9 + - cce7b18495e4 + - 6a457678efcb + - f73435dc282b - 81e66674859e - - '841557158611' + - 26de3a7b1cb9 + - a6619171428e - 5a7c56a5cc08 - - b89cac5156ec - - f73435dc282b - c78f3d7dd1db - - d033ffc1c161 - - 3b8b5bde0bd9 - f04a1264e2a2 - - 26de3a7b1cb9 + - b89cac5156ec + - 107d3ba7024a + - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - e75442c7f4da - - b0af57c1a968 - 7a2092844346 - - 6a726db04d4b - - 4755f52427c4 - - a185b079b095 - - aa8cc71438cf - - 6283babe736e + - 3b96e92e8ec3 + - b0af57c1a968 + - e75442c7f4da - 6223845127ea - - df47d4845b62 - 88c4aa435ded - - 3b96e92e8ec3 + - df47d4845b62 + - 4755f52427c4 + - a185b079b095 - 02b8758214b0 + - 6a726db04d4b + - 5fcd1ece3a6e - 5b777002c2de + - aa8cc71438cf + - 6283babe736e - 659517798cc4 - - 5fcd1ece3a6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 0878b7fd5260 - - b8476e82ac20 + - 70acec670c30 + - d1c340a5664b - 111bd54f6bc4 - - f97743d52b87 - 524d31add34a - 24d024316465 - - 70acec670c30 - - d1c340a5664b + - f97743d52b87 + - b8476e82ac20 + - 0878b7fd5260 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - feb40665d7cd - - 9e10ba792be2 - - daddf188c13f - 4f6349228462 + - daddf188c13f + - 9e10ba792be2 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: - - 14ae456b8cc5 - - 83a69484cb87 + - ca337cce3888 + - 03ed9524dcd1 - a2099fb98cdb - - abf6dbe8c9d7 + - 2f1019071464 - 81804a978fc0 - - 7bb8726be37c - 36912871ccdc - - b7e297c2ede6 - - ca0d8cf80567 + - b6abccb1f25b + - 42a174224817 + - abf6dbe8c9d7 - 5f8727ff21e7 - - 03ed9524dcd1 - - 2f1019071464 + - 83a69484cb87 + - 14ae456b8cc5 - 9d61d3fa046c - - b6abccb1f25b - - 2fa9d4f1b48f - - ca337cce3888 - 8ad84c5753ea - - 3a43c3982401 - 437e28791761 - - 42a174224817 + - 3a43c3982401 + - 2fa9d4f1b48f + - 7bb8726be37c + - ca0d8cf80567 + - b7e297c2ede6 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - ba29b5e2a4be + - b1e68bbe4cef - 73a469f7dc96 + - a4b71be30c3c - ea30d3089354 - 29ff6a849eac - - b1e68bbe4cef - - a4b71be30c3c + - ba29b5e2a4be tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: + - 9b2b122d0415 - 91887494eb97 - - f1ccc8a6eb05 + - e88a7de55d6e - 15ac71df11a0 - 809e42326fc2 - dbe2b2204555 - - 9b2b122d0415 - - e88a7de55d6e + - f1ccc8a6eb05 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 0de398ea3..a0000981c 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: - - b502c227b5e6 - - 1aac2a13842a - f9242e01365a - - f6ced08779c4 - - 881d7645d1bf - - fc288950c3b7 - - 7d34178f2812 - 3f254c5ced1d - a1f0b3f4b781 + - fc288950c3b7 + - f6ced08779c4 + - b502c227b5e6 + - 7d34178f2812 + - 1aac2a13842a + - 881d7645d1bf 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 628b9beb4..751ad97ca 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: - - e4a053d67e24 - - 3bd420ec162d - - d00e15139065 - 2f7702fd0a4c - - c0e71cb2bd1b + - 6ab1a261520a - eb085b3dbaf8 - - 5b85006245f3 + - 3bd420ec162d + - d00e15139065 + - a58f7eb0df2c - ca90d17ff51b - - 6ab1a261520a - 7fbec959cf2b - - a58f7eb0df2c + - e4a053d67e24 + - c0e71cb2bd1b + - 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 3fcc7f29f..0d6dddd3c 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: - - ece627528a78 + - 0a18ac48ac53 - 277dc652246e - - 4c177985028a - b574b84afc4d - b18329a8ac14 + - 4c177985028a - f28ad96b76dc - - 0a18ac48ac53 + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - b41107d8fe89 - - bf06d196e23d - e988563cc6e5 - - a9a28e46d54a - e215f71d7983 + - bf06d196e23d + - b41107d8fe89 - 525f201b86c1 + - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 56da27be956a - 4fbffddde8cd - - bb6397b94018 - 8da3511c9467 + - bb6397b94018 + - 56da27be956a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - f23d67e28cc8 - - 890845926d4b - - a8157342d9a3 - 528fb09022be - b8c79e70516d + - a8157342d9a3 + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - 25b83cbd596a - - ae304a72db7b + - 59e85306eae5 - 80600735685d + - ae304a72db7b - a95a82eb4d50 - - 59e85306eae5 - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d + - 83aac7741200 - e0669b1854b1 - - 611d80c0e29d - - ed9ed1e6cca2 + - 798da6bdff3d - f1897eb07081 - - 83aac7741200 + - ed9ed1e6cca2 + - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - a7fb9b395ddf - d426a9107a6c + - 5a35e3a8d013 - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - 82f6c2f4332d - df2187f9013b - - 91f0f5922011 - cc430977c8ff - - 82f6c2f4332d + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - d2483487e077 - - 10566783d718 - - ba92b59cd529 + - 043f9c91f686 - c5aa9fca18c6 + - ba92b59cd529 - 1693b2126f30 - - 043f9c91f686 + - d2483487e077 + - 10566783d718 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: + - bf0728e000cd - 9fa3dbf06f17 - ae4dc0c041f9 - ff8c9e0e8a7b - - bf0728e000cd 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 @@ -137,16 +137,16 @@ 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: - 0d2e93e01e68 - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,9 +158,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - e66f552a3c47 - d286ff4600dd + - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -180,16 +180,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - 837224ad1694 - - 37d669de2828 - - 4d17fcdeb8ff - - 97a7f34fcb6a - - 9c52362ae7bb - - e42225f8a659 - - 2133b0be850a - f522c08e900c + - 2133b0be850a + - e42225f8a659 + - 9c52362ae7bb - 7f432d87c82c - 1f39c833f65f + - 837224ad1694 + - 4d17fcdeb8ff + - 97a7f34fcb6a + - 37d669de2828 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,44 +201,44 @@ tools: - name: metaquantome_db owner: galaxyp revisions: + - 85b8866f06d7 - 0ed07016d668 - - a72ac2c7cc5b - e63db1aa82ee - - 85b8866f06d7 + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 990b4560ead7 - - 1974224d63c2 - - 352b37c66d97 - 767c1d761aaf + - 352b37c66d97 + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - deaf035bbe9f - - 35cc7ca0bdc7 - 4f359549383c + - 35cc7ca0bdc7 - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 06f6826d380c - - e79958768a2c - c1343e3389ca + - e79958768a2c - c7745841de24 + - 06f6826d380c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - d2eac53666f0 + - b9d453dca8d3 - da986f83631b - d46d64e7964d tool_panel_section_label: Proteomics @@ -246,17 +246,17 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - 8bd7734309f6 - 944b43462104 - - 9bf325045235 - 1199751329b0 + - 9bf325045235 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -270,9 +270,9 @@ tools: owner: galaxyp revisions: - de7593c29499 + - 593839e1f2c3 - 28434abe6c5c - 8212e342e482 - - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -285,64 +285,64 @@ tools: - name: openms_consensusid owner: galaxyp revisions: + - 01dbaf6a57e0 - 8960fb791701 - f4be248c3d47 - - 01dbaf6a57e0 - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: + - 06cca574e337 - 25529df60a81 - 370141bc0da3 - - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - 518b1730cf2a - - 9cdf15d3cfc8 + - 6ccbf9a2072c - f7fef900f5b2 + - 9cdf15d3cfc8 - c9eff69a7c62 - - 6ccbf9a2072c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: + - 5e948629bc73 - dff6c756eee5 - 9876bda3ec53 - - 5e948629bc73 - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 1595601708ec - - 658494a2cb00 + - 41859bbdc16e - 890025d6e426 + - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 9b7977080f6d + - 2a93a25f0599 - 6634cad7d797 - 5ad0b5bf1deb - - 2a93a25f0599 + - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 05d5e1ddc985 - 0bb5056cb775 - fe4e4587d265 - d6878d27f051 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo @@ -359,17 +359,17 @@ tools: revisions: - 92352a475eed - 39e8fde08881 - - 27cba4c5fc42 - b2fc8da99bcc + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d3546bb9fd8e - d413dc49d650 - 0efbc235f314 - 9e26f5c770f8 + - d3546bb9fd8e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver @@ -384,20 +384,20 @@ tools: - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - - c427a8628cbe - ca799a7246e7 - - a5d785af0ad8 - 382cde407f81 + - a5d785af0ad8 + - c55dddc5844a + - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - b5d0905419da - - 39caaa778d2e - - adca857b4884 - 8ddb7bab1138 + - adca857b4884 + - 39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger @@ -405,27 +405,27 @@ tools: revisions: - f817513840a9 - 34e7afee141d - - 8d4db262964c - 1c5f31b8d632 - 18f93351f8b6 + - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - 5d9f175dff81 - c69f69d7867a - - 111c3a00136d - 986e03d3201e - - 5d9f175dff81 + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: + - 476b5e296979 + - be74a8cd7d66 - 0e52c85f3b15 - 4204882495f2 - - be74a8cd7d66 - - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -438,43 +438,43 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - f5ec766d80cf - c18d8efa4474 - - a407b6790342 + - f5ec766d80cf - 2b2a7551a857 + - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - d0304fb829c0 + - 4e66c4e73909 - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - 8098330f6d91 + - 2735db4dd8d9 - ee860980edc6 - bf32e0bcf554 - - 2735db4dd8d9 + - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: + - a2a6e9551046 - 08488066d588 - 0ced5bc9f4dd - - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: + - 8c01da82292c - de7a553552a6 - 2a9ff56cb279 - - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -496,101 +496,101 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - - d4396637b9f5 - c99d5004b74f + - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - 8b814eafce2c - - 89254095cbf6 - 4bb198c0bd3e + - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - - f82b320ceb90 - f9ed7e074900 + - f82b320ceb90 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - 18826fb8e5db - - d31426ef20f6 - 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 owner: galaxyp revisions: + - 3d8d4ada5405 + - 6b01678ec2fc - 5ae104d0da6e - decc397c3b7e - - 6b01678ec2fc - - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - e039cc5c7aed - - d6aca689dd48 - - dd173849c3d8 - 5182338d5e7c + - dd173849c3d8 + - d6aca689dd48 - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - - d426affe977c - 16026cdb1330 + - d426affe977c + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 9c70a651a53e - dd71e020e2aa + - 9c70a651a53e - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: + - 9020199dba0a - d063e2fe4ba4 - 1b03536aa3c9 - - 9020199dba0a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - ad2ba3a95a02 - 78c080d36945 - f036e8cf1a55 + - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 5c2a97a234d6 - - fb52e95a370c - 7f6a1f27553e - c8b225c69a7f + - 5c2a97a234d6 + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -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 - - 07ff622ec007 - - 3ec27b4cee7c - 1beff3ddce58 - - 7fdd9119cc4f + - 943a34df6047 - a72c48001f7c + - da885ca16cb2 + - 7fdd9119cc4f - 3634c90301af - - 943a34df6047 + - 3ec27b4cee7c + - 07ff622ec007 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: - - 265c35540faa - - a371252a2cf6 - 12692567c7f9 - 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 4675061a5..cbdf887f5 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,9 +2,9 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 42201b90e3f4 - - 110a346daf36 - 289b7d6b69a4 + - 110a346daf36 + - 42201b90e3f4 - cd5f98911089 - 2f1d464ebfd2 - e345aadf914f @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - - fcce77c09289 - - 42d9087b4789 - 0cd2df8af811 - - 8501601a118d + - fcce77c09289 - c207119ba5f6 + - 0345dbaaa79b + - 8501601a118d + - 42d9087b4789 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - 405a212b32ab - 33486216eec0 + - 405a212b32ab + - 04db7fd6b238 - ad5ab22ffe24 - - 89eb29319bf4 - 421c33b8bf17 - - 04db7fd6b238 + - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -55,10 +55,10 @@ tools: revisions: - 1d839ead7ad3 - 7b72fde3d27e + - 7370bb65bad4 + - eb784fa07f80 - fa51dc5e8386 - f6e91108b7b1 - - eb784fa07f80 - - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -71,11 +71,11 @@ tools: owner: iuc revisions: - 1544278c272e - - c9b77ced9a78 + - a3e86cd9cac7 - 3d70c2996730 - d30e36c48c93 + - c9b77ced9a78 - 8a55d29c8fcf - - a3e86cd9cac7 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: + - 887cf585cafc + - 564c33e5c3e3 + - e2db212d64ad - a5969aa9347e - 7b881f5f5ad5 - b242deb58952 - - e2db212d64ad - - 887cf585cafc - - 564c33e5c3e3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - 8cff84759bf6 - - b4bab607eb05 + - bd5ff77e2036 - e897c74a48bb - 9a171f9a450b - - bd5ff77e2036 + - 8cff84759bf6 + - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,11 +120,11 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 5e10f396979e - - 4f65e343ecdf - - 33f0793edf93 - 6dafad990086 + - 33f0793edf93 + - 4f65e343ecdf - adc7a7610d4f + - 5e10f396979e - 887e0991eb24 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: - - 43e3eeb2e0ec - - c287418eb288 - - c5d7050e4ad7 - - 17d39bf0a63a - 97575d01f06b + - 17d39bf0a63a + - 43e3eeb2e0ec - 4e280b27a831 + - c5d7050e4ad7 + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -155,10 +155,10 @@ tools: owner: iuc revisions: - d9bf483266a1 - - 0b8c84a7fdb5 - 9586f08634c0 - cd034465d4a4 - a819ec3b362d + - 0b8c84a7fdb5 - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -172,11 +172,11 @@ tools: owner: iuc revisions: - 2645575d1bf2 - - a9c34a289493 - - bf0e43ab0416 - - a4b4bd84f69e - 95351dd0fd3f + - a4b4bd84f69e + - bf0e43ab0416 - 69842dd5aa48 + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: + - cfb504394ae1 - d033e1ccb386 - - bb0475c884ff - d1fda11e602f - - 912f904a6e1e - 8a35a3bc6752 - - cfb504394ae1 + - 912f904a6e1e + - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - d504d945a655 - 95286af4139b + - d1fad35bdb4a 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 946d403b2..9aba65372 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: - - cf01dd6c6b1f - - 31f8063eedea - 7acb00fc980a - 2d4e3aff9dc7 + - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 703a2cb3fb38 - 125d20cb23d7 - - 32e542c2a773 - 7a5a2d28c539 - - 703a2cb3fb38 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -98,8 +98,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -123,9 +123,9 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - - 3b36efd62b3e - e3b16fd7dd08 + - 3b36efd62b3e + - 0693ccd171c4 - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -138,13 +138,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 24a09ca67621 - 0696db066a5b - d027d1f4984e - - 6a3a025714d3 + - 24a09ca67621 - 9a882d108833 - - 8fe98f7094de + - 6a3a025714d3 - cd9874cb9019 + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -156,11 +156,11 @@ tools: - name: dexseq owner: iuc revisions: + - b47c006d90c5 - 62adf13b86ea - 2872c633f07e - 9a7c5b6d8f1e - df929f257179 - - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -172,18 +172,18 @@ tools: - name: edger owner: iuc revisions: - - 334ce9b1bac5 - - 555659de7321 - - 5bf899c13979 - - 3d89af8a44f0 - df0c8d0a5992 - - ae2aad0a6d50 - - 9bdff28ae1b1 - 0cb907a2a810 - - a8305cf0c951 - 6e53e565fc6a - - 070900306913 + - 9bdff28ae1b1 + - ae2aad0a6d50 - f2843df56434 + - a8305cf0c951 + - 3d89af8a44f0 + - 334ce9b1bac5 + - 555659de7321 + - 070900306913 + - 5bf899c13979 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -195,8 +195,8 @@ 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 @@ -214,17 +214,17 @@ tools: - name: featurecounts owner: iuc revisions: - - 38b6d12edc68 - - 90d16db017d7 - - f9d49f5cb597 + - f3a5f075498f - a37612abf7f9 - - e6a2a912677a - - 7db9d3ea71c9 - - af814359d244 - a56fbe2d6ba7 + - 38b6d12edc68 + - af814359d244 + - e6a2a912677a + - 90d16db017d7 - 6f66ae7c5f7a - - f3a5f075498f - ea04b737afa0 + - f9d49f5cb597 + - 7db9d3ea71c9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -254,9 +254,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - - 0f710191a66d - f99dd58de04f + - 0f710191a66d + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -274,13 +274,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6ab42baa56e9 + - f4af63aaf57a + - 26371a1df031 + - 3fb01a8c902d - 6c19daec423d + - 6ab42baa56e9 - d4b55e2beb12 - - 3fb01a8c902d - a86e80d3c09c - - 26371a1df031 - - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -298,9 +298,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 4418229c501e - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -318,11 +318,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - ce5d418183c5 - - 01247aaf0a10 - 5ae5c312d718 - - 1c75aa5de15e + - ce5d418183c5 - 87c11c05d238 + - 1c75aa5de15e + - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -334,10 +334,10 @@ tools: - name: kallisto_quant owner: iuc revisions: + - 40985510cd98 + - 4f9c4e6566e5 - 10c98fab6c5a - c971db6f0fe5 - - 4f9c4e6566e5 - - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -349,14 +349,14 @@ tools: - name: limma_voom owner: iuc revisions: + - 0921444c832d - 58c35179ebf0 + - e827f9aae031 - 97e06a4c7c75 - 119b069fc845 + - d6f5fa4ee473 - 32511f586472 - - 0921444c832d - - e827f9aae031 - 708348a17fa1 - - d6f5fa4ee473 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -374,8 +374,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -405,8 +405,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -424,21 +424,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - b9e04854e2bb - - c7c55b694974 - - c772497b2c32 - - 4074fc1940e2 - - 99b17b74a8cd - - 79de45b5069b - 5ec75f5dae3c - e132e7d02a3e + - 79de45b5069b - 4df95e2d7f61 - - 4014de1b6daf - 7ed2edc1337f + - 99b17b74a8cd + - b9e04854e2bb - 980d2a2e1180 - - 0a563fd2f22e + - 4014de1b6daf + - c7c55b694974 - 3ea5a2a63fa2 - b0f2be869d6d + - 4074fc1940e2 + - c772497b2c32 + - 0a563fd2f22e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -463,12 +463,12 @@ tools: owner: bgruening revisions: - ebab418107f5 - - 2c0ca397d302 - - cc05793bb896 - - 53e9709776a0 - e3d32471da11 - 15cd64d7c58b + - cc05793bb896 - f4d5237a84f6 + - 2c0ca397d302 + - 53e9709776a0 - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -483,21 +483,21 @@ tools: revisions: - c0fd285eb553 - 56242ff81c84 - - fab6ff46e019 - 8c28affc7c48 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - 258d696dbd7e - - 1ebd14235b92 - - cbf488da3b2c - 76d290331481 - - dd4df992d93d - 914cfcba0ec8 + - cbf488da3b2c - ae618321f34a + - 1ebd14235b92 - cef79931dda5 + - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -533,8 +533,8 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - d0d4cef4f967 + - 0db979fead3a - ffd1300599a1 - c6334cb383ff tool_panel_section_label: RNA-seq @@ -548,10 +548,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 + - 74217fbfba4d - ba3720d7e68b + - bcc5f03f1900 - d6a479fd4281 - - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -563,10 +563,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 2fb4ee002432 - - c2b82a94493e - 478f36effca1 + - c2b82a94493e - 56162e446004 + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -578,9 +578,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - fab23c3b5258 - 3f4094b6a565 - 9ff3765e7172 - - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -593,9 +593,9 @@ tools: owner: iuc revisions: - 870ac06dff8e - - be3f26533209 - - 34a018cbee9c - 4687ecf0eb2d + - 34a018cbee9c + - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -608,8 +608,8 @@ tools: owner: iuc revisions: - 05ab8d5e04a2 - - c5fbddcac63a - 5192f657f305 + - c5fbddcac63a - 65e7dea767ea - 33406f5a445c tool_panel_section_label: RNA-seq @@ -624,9 +624,9 @@ tools: owner: iuc revisions: - a35cba31d904 - - 6f0fb35b799c - e406ac71165d - 1fdb25a8384d + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -638,10 +638,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: + - 7c7fbf13aadd - c2c039e421af - - 37a1129c89d2 - 964b7efe2639 - - 7c7fbf13aadd + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -653,10 +653,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 - - 1d689e4e1caf - eafea3083352 - 24e94d84adc9 + - 047c22569787 + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -668,10 +668,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - 3a4ac03d1266 - - 1812dbc5bb7b - 04bb8bb7c198 + - 1812dbc5bb7b + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -695,15 +695,15 @@ tools: - name: trinity owner: iuc revisions: + - d84caa5a98ad + - c9cfec002f71 + - 32b86cd8eb50 - d2bc35f3d1c5 - - 9fa24d5aac68 + - cee61b3fcf78 - 8f1c3df4dd49 - - 32b86cd8eb50 - db1f362cca3e - 48636f857c4b - - c9cfec002f71 - - d84caa5a98ad - - cee61b3fcf78 + - 9fa24d5aac68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -715,10 +715,10 @@ tools: - name: trinotate owner: iuc revisions: + - 9e61bc67866f + - 4383070d29ed - 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 700ffb5e7..636b5a8af 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -3,8 +3,8 @@ tools: owner: nilesh revisions: - 27e16a30667a - - 473382134e56 - - 1a052c827e88 - 080fd5739bb4 + - 1a052c827e88 + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 668aa40a7..c5c1fde5c 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - 88eedb4abea0 - - 10184eaa85fc - 3c661e57a88f + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -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: - - 9c1c0b947e46 - ef11139d4545 + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - 30a201c9c310 - - e7fd6754d093 - 19ece8afbaab + - 5f8e69cc4c6e + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -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 @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: + - 12749212f61b - 9149ad20699a - - 46c6639921f1 - 6856f8a01905 - - 12749212f61b + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 92ec40abcdcf - 26b4f9f98aca - - 33208952b99d - 06dc50b7b711 + - 92ec40abcdcf + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - - 66e23b11feae - b3d99709fe1a - - 720217c23995 - b906586a6596 + - a8d69aee190e + - 720217c23995 + - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -221,18 +221,18 @@ tools: - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - db17d5321bad - - 22970df7a40e - fe34990e5ce7 - - fefd89ab563c + - db17d5321bad - cc61ade70eb8 + - fefd89ab563c + - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,10 +244,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 88b8c2916784 - 811fc2d75ad4 + - 88b8c2916784 - 7def34e6cf4d + - fa5d3e61e429 - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -260,18 +260,18 @@ tools: - name: samtools_markdup owner: iuc revisions: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - 36677f429310 - - 65a38e8c8e2a - - b40e2d865d52 - cae2794d2deb + - b40e2d865d52 - 740ce0a18f0d + - 65a38e8c8e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -280,8 +280,8 @@ tools: - 9da0311ab1dd - 329deb17a9f7 - 583abf29fc8e - - fa7ad9b89f4a - b61f5d6a7f25 + - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -293,8 +293,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 85e38b31e8b3 - bb8cfc6f6e0c - db000c6007a0 - 30388d878f81 + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -342,8 +342,8 @@ tools: owner: devteam revisions: - cab3f8d35989 - - e613c1ad4c4c - 6c2c1836728b + - e613c1ad4c4c - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -357,11 +357,11 @@ tools: owner: devteam revisions: - bcedabb53ddf - - b7f7826ef1cd - 135c85f4cfaf - bd850490c7f1 - - 818030fa6bbf + - b7f7826ef1cd - 5d9ae78f34d3 + - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -374,10 +374,10 @@ tools: owner: devteam revisions: - 24c5d43cb545 - - 541082d03bef - - 1cc79f49b8d5 - 145f6d74ff5e + - 1cc79f49b8d5 - 3a0efe14891f + - 541082d03bef - 5a08c09b9311 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - 0dbf49c414ae - - b01db2684fa5 - - bf328cec6a42 - b72793637686 - - 32dc5f781059 - - 350bbc5c2ffd + - 5826298f6a73 - 2dce91e11ca7 - - c370440f901e + - 350bbc5c2ffd + - 32dc5f781059 - 6be888be75f9 - - 5826298f6a73 + - bf328cec6a42 + - c370440f901e + - b01db2684fa5 + - 0dbf49c414ae 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 47ebc57d0..4c2cfd112 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,12 +2,12 @@ tools: - name: ena_upload owner: iuc revisions: - - d147d6455873 - - 5cb6146337d8 + - 59bb6d34fca6 - ea5e944f447d - - 6f6537780379 + - d147d6455873 - a62c4a11a67d - - 59bb6d34fca6 + - 6f6537780379 + - 5cb6146337d8 - 480d9e9d156b - 4aab5ae907b6 tool_panel_section_label: Send Data diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index e56be3716..dec52b62a 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,31 +8,31 @@ tools: - name: alevin owner: bgruening revisions: - - c9944a2600f1 - f2000bc73102 - - e32b215b7c04 - ecb9ea6269ee + - c9944a2600f1 + - e32b215b7c04 - e4c01dcece8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - c0b037b12765 - cfaf5a405371 - 707023fa62fe - e1c3c2f2a834 + - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 93dd15e13e6a - 55e35e9203cf - - d330b3082107 + - fb9e030ffae4 - 32e547223c9e + - 93dd15e13e6a + - d330b3082107 - 00712416fdaa - - fb9e030ffae4 - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: + - 038e32885fec - 0bf7fddf90c7 - 39e945f0b2c1 - - 6f0d0c784f09 + - ee98d611afc6 - b9fac48532eb - - 038e32885fec - 688357ad5e61 - - ee98d611afc6 + - 6f0d0c784f09 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 3d748954434b + - b85871dd69f9 + - 43cb7b5a6fe7 - d4af736e7b83 - - 9bd945a03d7b - ed4996a16f7f - 7e8c677a7b71 - - 43cb7b5a6fe7 - - b85871dd69f9 + - 9bd945a03d7b + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -81,25 +81,25 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: + - a4774b7b2e85 - 2e8022f1923c - fe75d2414dc0 - - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 0e70b2dfe4be + - 769d815e4b0d - 4fff5a293013 + - 0e70b2dfe4be - 02b1fe7aed76 - - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - aa4a6f0916b4 + - c29e7bb492bf - 344c2af50552 - a90f8efe08b4 tool_panel_section_label: Single-cell @@ -107,19 +107,19 @@ tools: - name: baredsc_combine_1d owner: iuc revisions: - - b13d3e4c48e1 - 050cf43887d3 - - 5b7c81b35b89 + - b13d3e4c48e1 - c32347702e12 + - 5b7c81b35b89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 02fc39c8610d - - ae969fdb8442 - 239193b96d72 - 1d77986f9ddc + - 02fc39c8610d + - ae969fdb8442 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: - - cfe1e6c28d95 - - cdf4443d5625 - 2c1200fba922 - - 8855361fcfc5 + - cdf4443d5625 - a9caad671439 + - 8855361fcfc5 + - cfe1e6c28d95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -195,15 +195,15 @@ 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 @@ -272,22 +272,22 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 3a6a5381db36 - 4401ed529d2c + - 3a6a5381db36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - 2ba6cee8e4db + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix @@ -300,15 +300,15 @@ tools: - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2786a931cad2 - 2b4d6a8dab36 + - 2786a931cad2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - 0410b6aada45 + - ffc33339cd3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad @@ -328,15 +328,15 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - 7f7c6ead2d0d + - 409396ea5cf0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -349,8 +349,8 @@ tools: - 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 @@ -363,8 +363,8 @@ tools: - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -377,15 +377,15 @@ tools: - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 11f39d7f6c64 - 6326cd29c1c3 + - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -398,8 +398,8 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - ea8fb5e899e8 - 21d859ad4502 + - ea8fb5e899e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -431,18 +431,18 @@ 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: + - 7784821452ac + - eeab712b0b99 + - 4b0adaa31c95 - 59be31ac9dc3 - 0f1aaff9b22d - - 4b0adaa31c95 - - eeab712b0b99 - - 7784821452ac - e98619de2776 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -455,23 +455,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 282819d09a4f - 7ffaa0968da3 + - 282819d09a4f - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 2ba99a52bd44 - 56371b5a2da9 + - 2ba99a52bd44 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -490,10 +490,10 @@ tools: owner: iuc revisions: - c4f39bf4a068 - - 0bff0ee0683a + - a4b734cd253b - f911a64454fb + - 0bff0ee0683a - 7e014059a88d - - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -505,9 +505,9 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: + - 7608d5faee41 - b83fbc90161e - 43c146e25a43 - - 7608d5faee41 - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -520,8 +520,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - f3eb2291da05 - 37a47c4fd84d + - f3eb2291da05 - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -548,11 +548,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 44b935f2271b - 72979cac22b2 - - 2af7c5086a96 - - c92d0f9338c5 - e93b008c637a + - 44b935f2271b + - c92d0f9338c5 + - 2af7c5086a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -576,15 +576,15 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - - 77b91b9bdf52 - - edec35114f72 - - f9353ee6a0d4 + - 6acb08931836 - 4d8f983cd751 - - aaa5da8e73a9 - 6f83f8fd381f + - aaa5da8e73a9 + - f9353ee6a0d4 + - 77b91b9bdf52 - 38db3fef7aad - - 6acb08931836 + - b2df381a6004 + - edec35114f72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -596,14 +596,14 @@ tools: - name: scanpy_filter owner: iuc revisions: + - a97abb8cd15b + - 3c86f71498bc + - 277313130da5 - 8cb783c81905 - - d636ce5cde16 - b409c2486353 - 72a6bebab2a5 - - a97abb8cd15b - - 3c86f71498bc + - d636ce5cde16 - a03ff8633507 - - 277313130da5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -615,17 +615,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - d1cd8c147809 - 18262103fa61 + - 6c145a6868cc - c0a80a16560f - f54f0f0598ad - - 6bd82ed14acd + - 3081ff5c84a3 - 5e9171dc8244 + - 6bd82ed14acd + - c5d3684f7c4c - 5c3ebe2adc77 - - 6c145a6868cc + - d1cd8c147809 - cc0deb593fc8 - - c5d3684f7c4c - - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -637,15 +637,15 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 9f354c7c8c92 + - a407e7f8bdc1 - ab55fe8030b6 - - 94c19fb1281c + - 9f354c7c8c92 - d844935c906c - - a407e7f8bdc1 - - 3bcd5445cd7a + - 56c0d4acef02 - 7b9fafe32c86 - c9cb76cf8d6c - - 56c0d4acef02 + - 3bcd5445cd7a + - 94c19fb1281c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -657,16 +657,16 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 6f5349dd5c49 - - 1072ce66b426 - - 0185bd174ea0 - - 6adf98e782f3 - 95777145cb92 - - aa0c474463c2 + - 7647e5cd1b8b + - 6adf98e782f3 - f7446fd8d5e7 + - 0185bd174ea0 + - 6f5349dd5c49 - dbbe1ea8ecb1 - 9b0cdb8cf6be - - 7647e5cd1b8b + - aa0c474463c2 + - 1072ce66b426 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -678,15 +678,15 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - bf2017df9837 - - 9fb627495ec2 - - d18e7a6e5cd4 - - f2f6c703da06 - - c65fce500915 - - 215733a383f2 - a39040ae0a38 - - 458e8f43a775 + - c65fce500915 + - d18e7a6e5cd4 - 73ab2ac53d06 + - 458e8f43a775 + - 9fb627495ec2 + - 215733a383f2 + - f2f6c703da06 + - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -698,9 +698,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - b834074a9aff - 8f333f90d8d6 + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -712,9 +712,9 @@ tools: - name: scater_filter owner: iuc revisions: + - 7a365ec81b52 - b7ea9f09c02f - 652923ce664f - - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -732,9 +732,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 2e41b35b5bdd - - 81e5bdff4853 - ef4c80837bc5 + - 81e5bdff4853 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -752,8 +752,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - 46fc6751d746 + - 9e5c0bb18d08 - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -1002,8 +1002,8 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 88192fe25375 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -1029,8 +1029,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index ac6c0843f..df0f80463 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,9 +32,9 @@ tools: - name: datamash_ops owner: iuc revisions: + - 562f3c677828 - 746e8e4bf929 - 4c07ddedc198 - - 562f3c677828 - 419027d822d6 - 2f3c6f2dcf39 tool_panel_section_label: Statistics @@ -42,15 +42,15 @@ tools: - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: + - cb1c59d69557 - 7a15159140d1 - 6c29c7e347e8 - - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,32 +120,32 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e - 9c3e1d3235c8 - aef56d0e7a61 + - 4c4ec859c31a + - 7442b94d6a1e - 840f29aad145 - b1eda492f063 - - 4c4ec859c31a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 + - 375bbd555f4a - 30d21a6041f6 - 9fda0b82f419 + - d0352e8b4c10 - 07843f917990 - - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d - - 4cc980df6265 - - 8b1b2b91f8d0 - cd02bf168d23 - 2c58b83c9bad + - 4cc980df6265 + - 7ae443e6217d + - 8b1b2b91f8d0 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering @@ -153,10 +153,10 @@ tools: revisions: - 4bbaf77573ef - bb9fc9d46ea4 - - 1dd433d2c92c - - ad7e0b4291ee - e10e776f2109 + - 1dd433d2c92c - 7dd3fb35904f + - ad7e0b4291ee tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index 85e53a66d..decd70463 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: - - 9cd341095afd - 464b9305180e - - be25c075ed54 - - 626658afe4cb - 6e8d94597139 + - be25c075ed54 + - 6595517c2dd8 - aff5135563c6 - 02026300aa45 - 13b6f0007d9e - - 6595517c2dd8 + - 9cd341095afd + - 626658afe4cb tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -54,8 +54,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 90f657745fea + - 557ec8d7087d - 37cde8134c6a + - 90f657745fea - 9cc411a62277 - 34d29339abab - - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,22 +107,22 @@ tools: - name: merge_cols owner: devteam revisions: - - f2aac0c5c60d - ae7843d06f8f + - f2aac0c5c60d - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 83069b38aa85 - - 3a6b78c39dca - - cf4397560712 - - 623f3eb7aa48 + - 2e8f945f7285 - 1ea4e668bf73 - - 33d61c89fb8d + - cf4397560712 - cf34c344508d - - 2e8f945f7285 + - 33d61c89fb8d + - 83069b38aa85 + - 623f3eb7aa48 + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -144,8 +144,8 @@ tools: revisions: - f768f6183386 - b722161a845a - - bce29ec10b78 - c4d18aa4ec4a + - bce29ec10b78 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: - - f46f0e4f75c4 - d698c222f354 - - fbf99087e067 + - 74a8bef53a00 - 0a8c6b61f0f4 - - a6f147a050a2 + - f46f0e4f75c4 - 9ff72e942410 - ddf54b12c295 - - 74a8bef53a00 - - 12615d397df7 - 86755160afbf + - a6f147a050a2 + - fbf99087e067 + - 12615d397df7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index 781669468..e1eea58eb 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.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 @@ -34,57 +34,57 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 + - a5937157062f - 156b60c1530f + - 04fa42777df9 - ef2c525bd8cd - 57def2d7c093 - - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - e61c9ac190ad - - 09d6e4693887 - 791f73caa0c8 + - 09d6e4693887 - 435b157bed6d + - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 65432c3abf6c - e1461b5c52a0 - 3b4b2121842f - - dfadc322b065 - - 4805fe3d8fda - 074d44697036 + - 65432c3abf6c - 03627f24605f + - dfadc322b065 + - 4805fe3d8fda tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 9cb929f21cfa - 701d134358ad - 7dfca164d2e3 + - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - c27549b9aa1f + - 971e07ca4456 - f4473557ffc7 - 426d707dfc47 - - 971e07ca4456 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 @@ -96,18 +96,18 @@ tools: - name: sniffles owner: iuc revisions: - - 93c4b04a0769 - 43fffeed243f + - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - - c9a8ef2aa380 - - 5bbf9eada9c2 - - fa016f1eea1a - d220115f882b + - fa016f1eea1a - 9bccc8404a3c + - c9a8ef2aa380 + - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -149,20 +149,20 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - ee4a90760848 - e7aff4a85df5 - - 40f0591deda0 - 3b1e7c170b10 + - 40f0591deda0 - 32f14a2723ec - - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 4934c0ac6197 - - 9793bc5d741b - 02d81b994ef5 + - 9793bc5d741b - 42818629ec4c + - 4934c0ac6197 - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 972e704e9..423fab309 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: - - ebe5fc018e72 - - e075b1be5abb - - b7ea370b8f5d + - 6a88248893c4 - 8a2e296c07ef - - 265fe0f9ea64 - 95815a0bb307 - - 6a88248893c4 - 2c372041ed8c + - b7ea370b8f5d + - ebe5fc018e72 + - e075b1be5abb + - 265fe0f9ea64 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -22,12 +22,12 @@ tools: owner: iuc revisions: - 1001172b5089 - - 0fba2c15b40d - c37b684e7f4e - 22637b1a55bf - - 21687e35f066 - - b03984136ce4 - 544cb432072b + - b03984136ce4 + - 0fba2c15b40d + - 21687e35f066 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - ccb83bf54de0 - - bf1f4994f104 - - 8627b2b383b4 - - 01d6b7d6365e - 8ca3647c90fd - 3a7084316a6e - - 0238f68ad641 - 143796b504eb + - 01d6b7d6365e + - ccb83bf54de0 - 8408bffd5616 + - 8627b2b383b4 + - bf1f4994f104 + - 0238f68ad641 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -60,13 +60,13 @@ tools: owner: iuc revisions: - 62ca6da715bf - - 81426b3cf18b - d144af39073a - - 03e0645395d2 - 9b5abbf50d23 + - abd489215f73 + - 03e0645395d2 + - 81426b3cf18b - f430a1ec7ee4 - 6b6c992d3a14 - - abd489215f73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,13 +78,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - e522022137f6 + - d3081540d175 - 95c6f3f4c77f - - 8aa352093d73 + - 1829900b5dcd - d37e313a41be - 2363ef414c9b - - 1829900b5dcd - - d3081540d175 + - 8aa352093d73 + - e522022137f6 - 1171446da5db tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -98,13 +98,13 @@ tools: owner: iuc revisions: - 012656fd329f - - 348cd212dbad + - 09f37afb3621 - 1137ce8efc1e + - 9b29129fb491 - b14ff40958cb + - 348cd212dbad - d58d2e8c7a57 - 92c0aff8b53e - - 09f37afb3621 - - 9b29129fb491 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 1f2183a23823 - 7291189e98b4 - - 367ba501b6eb + - 1f2183a23823 - 55c0e906c14c - cfd81f17580b - de68c11034f6 - ecc9192912b8 + - 367ba501b6eb 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 + - 7cbf3c66d4ad - 64a8f7dae3ad - 6c790a091c7c - - 7cbf3c66d4ad - - d237eaef451f - - ae68ceb4cca3 - e6f4badbe6f3 + - ae68ceb4cca3 + - 039ea3f1dea9 + - d237eaef451f 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: - - e7452697afd9 - 963a3635b2e1 - - 46fcafba49ec - - 33bd9301568c - - 5d6653c989cb - - cdb7b4927742 - 6ea7170a016d + - 5d6653c989cb - 277719af4dd7 + - cdb7b4927742 + - e7452697afd9 + - 33bd9301568c + - 46fcafba49ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,12 +171,12 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 7b4454382d39 + - 26d97cdd5410 - 91c1e57d5c7f - - 501bfb078342 - - b7f0f59baa7e - a1213a0b7b66 - - 26d97cdd5410 + - 7b4454382d39 + - b7f0f59baa7e + - 501bfb078342 - 5a321fab1fe4 - a29a2f40b665 tool_panel_section_label: VCF/BCF @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: + - 15da1ddcfeff + - 97d19c008d15 + - 39bca000353d + - c803c34361e0 - 5f27e814a119 - 709dd8291b83 - 768d04526638 - - d7d1663559e9 - 81e4014fa809 - - 97d19c008d15 - - 15da1ddcfeff - - c803c34361e0 - - 39bca000353d + - d7d1663559e9 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: + - 5b006286a458 - b931e65638b8 - - b1eba148b35b - - 86296490704e - - 85ee7e6c4204 - 2215287d5cc9 + - 85ee7e6c4204 + - 86296490704e - b84fda8ebef0 - - 5b006286a458 - 7ba36babba2d + - b1eba148b35b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: + - f506df85c652 + - cf06b44624c7 + - 31ea13dfe5e6 - 56556e1267de - - 37757ffb4c5f + - 9c711df3258d - 4e1d23e5c691 - - 31ea13dfe5e6 - - ce9396ddcb2b - 5660b21a0dbd - - 9c711df3258d + - ce9396ddcb2b + - 37757ffb4c5f - 0a5dcc9a8ec2 - - f506df85c652 - - cf06b44624c7 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: + - a404f786a94c + - 271965b55437 + - 19905c025d2a - 1ca7418e46ee - 021693fdadaa - 6deb4d549bc9 - - 19905c025d2a - - a404f786a94c - 48291658fdf6 - - 271965b55437 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - dadbd61dc4cf + - 97e8145d7e30 - 3f6fadf8b8ff + - c450406f722b - f7879f1e77f9 + - 69d8b7567281 - 71c78e0eea52 - 5ad5d4243987 - - 69d8b7567281 - - c450406f722b - - 97e8145d7e30 + - dadbd61dc4cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -288,13 +288,13 @@ tools: owner: iuc revisions: - 0fe007201caf - - 2514e684f8a3 - - cc7f9a4e186b - - 283911fe7e1a + - d31a2e310a52 - 79f7a1acc2cd + - cc7f9a4e186b - 6cf13a657cf6 + - 283911fe7e1a - 52f9e4a660e3 - - d31a2e310a52 + - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 75ddd081f608 + - 6963a6841d22 + - 230e424bde67 + - 026a989b7cee - a12844ca467a + - 75ddd081f608 - 1411bef27a75 - - 230e424bde67 - - 0a62420cb9cd - - 6963a6841d22 - 80e6e399ccd0 - - 026a989b7cee + - 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: - - 450a265f92e8 - - 444e6a756c35 + - bca7ce81688f - b10d1510fa84 - - e493702b19eb - 5acfca5a76af - 5808f77b2bb6 + - e493702b19eb + - 450a265f92e8 + - 444e6a756c35 - ba20340426fe - - bca7ce81688f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -346,12 +346,12 @@ tools: revisions: - dd72ff87cfd0 - 157ffcdd3fa7 - - f2482aa4862e - - 68fec03a63b7 - d52b8947b269 + - f2482aa4862e - c43399f161f4 - 12152af85697 - 4d236c696844 + - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 8dbce095986c - - 29ba253e2e05 - - cbe39e530cbf - 75becf493cd3 - - 8f2fc0ab30fb - 0e5d11004815 + - 8f2fc0ab30fb + - cbe39e530cbf + - 8dbce095986c - 6f8e223f78f3 + - 29ba253e2e05 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: - - a367a15c6de5 - - 9708e3086f32 - - f544f71adb73 - - 88bb477f45f7 - - 8f5962c43868 - 3ff5654b4e7d - a8630d4fbaf8 + - f544f71adb73 - e0a856def0b0 + - 8f5962c43868 + - 9708e3086f32 + - 88bb477f45f7 + - a367a15c6de5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -400,14 +400,14 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 4ed46189d6c6 - 34dc0bbc7e93 - - 6ce175385dd9 - - 96d0145c041a - 5c9729d54721 + - 31c096c6b156 + - 6ce175385dd9 + - 4ed46189d6c6 - 03e30f06f15f + - 96d0145c041a - 8b260d252ff4 - - 31c096c6b156 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: + - 11af7fce71cf + - a730269af659 + - 09f5e45a8212 - 2c4941386820 + - 46eb13bc2c73 - a1aad8b559c6 - - a730269af659 - 681bdf1e22ff - - 46eb13bc2c73 - - 09f5e45a8212 - 40daf124be88 - - 11af7fce71cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - b74b8cbfc1f1 + - 743cd1472aeb - 8cb121b6a1d2 - - f272b8ba0983 - - 882b2e649602 - 3897eaadfbff - - 0594ea1417c8 - - 12038f59c0f4 - - 743cd1472aeb + - 882b2e649602 - 6cbb9c47795c + - b74b8cbfc1f1 + - 12038f59c0f4 + - 0594ea1417c8 + - f272b8ba0983 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,13 +458,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - cced6715f926 - - 18cf9de1cf73 + - eccb508bb678 + - adee7e8b746f - dba06328556a + - cced6715f926 - 238f78e38a8b - - eccb508bb678 + - 18cf9de1cf73 - a9826db86d9a - - adee7e8b746f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,13 +476,13 @@ tools: - name: bcftools_query owner: iuc revisions: - - 9f36041495a3 - - 31a1b89eab9b - - e0ad88dec40d - - fdec14f69010 - 3ce32adc55b2 - - c9935c9e8a24 - e53501abf992 + - e0ad88dec40d + - c9935c9e8a24 + - fdec14f69010 + - 9f36041495a3 + - 31a1b89eab9b - f64e7ca2efd2 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: - - 3b7b1fe7b937 - - d68c43202172 - - 2331ddcbd5aa + - d43eb39b989e - fd3539749127 + - d68c43202172 + - b7be725976b6 - 79489d5685dd - 4db0695a6fc7 - - b7be725976b6 - - d43eb39b989e + - 3b7b1fe7b937 + - 2331ddcbd5aa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,12 +514,12 @@ tools: - name: bcftools_roh owner: iuc revisions: - - b0d39ef600a7 - - 5296d26b0373 - - 1a989b4110da - - 58091e1be01b - 6a636d58dfc2 + - 1a989b4110da - 78cd8b69da4c + - 58091e1be01b + - b0d39ef600a7 + - 5296d26b0373 - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: + - bf8325a07ce7 + - baa8823f8073 - e8af591435d1 + - 4d3ce9dc1525 - b641062a2587 + - b17394940c7a - '388983871932' - - baa8823f8073 - - 4d3ce9dc1525 - 591cc8518033 - - bf8325a07ce7 - - b17394940c7a 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: - - d1f8f55f564d - - e6b5cbbf449b - - 59fa8742285e + - 1a2ef636f48e - 38d75661c235 + - c2ab91a0d506 + - e6b5cbbf449b + - d1f8f55f564d - 3a233c8eb814 - 3ca3de4e5291 - - c2ab91a0d506 - - 1a2ef636f48e + - 59fa8742285e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -570,29 +570,29 @@ tools: - name: vcf2tsv owner: devteam revisions: - - e92b3c0f9224 - 285060661b45 + - e92b3c0f9224 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -605,8 +605,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -619,8 +619,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -649,15 +649,15 @@ tools: revisions: - eae7c08ebb6f - 4bdc111b2470 - - fa24bf0598f4 - 6b935ab36d7b + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -670,8 +670,8 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -698,8 +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 @@ -712,16 +712,16 @@ 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: + - f0580efedada - ee60203e68d9 - 5b7120c66efc - - f0580efedada tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -751,7 +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/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 73b1aa0c3..9cbcfa975 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - - c2ef298da409 - 78c75f134c16 + - c2ef298da409 - 6e9aea89e388 + - 3f3e247c053d - 4efdca267d51 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 @@ -41,15 +41,15 @@ tools: owner: iuc revisions: - 3e1f6f6d557e + - a79ee60b6926 - fe3ca740a485 - - 133f36c29579 - - 1aae04680c4b + - f29602ae449e - cd2480f35935 + - 4f2967b27e67 - 44018dd6b447 - b5d8e5475247 - - 4f2967b27e67 - - f29602ae449e - - a79ee60b6926 + - 1aae04680c4b + - 133f36c29579 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,34 +62,34 @@ tools: - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 - 6519ebe25019 + - dc027fa56d55 - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: + - 09855551d713 - 28433faa6e42 - ca6d970d931c - - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - 92eee5f31117 - da5f1924bb2e - - d77802fe76f7 - 728dacaf08a9 + - 92eee5f31117 + - d77802fe76f7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - 8fd427007e93 - fe48aa4ccd5e - 7355bbf5e05f - - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -122,9 +122,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -148,61 +148,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 756376aeb1ae - b6b5cd37f2a2 - - 9c15ca7e764e - 3bbe70fef6df + - 9c15ca7e764e - 14f588312c56 - - 582fd74dc2a1 - 9f2455341fac + - 756376aeb1ae + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - a230ea445788 - - 1691af4a0d17 - - 0ffe5be70caf - 989f7c061f35 - - 30fb23d4c31c - - 8e1ace8f77c6 - 73428a792541 + - 0ffe5be70caf + - 8e1ace8f77c6 + - 1691af4a0d17 + - a230ea445788 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 30f08d74024f - - 5a5ae61da69c - - 563a19373357 - - e94187d661df - 0418d28136de - 57c6718cbfcc - 494f0bb4a993 + - 30f08d74024f + - 563a19373357 + - e94187d661df + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - - 1bc5a03faf2e - f77d7b685bb3 - - 2bba2ff070d9 - 4b96ced19f75 + - f31125bb85ea - d6c7106b7b2e + - 1bc5a03faf2e + - 2bba2ff070d9 - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 52af33194019 - d3af38b9c7e1 + - d77fdcca400e + - 52af33194019 + - fed64e676186 + - b3cf4684e9c7 - 54961e026fe4 - 520e30695ec3 - - b3cf4684e9c7 - - fed64e676186 - - d77fdcca400e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -214,9 +214,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 07d7991bf205 - - 79261884facd - 2aea122fbd25 + - 79261884facd + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -229,9 +229,9 @@ tools: owner: iuc revisions: - 43798b4caee0 - - ef2ad746b589 - - 8b3e3657034e - 602de62d995b + - 8b3e3657034e + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -290,18 +290,18 @@ tools: owner: iuc revisions: - 3c1a01127868 - - 370c210d9541 - d46d803ca6cc + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - c8ac28e8ac44 - - b815ec682418 + - 624606f7c996 - 033755194fe9 - e95d52d295d7 - - 624606f7c996 + - b815ec682418 + - c8ac28e8ac44 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -349,10 +349,10 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - bf68eb663bc3 - a17498c603ec - d643e3b03500 - - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -396,22 +396,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5b80f544c67f + - 6322be79bd8e - cfcf33df7fc0 - - 68693743661e - 268d162b9c49 - - 6322be79bd8e - - 5a29ab10dba6 - 8f92c2b26e6d + - 5a29ab10dba6 - 5c7b70713fb5 + - 68693743661e + - 5b80f544c67f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -430,24 +430,24 @@ tools: - name: tbprofiler owner: iuc revisions: - - 4839e590cb26 - - d03af1c7002c - - 51dd22484644 - - 45083d070fb8 - - e1a9d6fd258d + - 200c378d85f3 - 809dfc93d593 - - 37213cf56392 + - e1a9d6fd258d + - 45083d070fb8 + - 51dd22484644 + - ba6f87115e13 - ac8250086ac3 + - d03af1c7002c - 037a11682176 - - ba6f87115e13 - - 200c378d85f3 + - 4839e590cb26 + - 37213cf56392 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 f80c7305b..5d151a55b 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,44 +2,44 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - d6d5ccc2c581 - - 8f1b150a2487 - - a929ce596a34 - - 553bfe8bd0b5 - - 0e93176640ac - 841084c5fc46 - fa5259cc561b + - d6d5ccc2c581 + - 0e93176640ac + - 7547fcab5d19 + - 553bfe8bd0b5 + - a929ce596a34 - 890b794c997d + - 8f1b150a2487 - 0124fce4654a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 067592b6b312 - ddddce450736 - - 94fe43e75ddc - b2860df42e16 - - 21e491ad532a - b9e31c5c01c7 + - 21e491ad532a + - 067592b6b312 + - 94fe43e75ddc 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: - - 22286dab5aa1 - - faee8629b460 - - 5258e18bbe23 - 3371c5bdc17a - a7f16f24e9a1 + - 22286dab5aa1 + - 5258e18bbe23 + - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -52,30 +52,30 @@ tools: - name: busco owner: iuc revisions: - - 602fb8e63aa7 - - e824f5d958d0 - - 46ae58b1d792 - - 2babe6d5c561 + - bb935709506a - 41030a6c03b7 - 2dd755c1c6ff - - bb935709506a + - 2babe6d5c561 + - 1e62c28ba91d + - e824f5d958d0 + - 1440ae06552f + - e4bd1e99bacf + - cf13a1e03e5b + - 94170eee0ad8 - 4048d82f0c88 + - 46ae58b1d792 - 5ecdeca79a0d - - 94170eee0ad8 - - 1440ae06552f + - 602fb8e63aa7 - ea8146ee148f - - 1e62c28ba91d - - e4bd1e99bacf - 0d243f458b53 - - cf13a1e03e5b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - c5b7390290b1 - - 5732f959936a - 86f150c8019d + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -87,22 +87,22 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 - - 291923e6f276 - 3e4f8642c77e - - e27815e82dd4 - - cb8dfd28c16f - - 1f0769f0b56b - 8d4f03b5fe9d - 1ce9b1d72ec3 + - 291923e6f276 + - e27815e82dd4 + - 276f5d8712d5 + - 1f0769f0b56b - 3ee0ef312022 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 3169a38c2656 + - b2f674562a18 - 01210c4e9144 - 460fad600dce tool_panel_section_label: Assembly @@ -110,19 +110,19 @@ tools: - name: getorganelle owner: iuc revisions: + - ba88bc5a6446 - 06bcf65179fb - 8b330a577046 - 7348b69e5109 - - ba88bc5a6446 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 3fba9c77550a - 3ef480892a9f - 690c2caa367e - 5127a713de83 - - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -134,23 +134,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 045c7c3d8e59 - - ec9e21e9c71b - - 0ee0c3089254 - - 60024a528cbd - - 9ef6920c3089 - - 71740308d412 - df25d4fb79b7 - - 6505bd37670d - - 5f625c63b8bc - 3f7be05a1597 + - 2061fb3b81b4 + - 60024a528cbd + - 0ee0c3089254 - da9d8bf98802 - - f3c89da3af16 - 5bec28269d95 - - 366a11d316a7 - - 41cea2aa2dce - - 2061fb3b81b4 - 284a1cb82b61 + - f3c89da3af16 + - 6505bd37670d + - 045c7c3d8e59 + - 5f625c63b8bc + - 71740308d412 + - 41cea2aa2dce + - ec9e21e9c71b + - 366a11d316a7 + - 9ef6920c3089 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: + - 7518ee87b53d - a96f3ad4e0d8 - - de387b2b2803 - 14ddfc8ffb93 - - 7518ee87b53d + - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - 09c589057ee8 - - f8113c25bc6b - - d7edbc9c3a07 - - 9d79beb19ac3 - eb7b00ec347d - 39edec572bae + - d7edbc9c3a07 + - f8113c25bc6b + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - - 29dabd8db6f2 - 51c2360aa807 + - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 606b09cc9860 - - f338e9942b27 - eb7a370f6588 - - fd128c111ab0 + - 99ecfdafc64f + - f369ef5f210b - 3ca2d2a9068c - - 2ecf5a570907 + - fd128c111ab0 + - 606b09cc9860 - e731ea24e48d - - f369ef5f210b - - 99ecfdafc64f + - f338e9942b27 + - 2ecf5a570907 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 - - b799a615995d - a7b889b90140 - 73a3846701e1 + - b799a615995d + - 8b6d0d85252b - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -244,8 +244,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 7c2f5268d01c + - 64a1c751d99b - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,46 +258,46 @@ tools: - name: pretext_map owner: iuc revisions: - - dfb8a4497339 - - 02831bf9e95f - - d256a51a656b - bbe19ef04a74 - 2b16ba799da9 - 8fef980d48b5 + - d256a51a656b - 79b48f02db49 + - dfb8a4497339 + - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - e9bd16ba5ebd - - a315c25dc813 - 76d4cbefff85 + - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - 7594365c546b - - 342a1d1fed7b + - ebb0dcdb621a - 675488238c96 - - 6fcbee531de6 - 875d0f36d66f - - ebb0dcdb621a + - 59db8ea8c845 + - 6fcbee531de6 - 72472698a2df + - 342a1d1fed7b - 3061c8b029e5 - - 59db8ea8c845 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 + - 78c533842eeb - d865b62f501c + - a199cd7ac344 - cd06929b224b - - 78c533842eeb - - 39bed8de8017 - aa39b19ca11e + - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -310,10 +310,10 @@ tools: owner: iuc revisions: - 2b2a352488fa + - f11b994b7eb2 - f8564b2d7f63 - 33b7d8481a76 - 5c55448d0f33 - - f11b994b7eb2 - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -327,13 +327,13 @@ tools: - name: rnaspades owner: iuc revisions: - - ef69617ecb42 - 1d06c8b38e77 - - 5fc94b3a4704 - - e122f9101584 - 53c2bc8c2ae3 + - e122f9101584 - 28189050e437 - 378e55aeeb25 + - 5fc94b3a4704 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -346,10 +346,10 @@ tools: owner: iuc revisions: - 865119fcb694 - - ad80238462c1 - - f698c7604b3b - ee17a294d3a3 + - ad80238462c1 - 83ead2be47b2 + - f698c7604b3b - 196a599ec43d - d9f6a00b6db7 tool_panel_section_label: Assembly @@ -357,80 +357,80 @@ tools: - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - - 5e0825476fb7 - 24e471d13fe9 + - 5e0825476fb7 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - c33a476f4001 - - 7490b213baa9 - 051fd2db8a27 + - 1fc82fe7ebef - 1bb12736175c - 904bf932cf78 - - 1fc82fe7ebef + - 7490b213baa9 - 604782a8a53a + - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - ad8b536d1caa + - 34305b013402 - 9678993ca5bd - fee85957cebe + - 655fa188c3cc - 808b3a0a6716 - - ad8b536d1caa - d6e617c4e338 - - 655fa188c3cc - - 34305b013402 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - e5a3b75a271f - - 21da31ed41a1 - - b8002c3f7141 - - 8d4b90bf9caf - 7e27faaad80e + - 8d4b90bf9caf + - e5a3b75a271f - 6b5a5842531e + - 21da31ed41a1 - 037f9927c4ff + - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 328aa71f0f3c - - 5b26685e5d3b - 2a10645aeadd - f1532cb33c75 - - 9de69775f512 + - 5b26685e5d3b - 7922870efcca + - 9de69775f512 + - 328aa71f0f3c - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 8cc856b935ee + - 6aad515a5270 - 1708851f8804 + - 340bc17f49cf - 85fb02c43042 - - 6aad515a5270 + - 8cc856b935ee - e41dcb0e913b - - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - b65a43f70b99 + - 6357b127161e - d5fb354f745d - - d159735a6a9f + - b3490b036c5a - de1260f8a300 - 249f6a28c751 - - b3490b036c5a - - 6357b127161e + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades @@ -439,9 +439,9 @@ tools: - 7897763d14ec - d5887ace0dd4 - a90db5dbaaf3 - - b7829778729f - 9006e5836729 - 33368fec3b70 + - b7829778729f - dd7ad84f3943 - d2d1df21dfb9 tool_panel_section_label: Assembly @@ -449,23 +449,23 @@ tools: - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - - ed2425b9fd27 - ced385aa976d - - 6f4c8ad6ea01 - 8f631679571f + - 505a9833ab5d + - ed2425b9fd27 - 189e837009c9 + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - e59bee4565b3 - - 19bdfd1e6fe3 - - f31d376ce725 - 9ded6109434a - - d40ed4eb0c0e - 356afed970b4 + - d40ed4eb0c0e + - 19bdfd1e6fe3 + - f31d376ce725 + - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition @@ -473,21 +473,21 @@ tools: revisions: - 4688ae3b49b5 - af40e971a8cc - - 80a17897564d + - ebd801e712bc - b23249f81bc4 + - 80a17897564d - 6dd935e4984b - - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - b5e35a2ca4f3 - - bb11fefb23a3 + - 937ea677d437 - cb1e3db43020 - - 59bd28f6265d + - bb11fefb23a3 - b64696992ee9 - - 937ea677d437 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample @@ -495,10 +495,10 @@ tools: revisions: - cb4768eeca3b - 6bfab4a4a988 - - 05bd7504fdb2 - - 6015aa0303f2 - 2628f6790eda + - 05bd7504fdb2 - 383bb5ad32e2 + - 6015aa0303f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler @@ -516,18 +516,18 @@ tools: - name: velvet owner: devteam revisions: + - 5da9a0e2fb2d + - 8d09f8be269e - 08256557922f - 920677cd220f - - 8d09f8be269e - - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 82398ba86ba7 - - 37d88f41c810 - 4a53b89fa703 + - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -539,8 +539,8 @@ tools: - name: yahs owner: iuc revisions: - - 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 4eab817f6..10e54112a 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -3,25 +3,25 @@ tools: owner: iuc revisions: - bfd290fe1588 - - 1ae00120dd24 - - 4768f7f8e93f - 392f100eebcd + - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 1f5641a52664 - ded48b36f3b7 - 31812e7a1315 - 8e8dc9a1e3e5 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - - 24a7a95867b0 - 17fcac7ddf54 + - 24a7a95867b0 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index a32d1e0ff..b198fca64 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: + - d1f62024a08b - 159b04e36791 - - 7beb76ffbc0f - 0840ba83860c - 1c427e24fb79 - - a9c9d768b751 - 204a131e47db - - d1f62024a08b + - 7beb76ffbc0f + - a9c9d768b751 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 f004a761c..13e54546d 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - a8eabd2838f6 - - b28e0cfa7ba1 - - dde39ba9c031 - - e19bebe96cd2 + - 589e7e57fd6d + - ce3c7f062223 - 64e2edfe7a2c - a68aa6c1204a - - 589e7e57fd6d - - a1a923cd89e8 + - a8eabd2838f6 - 07e8b80f278c + - a1a923cd89e8 + - e19bebe96cd2 - 87ee588b3d45 - - ce3c7f062223 + - dde39ba9c031 - 0a5c785ac6db + - b28e0cfa7ba1 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 d71b9f720..fc0bebec7 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,24 +8,24 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - 54f751e413f4 - e8ac2b53f262 + - f921014aba5a - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: + - 5edc472ec434 - a52d2d93e595 - - 0e3cf9594bb7 - 2889433c7ae1 - - e25d3acf6e68 - - 5edc472ec434 - - cbf3f518b668 + - 0e3cf9594bb7 - 6f386c5dc4fb + - cbf3f518b668 - d999e774072a - acf4e47b734c + - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 3807d2940..242082a20 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - c8cdde00b105 - 710301bc46fa - - 27ee142314a9 - da6bd1975a71 + - 27ee142314a9 - f4230f116196 - 6ca543ec1bf8 - 095ad4d096d1 - - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,14 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 + tool_panel_section_label: ChemicalToolBox + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ctb_im_conformers + owner: bgruening + revisions: + - a4b1474efada tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_rxn_maker @@ -124,9 +130,9 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 0fac8e2afc13 - - 88076940fa94 - 3b8a9d5ced85 + - 88076940fa94 + - 0fac8e2afc13 - 79cfd9ead848 - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox @@ -134,64 +140,64 @@ tools: - name: gmx_em owner: chemteam revisions: - - eb6564a60136 - - 55918daa5651 - 715cd0e87781 - d532b7e5f64b + - eb6564a60136 - b46d4b4d995c + - 55918daa5651 - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - dae135dfd519 + - 5579659312e6 - f26afd1b7104 - d2f955aea23a - - dae135dfd519 - fdf2cc80adb5 - - 5579659312e6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - bc31d02be922 - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - - cac1886249a2 - - ed736e6eee39 - - 4da9ee404eab - 2c349b027a01 + - 4da9ee404eab + - ed736e6eee39 + - cac1886249a2 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - d1f803b5943c - 807aa4c9293d + - c0c9a5024177 + - d1f803b5943c + - f197e34c33a9 + - 73008ef1f487 - 2e219a2d9327 - da8753545526 - - 73008ef1f487 - 525ca7c8065f - - f197e34c33a9 - - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: + - 2c8ed1b52bf7 + - 27ea4e1a3f95 + - c4fbab8e03c5 - 61094e01eff9 - 1809414a9454 - 7568ae18908a - - c4fbab8e03c5 - - 27ea4e1a3f95 - - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -203,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - 730ef07b90ae - 79e8ab8f1e81 - ccfbd956a2d3 - ba83f0923369 + - d7ec25187599 + - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -262,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - e6011617c748 + - 4242b4d68e9c - b59c91adeac1 - e2c36f62e22f - - 4242b4d68e9c - - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -277,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 7672039a0bb0 - 75ee9c410951 + - 7672039a0bb0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -344,10 +350,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 9b48456a96fe + - d4c67ced6abc - 85fad59f8168 + - 9b48456a96fe - bf99565cec1f - - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 647187a97..d3ab19cbb 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -3,9 +3,9 @@ tools: owner: bgruening revisions: - 163688bb8f73 - - 2605cbdaa7d8 - - c97a786e8fb5 - fa56d93f7980 + - c97a786e8fb5 + - 2605cbdaa7d8 - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,18 +18,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 424aefbd7777 - - f5d67c722d67 - - 495a4173006f - 86e2413cf3f8 + - f5d67c722d67 - 640d3af5d833 + - 495a4173006f + - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index da9122084..9baa0ab20 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,17 +9,17 @@ tools: - name: collapse_collections owner: nml revisions: + - 830961c48e42 + - 25136a2b0cfe - 90981f86000f - 33151a38533a - - 25136a2b0cfe - - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,9 +31,9 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - - 0046692724f9 - 2dae863c8f42 + - 0046692724f9 + - 6cbe2f30c2d7 - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 7132e631e..454e987e5 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - ab9350a8ab4d - - 5e1240a87bcb - - 6ef0b5664c69 - - 3b6f97e7094c - - f3a19509108a - - 4a6ee918c13a - - e3cbd2287f63 - a3b86937ead6 + - f3a19509108a - 367b1ed91207 - 0b3c3ad92827 + - 4a6ee918c13a + - 6ef0b5664c69 + - 5e1240a87bcb + - e3cbd2287f63 + - 3b6f97e7094c + - ab9350a8ab4d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 33c99804a32f - 72ed72122deb - e525f9ffb9ac - - 584008e574b2 + - bd46669113b9 + - 1b5fc03380d4 + - 54ccb7e1f49a + - d4d4e9febf5c - 091bb5922a82 + - 33c99804a32f - e177a8ea0bf1 - 501c21cce614 - - bd46669113b9 - - d4d4e9febf5c - - 54ccb7e1f49a - - 1b5fc03380d4 + - 584008e574b2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -58,8 +58,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -93,8 +93,8 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - 4dea02886337 + - 3e436657dcd0 - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,8 +120,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - 18dbde5680c0 - b9ea85dfaf45 + - 18dbde5680c0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -133,18 +133,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 2dcfbbf9071a - 68f57cc8fad0 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - 19e45916daf9 + - 26c6706bfb07 - b9b385097f13 - 92ac8e086317 - 63769c4217a7 - - 19e45916daf9 - - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -156,15 +156,15 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - 3c6f9e8a4c17 + - 8067dfa00ed2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - - a2f83a375bf2 - 98704d357ede + - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 54269a63e..800517b4a 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,183 +2,183 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 29451af70c52 - - e821645ef8fc + - 5f6d123679f4 - de72ba3ed6f2 - - c929a006727f - 268e91e540ee - - 5f6d123679f4 - a1ca9bccc7f2 + - 29451af70c52 + - c929a006727f + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - - 12af64f93288 + - 2d2cf5c1ea8a - 0e143b4c3987 - 7a7fd0f5f15d - 0e49b109abc2 - - 2d2cf5c1ea8a + - bb1e4f63e0e6 + - 12af64f93288 - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 7c1beb6d6eca - c06951d10364 - dc059492a995 - - 1d848bc4585f - 195e98217334 + - 7c1beb6d6eca - 81b1e3e1fc6c + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - 26e7304d6737 - - 71aa86af6762 - bfff7454b59a - - 3d211717a775 + - 71aa86af6762 - a67ac707496a - 93eb012d9eed - 07418a30ed01 + - 3d211717a775 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 5be24eba848d + - 2bc10a9ca58b - 26983857c91a - - dd0b7398bb96 - 29fcfd36e90a - - b8858746dc1f - - 2bc10a9ca58b - - 5be24eba848d + - dd0b7398bb96 - 56d5b797ce84 + - b8858746dc1f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - ee3a1b0f45f1 - - 7ef978dc1b8a - - 7e6bcd2e5128 - 72bfafe3330b + - 7e6bcd2e5128 + - 7ef978dc1b8a - e6d0bff01239 - c3e012dfe21f - 9384cd033f30 + - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 - - 9470f29702f8 - - fb9cf9c97ec4 - - fd1275e01605 - a60c359ec43c - b73e213add0c - - 514fa53b5efb - 167788df3b46 + - 9470f29702f8 + - fd1275e01605 + - fb9cf9c97ec4 + - d9a637e83828 + - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - - 2c37ce318bc3 - 5bffaa8354a1 - e479c7ca5570 + - 2c37ce318bc3 - a02cfa31e9cb - - 86febdcc4283 - c34d11ea4ba6 + - 86febdcc4283 + - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 - 78f405266706 - 192ef85c0b0b - - 2d466b530754 - - 004aea905d4d - - 1fcb7adc39b8 - 69a8621ca2f0 + - 1fcb7adc39b8 + - 004aea905d4d + - 01fb6a7654e6 + - 2d466b530754 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 2f9e4843f480 - 9ecba5e225a6 + - 459cfa861f0b + - d580d6acd1df - db940c262830 - 137c4beed34b - - d9ce4897dbb2 - - 2f9e4843f480 - 3c9f0c486cca - - d580d6acd1df - - 459cfa861f0b + - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - fd408d755394 - - bad3ca889618 - 32e451def88c + - f264afa9fa6f - fbe773640707 - - 2c66e43f1c86 + - bad3ca889618 - bd7db9e2f2cb + - fd408d755394 + - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 3b9d990a0a0e - - 56bce3c82278 - 4e12ea27f788 - 7e361d147872 - - 231994413f89 - 7fda5607e777 + - 56bce3c82278 + - 231994413f89 - 9368fbc49c8b + - 3b9d990a0a0e tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - c03c3384cd81 + - ce4ce3316f74 - d9114ef1c8a5 - e65d16fb2724 - - 94ca68515826 - b1779366c8e9 - - c03c3384cd81 + - 94ca68515826 - 4431f39ede55 - - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 4ed32329e0ed - 793665fff0f8 - b88ebb3672a1 - - 4ed32329e0ed - d57251071381 + - f8fc4e5aff9d - 2da482e408b8 - 23f7c5f1fdaf - - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 010e58e9d822 - - ba6efa77fb79 + - 25d830337d31 + - e4c7985d4585 + - a4dfb122e52b - c60570fa602f - 512155688d98 - - a4dfb122e52b - - e4c7985d4585 - a7849312d328 - - 25d830337d31 + - 010e58e9d822 + - ba6efa77fb79 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca @@ -186,21 +186,21 @@ tools: revisions: - c899e0ccff8c - aa200e4f3939 - - 38e3f226248b - - 69264da0ce77 + - 4d678170d29b - 00d869ea03a1 - 443d9a9d6d11 - - 4d678170d29b + - 69264da0ce77 + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - c361b12d207a - aac8444d6681 - 10301d137111 + - 6662b1a8d326 - a2d70c4fd406 - - c361b12d207a - d806504e96d9 - - 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 8eff59553..83a0942c9 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -2,15 +2,15 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - d50dc96e3ce9 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -37,29 +37,29 @@ tools: - 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 owner: iuc revisions: - - b6d9ea2fb41b - 12b9e285ca1c + - b6d9ea2fb41b tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 4cf47c504672 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index caecd371d..2a6d2feda 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 + - 63dd26468588 - ce385837c160 - 832c20329690 - - 63dd26468588 + - dba489bfcd62 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index ab731264a..68f49c8e3 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 29bdbc353f20 - - cf1322aeb137 - - d82648ad25a3 - 6da3972210ee - 62f5fab76dfb + - d82648ad25a3 + - 29bdbc353f20 + - cf1322aeb137 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 b531a3db7..4da737153 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -9,40 +9,40 @@ tools: owner: lparsons revisions: - 5915ea1ec9b1 - - c5e2e5902201 - - 4e5056fefd88 - 64172f1c1202 - - c053d4cad713 - - 5eb7e84243f2 - - 49370cb85f0f - - 660cffd8d92a - - fe74900d6dc7 + - 4e5056fefd88 + - 288f97432497 - de6cebe3c043 - 135b80fb1ac2 + - 660cffd8d92a - 44e2cc14f75b + - 8665bcc8b847 + - b1c926deaa2d - 8c0175e03cee + - c5e2e5902201 + - 49370cb85f0f + - e4691e1589d3 + - c053d4cad713 - 48f587c13075 - - c4b82dce8335 + - fe74900d6dc7 - 093678460093 - - 8665bcc8b847 - - 288f97432497 - - e4691e1589d3 - - b1c926deaa2d + - 5eb7e84243f2 + - c4b82dce8335 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - f666895cbebd - - 8889eb864cef - 9db07fd39f85 + - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -60,16 +60,16 @@ tools: - name: fasta_formatter owner: devteam revisions: + - 859422bcb689 - 516b97a23d7e - 9457a20156db - - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -83,10 +83,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd + - 9c620a950d3a - cd0874854f51 + - 56022eb50bbd - 0dbb995c7d35 - - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -95,15 +95,15 @@ tools: - d60c3f704da0 - dbf9c561ef29 - 65b93b623c77 - - 1d8fe9bc4cb0 - c59d48774d03 + - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -137,8 +137,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -151,15 +151,15 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -167,8 +167,8 @@ tools: owner: devteam revisions: - 045f0e1043f7 - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -181,8 +181,8 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - b63b2bfb3ea3 + - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -194,34 +194,34 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - 09070cacefd8 - 529bccd5e4a1 - d5e9e83cd3d8 - - 09070cacefd8 - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - 8abdedf55101 + - 4bedca26c133 - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 - bdf1ce174e39 - - 90858c306551 - 736b8f6ee456 + - 90858c306551 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - 07497255281e + - 7ce1891db6f5 - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -229,17 +229,17 @@ tools: owner: devteam revisions: - f984bb114520 + - b29d37ca9e41 - 02f8a17a4ebd - 3599f5451ee2 - - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - e246088b6e34 - 0c2907307ba4 + - 6027ef51ef91 - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -247,9 +247,9 @@ tools: owner: devteam revisions: - 547e8d00f11c + - 73194cdd4f57 - 377ac2829eac - 61b4cedc8934 - - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -261,10 +261,10 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - - f69501361cec - b4c6f054210a + - 2f804526f5fd - 037f0acc7830 + - f69501361cec tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -277,8 +277,8 @@ tools: - name: seqkit_sort owner: iuc revisions: - - fdc21382376d - 61eb4cfc7313 + - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -291,33 +291,33 @@ 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 owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - bf04bd405d5b - 71f649c23021 + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - e654095ab143 + - 8250ea3a1501 - 24013bf85a6f - - b557acca0b56 - a535cf1e5da4 - - 8250ea3a1501 + - e654095ab143 + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -329,13 +329,13 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 - - f3759eec3018 - 015cf18f4a15 - - 27ac32a22ad2 + - 7accf7407811 + - f3759eec3018 - 9fa7803d1c51 + - 6a675c3aa610 + - 27ac32a22ad2 - 828dba98cdb4 - - 7accf7407811 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -347,7 +347,7 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 953b4821b183 - 4c8a1c7d3608 + - 953b4821b183 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 64ad8d312..f77470fa4 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -4,28 +4,28 @@ tools: revisions: - e41385662e5e - ce9cd02d5b88 - - 7b4468117008 - 64e9a6afdd0c + - 7b4468117008 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: - - ff9530579d1f + - 9da02be9c6cc - 2c64fded1286 - 3d0c7bdf12f5 + - ff9530579d1f - f2e8552cf1d0 - - 2b0c9d9fc6ca - e7b2202befea - - 9da02be9c6cc - 5ec9f6bceaee + - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -47,32 +47,32 @@ tools: - name: fastx_quality_statistics owner: devteam revisions: + - 7306ec78632a - 59003d0543cd - cc0fd298cc17 - - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - 8880fb74ef56 + - a72af9de6bf5 - 1f296803dfa3 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 5e33b465d8d5 - - bf675f34b056 - - 3d93dd18d9f8 - - 1c2db0054039 - - f7e2f1eb3a16 - 75c93c70d094 - - abfd8a6544d7 - - c1a4b5f3b432 + - 1c2db0054039 + - 5e33b465d8d5 - 9a913cdee30e + - c1a4b5f3b432 - b2f1f75d49c4 + - abfd8a6544d7 + - f7e2f1eb3a16 + - bf675f34b056 + - 3d93dd18d9f8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index b747339b5..950bfb9dc 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -9,15 +9,15 @@ tools: - 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 owner: peterjc revisions: + - 85ef5f5a0562 - 83a19df00eab - 141612f8c3e3 - - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 5e380ba73..38fbbf8dc 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,9 +16,9 @@ tools: - name: gemini_annotate owner: iuc revisions: + - 8f53b238a360 - f2f3bc622a16 - 0c8f7322f8fc - - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -38,15 +38,15 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,8 +59,8 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: - - b2c25142267e - - 45296e47d565 - cf61daf064fe + - 45296e47d565 + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -101,30 +101,30 @@ tools: - name: gemini_mendel_errors owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: + - 840fb4850be3 - 666f60a9331a - da74170c55c7 - - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -144,22 +144,22 @@ tools: - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats 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 1445c9d17..2e186f768 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 70c9f2c61..2214cf40b 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee - b39347891609 - 983bf725dfc2 - e9df53a75f3c + - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -18,53 +18,53 @@ tools: owner: iuc revisions: - e063168e0a81 - - 1c58de56d587 - 28587613264f + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - f5ea3ce9b9b0 - - 8848455c0270 - - 6591f049cf7e - - e407b9da183a - - c441583adae5 - - 4317d3cb6cba - - 734abc7ac21d - - ba931a59dd59 - - 653e89d73fc4 - - 1790dcf3c32d - - f8054ea1c365 - - 6ea73833cf67 - - 7068f48d0ef9 + - e08a7ad4378b - 4df8de2d0e48 + - e407b9da183a + - aad3885b3216 - 5e6237d58b0c - - 83c7d564b128 + - 6591f049cf7e - 516a54ddf218 - 1ec814014652 - - aad3885b3216 - - 9a776b080193 + - 8848455c0270 + - f5ea3ce9b9b0 + - 734abc7ac21d + - 6ea73833cf67 + - 83c7d564b128 + - 7068f48d0ef9 + - ba931a59dd59 + - 4317d3cb6cba - 69ebb7f46e45 - - e08a7ad4378b + - f8054ea1c365 + - c441583adae5 + - 653e89d73fc4 + - 9a776b080193 + - 1790dcf3c32d tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 75b3b3d0adbf - 21a560af5913 - - 34758ab8aaa4 - 9aaa46d45472 - - 75b3b3d0adbf + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a - 95fb5712344f - - 054483e27a35 - - af5eccf83605 - 468c71dac78a + - bfdc6a7ffd3a + - af5eccf83605 + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index af5b96571..0ed8ad3ef 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: + - 290a11559985 - 4b519282a05b + - 740057a5126d - a64dc31ab7f2 - - c4bde687c846 - fd59d783248a - df7356989ac1 - - ae9994cf526f - - 740057a5126d - - 290a11559985 + - c4bde687c846 - 7f13dc906cb9 + - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,8 +28,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - f95284aa2946 - 867ab348287d + - f95284aa2946 - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,29 +42,29 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 3b37b1b1c3a7 - 374e9062d874 - '566197475670' - ca7cb0eaad62 - 53460afd5115 + - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 1a72f938213e - - 391a4cc45fea - 10515715c940 + - 391a4cc45fea + - 3d059e9c2fba - d3a9e32672ec + - 1a72f938213e - da4c086cff5b - - 3d059e9c2fba tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca @@ -77,19 +77,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - 1acf88921176 - - 5298e06f14f9 - - d0fc8b746d57 - e3a675da7fd0 - 299307abd804 + - 5fe1dc76176e + - 5298e06f14f9 + - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 17b666467c32 - 0e7290688b50 + - 17b666467c32 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -101,15 +101,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -127,17 +127,17 @@ tools: - name: jbrowse owner: iuc revisions: - - fd5dbf0f732e + - 4542035c1075 - 1cfc579079a6 - - 667e17248bfe + - fd5dbf0f732e - 2bb2e07a7a21 - - ca2def38369c + - a6e57ff585c0 + - 836d1aa3e89a - 6cd09d7b5f37 + - 667e17248bfe - 17359b808b01 - - 4542035c1075 - 112eb40ba6cf - - a6e57ff585c0 - - 836d1aa3e89a + - ca2def38369c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -155,8 +155,8 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - f1691de443a7 + - fe154a7af404 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -169,10 +169,10 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f - - 85da91bbdbfb - 62e3a4e8c54c + - 1c5dcef5ce0f - f234e2e59d76 + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -191,9 +191,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: + - 6c571966cfb9 - 44c66e8d21e6 - 7c9417381ad5 - - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -205,23 +205,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 36b848d5f3ec - - 2824d77cd8f8 - - a1abfa420d9d - - 326a3db8d9d1 - 360df4999907 - - 14e7c35f3d00 - 4ac4e7083b7e - 7dd841a32245 + - a1abfa420d9d + - 326a3db8d9d1 + - 2824d77cd8f8 + - 14e7c35f3d00 + - 36b848d5f3ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 83c573f2e73c - - 2f557f6abbfb - 73b8cb5bddcd + - 2f557f6abbfb + - 44608d0193ed 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 ff01522a4..12b14dea9 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -70,8 +70,8 @@ tools: - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - 9d76c3d6dff6 - c9da9192eee5 + - 9d76c3d6dff6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat @@ -84,16 +84,16 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - c354af93f567 - 6903bc865d63 + - c354af93f567 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - ff6decc0f432 - 9a2f72d7dbd2 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -113,8 +113,8 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 0387a2179f88 - 73d43034c860 + - 0387a2179f88 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -134,15 +134,15 @@ 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: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable @@ -190,16 +190,16 @@ tools: - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - ea91cfd0444e - 0f98603d0116 - 767a675b5254 + - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 3b183f2f5..b495975e0 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -5,47 +5,47 @@ tools: - 9edf8894a22d - 29f66c353bcb - a4c13ddcc8ee - - ed2cca6b5de4 - 921a2da49a0c + - ed2cca6b5de4 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - ec4b948dc6f0 - 5746d61f0a91 - - 78fb5e286609 - 755df866ad0c + - ec4b948dc6f0 - d404277cc87a + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - - 4d511437b1e5 - - 03dd3c16ae4e - 977dc15add20 + - 03dd3c16ae4e - 11fa44ee0603 + - 9e357a8b2ec3 + - 4d511437b1e5 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 3b5b54ed6392 + - 41dbf4d162a2 - 77919cc3618e - 0ba4f56a3613 - c3e5e2cf12b7 - - 3b5b54ed6392 - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e + - 12d51d7be66f - 7babd8a46fe0 - 9939786dd9c9 - - 12d51d7be66f + - b63363075c2e - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index b60a40240..9a5f1c6e6 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,28 +2,28 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 3df9f0a4bf34 + - 81f0cbca04a7 - 7db4fc31dbee + - 0c777d708acc - 8bccb36e055a - 699a5e9146b3 - - 0c777d708acc - - 81f0cbca04a7 - - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - - 5bc8cdc17fd0 - - 2436a8807ad1 - 0a53256b48c6 + - 2436a8807ad1 + - 5bc8cdc17fd0 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 9d47aabda459 - e576b73a2e2f + - 9d47aabda459 - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -31,8 +31,8 @@ tools: owner: imgteam revisions: - b1c2c210813c - - 77f7159d775a - 70316d792fc9 + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -52,11 +52,11 @@ tools: - name: bfconvert owner: imgteam revisions: - - fcadded98e61 - - 10eed33aa9b2 - - b07f4839ca77 - 85edbb7a436b + - b07f4839ca77 + - fcadded98e61 - f3360fbeda64 + - 10eed33aa9b2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -69,16 +69,16 @@ tools: - name: count_objects owner: imgteam revisions: + - b58447a2eed2 - 664232d2a3f7 - 5bf8eb50b280 - - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 + - eb6c08714244 - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -92,16 +92,16 @@ tools: - name: cp_common owner: bgruening revisions: + - 6070780813d9 - e7273daa5ae2 - 670975e92458 - - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - cdf8e3c57dae + - ef4aed1d34c4 - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,56 +109,56 @@ tools: owner: bgruening revisions: - 2484086dee41 - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - bace5a93a97c - 11f177b1a59e - f2ed92b011a9 - - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 3245681b2f6d - - ad271f78a87a - 31d195bedf6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - 6100a22bf4f2 - - ff1a86a87364 - c09dcda1143f + - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: + - b178453ea8d1 - 3a05117669cf - 667a513e67e4 - - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity @@ -172,33 +172,33 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 91e03287f285 - a32c3f810ade + - 91e03287f285 - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - 8536b1ae0254 - 5499dc6f8ac1 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - e972e07c7845 + - 6f4715b8540a - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - 980aed9e8fd5 - e52c75a28c4b - 407925835dd9 - - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape @@ -228,15 +228,15 @@ tools: owner: bgruening revisions: - 48102a685037 - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -262,15 +262,15 @@ tools: - name: image_info owner: imgteam revisions: + - 7b6d9412c7f8 - 236ec78b2e53 - f8b4eada923c - - 7b6d9412c7f8 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images owner: imgteam revisions: - - ca362a9bfa20 - 8dc02c854048 + - ca362a9bfa20 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index baef95431..964459c6e 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 - - 78bbd17d0703 - e4ee04da1c19 - - 1069f6db0a0e - - 3a72fede57ce - - e319b5b65879 + - 78bbd17d0703 + - a38934e303b9 - f362150bef41 - 3e4f434a69c6 - - a38934e303b9 + - e319b5b65879 + - 3a72fede57ce + - d6e72da3ec35 + - 1069f6db0a0e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 8f8df367470d - - 618297d23022 - - c88553ec696e - 7fe36019c073 - - f91cfb73d369 - - 0135f1d487a0 - - 2b95d5c04908 + - 618297d23022 - fcbeda41d0ac - 9537184d421f + - 0135f1d487a0 + - f91cfb73d369 - 72ddd32392cd + - 2b95d5c04908 + - c88553ec696e + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - 2cf4a1cafc16 - - fafb3d685fa9 - d7e79eb3bcb3 - ad0dc9f4c9e2 + - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 5dc33613c288 - - 7f1cfa4c0e32 - - 6a1515bb0687 + - 43aac8d29685 + - 3d18f8c3c0f6 - 28a6f1908fcc + - ee29337f905c + - 6a1515bb0687 + - 94df24c6bc00 + - 7f1cfa4c0e32 - 8d36959b000d - - ee2beb764a7b - - 3d18f8c3c0f6 - 9eaadf03e0df - - a1c2aecd7a0d - - 43aac8d29685 - bd2a7d1316b9 - - ee29337f905c + - ee2beb764a7b + - 5dc33613c288 - 8c05afb547fa - - 94df24c6bc00 + - a1c2aecd7a0d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - d37ede8589b2 + - bcaa0d571ce2 - 8858fa037a15 - - cb903c9dc33d - - db536ad45f28 - - 86a20ae274fc - - 5671e1d3d5ee - - e3bb03cf207a + - 9f978da6528a - c092052ed673 + - 86a20ae274fc + - db536ad45f28 - 5d6ed46cc101 - - bcaa0d571ce2 + - cb903c9dc33d + - e3bb03cf207a + - 5671e1d3d5ee - 364f4ffec275 - - d37ede8589b2 - a250929be21b - - 9f978da6528a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 194e3ceee923 - - 12d66d0d05ac + - abbc8041e8ec - 230b05597996 - - 49236b03e4fd - 38b91a3190cd - - abbc8041e8ec - - c5c9f02b6167 + - 584beffa972b + - f95f403841ad - e1a015876aa9 - 3b6a16d82c1b - ed28dd32141c - - f95f403841ad - - 584beffa972b + - 49236b03e4fd + - 12d66d0d05ac + - 194e3ceee923 + - c5c9f02b6167 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 dda02b21c..51c23fd7f 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -3,9 +3,9 @@ tools: owner: iuc revisions: - 0f1724dd59d2 + - f198773344e4 - 17e3b698dd52 - b8a457820315 - - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 47fe6c2e1..ebd81c4f3 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,35 +2,35 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - - 522137aaa9c4 - 66d7efc06000 + - 522137aaa9c4 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 4d81e3e2fb63 - f22a9297440f - 8a794e6d3388 + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: + - b6ef6d0cb6b7 - e1317b5502fa - 818f9b69d8a0 - f1b9a42d6809 - 2af1346e68c9 - - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - 05143043ca13 - 1588f9076e32 + - c80db5d6fd8c - 947c2eacccb8 - 8334dc98c48e tool_panel_section_label: Machine Learning @@ -38,63 +38,63 @@ tools: - name: model_prediction owner: bgruening revisions: - - 25b46af53232 - - 1552b8cb4a94 - 83228baae3c5 - - 9991c4ddde14 - 29e4122c90de + - 9991c4ddde14 + - 1552b8cb4a94 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - f3dfa4bdf87e - - 841a6cc5fc58 + - 53616c8b0865 - a07ab242b0b5 - - 1a53edc4b438 + - f3dfa4bdf87e - 060ca94ac049 - - 53616c8b0865 + - 1a53edc4b438 + - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: + - 40f4447733b2 - 2fc89dcd41c8 - - d4808d5b83da - - dc4b5fd604a6 - 927586a18553 - 91c4e3331208 - - 40f4447733b2 + - d4808d5b83da + - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 36e8d6d5d01b - - 25ab6b4e376e - e5a5ad882f1f - - 301e07345c93 - 7626ea9c2e1b + - 36e8d6d5d01b + - 25ab6b4e376e - c6ae57f774c6 + - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - 02d2be90dedb - f9639b488779 - - 0630258dcf35 - 80852884053f - - 02d2be90dedb - - 4ed102b922cb - b7c3e9a3b954 + - 4ed102b922cb + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - ec69cbe34b73 - caeb57858702 + - 14180f9c831e - 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 1251ff4ac..695ebd60e 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - f6877ad76b00 - - 0d4acadabb04 - - 937aa69e715f - - 749c918495f7 + - d5ceb9f3c25b - 017aba02828d - cd659e8cc5fa - - d5ceb9f3c25b - - a6d65b0c67af - 17062a0decb7 - - 03e9b2fbc005 + - 937aa69e715f - 3ba8d4563129 + - 0d4acadabb04 + - a6d65b0c67af + - f6877ad76b00 + - 03e9b2fbc005 + - 749c918495f7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -32,9 +32,9 @@ tools: owner: devteam revisions: - dfd8b7f78c37 - - 2477830927ec - 3fe632431b68 - 64f11cf59c6e + - 2477830927ec - e188dc7a68e6 - 53646aaaafef tool_panel_section_label: Mapping @@ -51,43 +51,43 @@ tools: - 60afcc2c1d05 - e7f19d6a9af8 - 3e1ea2facca6 - - 37b497aa133f - 2ff111fac1d7 + - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 09b53c1d4ab1 + - b3eab4b67562 + - c0c2d0941de8 + - 53c0b7a1a0c3 + - 5cc34c3f440d - be1d967337e4 + - 8c6cd2650d1f + - 77b2770508f6 + - 11a0d50a54e6 + - 3f4d6399997b - 6b1e195506a3 - 037c6e54df11 - f54f5baedfdd - - 53c0b7a1a0c3 - - c0c2d0941de8 - - 11a0d50a54e6 - - 8c6cd2650d1f - - 3f4d6399997b - - 09b53c1d4ab1 - - 77b2770508f6 - - b3eab4b67562 - - 5cc34c3f440d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 42ce70172b72 - - 1cd2511a396e - - 5ef7ec16b04f - - e403d27e8f24 - - 13022c3d3076 + - 45795f582ae9 - b8f5f6e87f5c + - 42ce70172b72 - ec9cbd6b9a49 - - 00fbfac99d39 + - 5ef7ec16b04f + - 9ee34ba73ebf - 79b885ce78d7 + - 1cd2511a396e + - 00fbfac99d39 + - e403d27e8f24 - 178bdbdb6d24 - - 45795f582ae9 - - 9ee34ba73ebf + - 13022c3d3076 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 d0111cac4..fadca8ff4 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 6cd2a9e6ac49 - 90dc951da294 + - 6cd2a9e6ac49 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -75,15 +75,15 @@ 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 @@ -103,15 +103,15 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - b576ed720711 - f04610d25411 + - b576ed720711 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 @@ -168,8 +168,8 @@ 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 @@ -224,48 +224,48 @@ 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: - - c53a97599181 - 79ad928a0dae - 7b42ee54d757 + - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - f3a18e020cdd - 149b9cc7499b - 18ec7635bac6 + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: + - 481d769e2f7a - dfebc82ba1f0 - 134be5abb208 - - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 9064aecc78a7 - 02c772a49998 + - 9064aecc78a7 - 51332c2520c7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - - b341cfd4baf8 - e7305ba0dd38 + - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table @@ -279,17 +279,17 @@ tools: - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - d7f5878a98c3 - 99d118321d5f - 24278c6b6d1c + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: + - ffbabefbd2e2 - d90187b0f247 - ea0758b41473 - - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index c24c572ba..3887e5021 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,23 +2,23 @@ tools: - name: bracken owner: iuc revisions: - - 1d4bd12f01cf - 0c7b6eb7e752 + - 1d4bd12f01cf tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: + - 0e63d03c8790 - 18676df0cb3a - 0094893f5001 - - 0e63d03c8790 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 @@ -90,68 +90,68 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 7c2100246a2f - - 76d3d2b10738 - - 65db807336bc - 63f86089423e - 5b5a7af9fbb4 + - 76d3d2b10738 + - 65db807336bc + - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 96336c6a2bb7 - - 00f5005840fa - - 84fd33a60b35 - 1c35dadbe76f + - 84fd33a60b35 + - 00f5005840fa + - 96336c6a2bb7 - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - a9f4a217dcd6 - - f732237754fc - 34e55239e68b - addaf9d22850 + - a9f4a217dcd6 + - f732237754fc - e8fba04706d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 5fe3edf19b9c + - 0776d824d896 - 04c15826a0b8 - 8c202e741d68 - - 5fe3edf19b9c - 75403243703a - - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: + - e96bbb9e24ea - 75c8945b0da2 - - 1c9b3bcd4261 - 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 - - 306a40d4bb8f - - 35176674168c - 5c865a382933 + - 306a40d4bb8f + - 1d75bd0595e2 - 84743da21318 + - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 555ccac8a4c5 - 32c9ea835770 + - 555ccac8a4c5 - 78faebd0879c - ac72310b038a - 8daf4564ccda @@ -160,31 +160,31 @@ tools: - name: dada2_plotqualityprofile owner: iuc revisions: - - a58e4a43f49c - - cae017b76acb + - d60df8727f59 - 7b8cb2b02978 + - cae017b76acb + - a58e4a43f49c - f947b4bb5107 - - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - 073608a50ac3 - - 7f3b59dee073 - 1bc3657cd694 + - 04144473e59e + - 7f3b59dee073 - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - d943081510da - - 9058d8943303 + - 0a1224c4b781 - 19299bb1c6af + - 9058d8943303 + - d943081510da - a7817705348e - - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -197,14 +197,14 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - f8f56dd6449f - - 5c7ba3d85a01 - - b907a3c0434f - - 65d52c693b8e + - dbf1798c0dcc - 4d9445dff47b - c4db8c4de66f - - dbf1798c0dcc + - 5c7ba3d85a01 + - 65d52c693b8e + - b907a3c0434f + - f8f56dd6449f + - a68b985913ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -217,9 +217,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6d364c65c946 - 6c84982ee6f7 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - 6aad8ca3918b - e66ab198ec15 - bd7a9c6efb10 - - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - b084117133af + - d77397f09da1 - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: + - cad93abecac9 - 9704f1a3b32d - 7f208f1eb64f - - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -281,38 +281,38 @@ tools: - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: + - c409a495841f + - e88b731dad59 - 31c6d107e7a5 - 79706f10d680 - - e88b731dad59 - - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 172920f67a84 + - 094ad9c068af - 71ea608ddfa3 - 714d5a28cc5c - d24841f5c3d2 - - 172920f67a84 - - 094ad9c068af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - a293a742194f - - 12fb63b5f63f - - 2bdd84912a2b - 4137b492233e - - d7e9a3c41657 + - 2bdd84912a2b + - 12fb63b5f63f - a4d7148ccee4 + - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -324,20 +324,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - a92c06a3afa7 - cf87759761eb - 6fcb8ac37a3e - - 64bc7acc22a9 - - e2c71b852aba - 75bedfb2078b + - e2c71b852aba + - 64bc7acc22a9 - 97f7bb0851e7 + - a92c06a3afa7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -349,21 +349,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - 4033827c76b8 - - 4e5e73d03f0d - 2d35528d2141 + - 4e5e73d03f0d - c82508e76ad1 + - 4033827c76b8 - 080ea153677c + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: + - 6b7622dda516 + - 95bf7479d53c - 2cd76b089570 - fc6c328c292f - - 95bf7479d53c - - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -430,10 +430,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - - 328c607150ff - - cdee7158adf3 - 20e2f64aa1fe + - cdee7158adf3 + - 328c607150ff + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -452,22 +452,22 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1c677354ab18 + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report owner: iuc revisions: - - bfae8da6082c - 27d65c78863c + - bfae8da6082c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -511,8 +511,8 @@ 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 @@ -549,21 +549,21 @@ tools: owner: iuc revisions: - 327d9f4cc95f + - 3cc4a60615c0 + - 27250f92a01a + - 2cff76cf35c6 + - e073891b2afc - 4fd3b5d8706b - 7f5d7b0e9884 - - e073891b2afc - 0270541aaf46 - - 2cff76cf35c6 - - 3cc4a60615c0 - - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - eb50e7eca3dc - 76bc4efa1aeb - 708abf08a626 + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -636,19 +636,19 @@ tools: - name: metaphlan owner: iuc revisions: + - ec368db926f4 - b89b0765695d - - 1a037928504c - - 1a6cdf55390f - ef65b083bd0c - - ec368db926f4 - - ff8f55893e7d - - 289b3807e80c - - a92a632c4d9b - 6dee4abadccb - - 2131d7dca455 - fd69c607b43f - - 740fd2d16a28 + - 2131d7dca455 + - ff8f55893e7d + - a92a632c4d9b - a16313517e55 + - 740fd2d16a28 + - 1a6cdf55390f + - 289b3807e80c + - 1a037928504c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -700,29 +700,29 @@ tools: - 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 owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -734,8 +734,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 8e2ac1b8f70a - 0ba7dfaa941d + - 8e2ac1b8f70a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -753,8 +753,8 @@ 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 @@ -784,20 +784,20 @@ tools: - name: staramr owner: nml revisions: - - be818ae858e4 - 4b9a8031ab74 - - 3b22de20bd4b + - 141afacabcfa + - aeaa20b96ef2 - 2fd4d4c9c5c2 + - be818ae858e4 + - 3b22de20bd4b - 4d83eccf5f81 - - aeaa20b96ef2 - - 141afacabcfa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - b3c7199d8786 - 9495df9dd6ef + - 576963db5f1b 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 a43ddad63..601b12a7f 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -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 @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 174c991f7..71893ebbf 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 94b8c6013083 - 80f03df2e2ce - a74dbfee5a86 + - bdfbaf0c10aa - 9baa871cb1d1 - - 8b67dd48fec1 + - 2263989660f5 - 9eeb13a92d79 - - cd07731e4434 + - 8b67dd48fec1 - 9422c5a87ee2 - - 2263989660f5 + - cd07731e4434 - 098506c54016 - 6ae5a7b5a0a2 - - bdfbaf0c10aa + - 94b8c6013083 - 48c13389050d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - d7ce0ec78e51 - - be78f13134e2 - - fc2e49f91e52 - - aaa0d6a8b808 - f14193ec1f50 - - 4a60927aaca5 - - bc3831dd65c1 - - '764845535798' - 2e093badc689 + - '764845535798' + - 4a60927aaca5 + - c18157c68134 + - d7ce0ec78e51 - c44f824c051a - - 5abf2c2249aa + - aaa0d6a8b808 - d390fe1567dc - - 3ff17bad4006 - - c18157c68134 + - be78f13134e2 + - 5abf2c2249aa + - fc2e49f91e52 + - bc3831dd65c1 - f0af8936ed41 + - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,15 +46,15 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -66,29 +66,29 @@ tools: - name: mafft owner: rnateam revisions: - - 15974dd17515 - - c5908940967d - - a65296ffb4a0 - f0d493f8f84f - - 6f28e90db932 - f1a5908ea2cb - bf28a8cff401 + - c5908940967d + - 15974dd17515 + - a65296ffb4a0 - 8e649f27aa0d + - 6f28e90db932 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - e8fdceffea4c - fbca557a4847 - b3acbb3a6af0 - - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - 5561a1193611 + - c9685bc0407c - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -96,31 +96,31 @@ tools: owner: iuc revisions: - 48823c9635a4 - - 57f042937ba7 - bcd65de9725b + - 57f042937ba7 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - fb43e8887350 - ebe3b0f84de9 + - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - e18267f90096 - - 636b049e6141 - 7cd7a55a678d + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - cf3c9489c088 - 959c1f8dae95 + - b4124df98b26 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 9f406ead7..627566ea1 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -9,35 +9,35 @@ tools: owner: galaxy-australia revisions: - 28928576e1ea - - 18a8d140ec6f - 7c47b3c9e493 + - 18a8d140ec6f 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: + - fc8804320156 + - cb34f00cc10f - 0e9e7fcdd543 - - 79e9a869f40e - 72b5e9dda577 - - fc8804320156 - a7228a7ea146 - - cb34f00cc10f + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - fa11aa8103b2 - d6cddc06aeae + - 18505fe2bdb1 - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -50,15 +50,15 @@ tools: - name: medaka_variant owner: iuc revisions: + - 222669c4afb6 + - edf6d4003fad + - eb746fa6f514 - 19f3b583a9b3 - 43815fa60f3a - - 222669c4afb6 - - ec699520444c - 0f5f4a208660 - 2bf63b38ee9b - cc36773a3681 - - eb746fa6f514 - - edf6d4003fad + - ec699520444c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -77,21 +77,21 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - - 0f1c34698076 - a3c4fe6f49ab + - 645159bcee2d - a38bdcec9e4c - - 7b379e98b9a9 - edbb6c5028f5 + - 0f1c34698076 - a02b8b3f5a0c + - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - - d219b6d8158a - 3b6f94fc7e1d + - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation @@ -105,17 +105,17 @@ tools: - name: nanopolish_polya owner: bgruening revisions: + - 449e9aeded2d - d376944466bf - 4857d5bcce52 - - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - bec636361cfd - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop @@ -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 @@ -168,8 +168,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 626b6c2be5c2 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -206,8 +206,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index d5cd57d22..ca07c8bab 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -27,11 +27,11 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - d74850cf4e42 - - 3e73c97f025d - - 97b1b5ad1cda - baceff842902 + - 3e73c97f025d + - d74850cf4e42 - adfd6bf710bd + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -51,19 +51,19 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - ed1518ce2237 - 2f27f3b86827 + - ed1518ce2237 + - 13851aefa67a - 19b6a2f0dbe2 - e4b4837f06f5 - 1e34d2e3d285 - - 13851aefa67a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -75,8 +75,8 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 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: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -104,8 +104,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -124,17 +124,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - b4b2b284230a + - 172815da3d41 - 27a6a256cd23 - 52b6a4d98009 - - 172815da3d41 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 @@ -160,15 +160,15 @@ 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 owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -193,36 +193,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - 2c61c30a57e7 - - 0cb27ea69dc1 + - 5fe20c915fa6 - d8dc037e3c13 - 9c43baa60906 - - 5fe20c915fa6 + - 4ba60cb14cb0 + - 0cb27ea69dc1 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: - - 9d09724f2bf1 - - aec831b54a5b - 0db22932bc39 + - aec831b54a5b + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 6e24e79d3d69 - - 29c738066906 - ed7a967cb11b - df30a2f1db55 + - 6e24e79d3d69 + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -248,8 +248,8 @@ tools: - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -261,8 +261,8 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - c520a52b5174 + - 64deddb6a8ec - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -270,8 +270,8 @@ tools: owner: devteam revisions: - 94a50db37d1a - - 9946bc39c834 - 625fd9476402 + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -795,11 +795,11 @@ tools: - name: salsa owner: iuc revisions: - - 9a22227bb6d0 - ba7b0f11e470 + - 9a22227bb6d0 + - ab5b7f6b7198 - 58a870ef434c - f77f7a7f3b83 - - ab5b7f6b7198 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 ddad5aefa..e7e5fdce9 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 26de3a7b1cb9 - - f73435dc282b - - 6a457678efcb - - d033ffc1c161 - - b89cac5156ec + - a6619171428e - 107d3ba7024a + - d7c7ef3353fe + - 3b8b5bde0bd9 - f04a1264e2a2 + - '841557158611' + - c78f3d7dd1db + - d033ffc1c161 + - 26de3a7b1cb9 - 81e66674859e - - d7c7ef3353fe + - 8834daeb9892 + - f73435dc282b - 3f59ebfbfe3d + - 6a457678efcb + - b89cac5156ec - cce7b18495e4 - 5a7c56a5cc08 - - c78f3d7dd1db - - 8834daeb9892 - - a6619171428e - - '841557158611' - - 3b8b5bde0bd9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 88c4aa435ded - - 5b777002c2de - - 7a2092844346 - - a185b079b095 - - 659517798cc4 + - aa8cc71438cf - 02b8758214b0 - - 4755f52427c4 + - 659517798cc4 + - 6a726db04d4b + - 7a2092844346 - 6223845127ea + - df47d4845b62 - 5fcd1ece3a6e - - 6a726db04d4b - - b0af57c1a968 - - e75442c7f4da - - aa8cc71438cf - 6283babe736e - - df47d4845b62 + - 5b777002c2de + - b0af57c1a968 - 3b96e92e8ec3 + - 4755f52427c4 + - e75442c7f4da + - 88c4aa435ded + - a185b079b095 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - f97743d52b87 - - 24d024316465 - 111bd54f6bc4 - - b8476e82ac20 - - c1d53e95327f - - 0878b7fd5260 - 70acec670c30 + - 24d024316465 + - b8476e82ac20 + - f97743d52b87 - d1c340a5664b + - 0878b7fd5260 + - c1d53e95327f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 4f6349228462 - 9e10ba792be2 - feb40665d7cd - daddf188c13f + - 4f6349228462 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: + - 83a69484cb87 + - 42a174224817 - ca0d8cf80567 + - 81804a978fc0 + - 8ad84c5753ea + - ca337cce3888 + - 3a43c3982401 + - b6abccb1f25b - 437e28791761 - - 42a174224817 + - 9d61d3fa046c - 2f1019071464 - 14ae456b8cc5 - - abf6dbe8c9d7 + - b7e297c2ede6 - 03ed9524dcd1 - - 83a69484cb87 - - 5f8727ff21e7 - - ca337cce3888 - - b6abccb1f25b - - 3a43c3982401 - - 9d61d3fa046c - a2099fb98cdb - - 8ad84c5753ea - - 36912871ccdc - - 81804a978fc0 - - 2fa9d4f1b48f + - abf6dbe8c9d7 - 7bb8726be37c - - b7e297c2ede6 + - 2fa9d4f1b48f + - 36912871ccdc + - 5f8727ff21e7 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 @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - b1e68bbe4cef - - ba29b5e2a4be + - a4b71be30c3c - ea30d3089354 - 29ff6a849eac + - ba29b5e2a4be - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 + - 15ac71df11a0 + - 9b2b122d0415 - e88a7de55d6e - f1ccc8a6eb05 + - 91887494eb97 - dbe2b2204555 - - 15ac71df11a0 - 809e42326fc2 - - 9b2b122d0415 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 e8aa0817f..0594cfbbe 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - fc288950c3b7 - - 7d34178f2812 - - 1aac2a13842a + - 881d7645d1bf - 3f254c5ced1d - b502c227b5e6 - - a1f0b3f4b781 + - 1aac2a13842a - f6ced08779c4 - - 881d7645d1bf + - 7d34178f2812 + - fc288950c3b7 - f9242e01365a + - a1f0b3f4b781 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index f2585565c..1e3098252 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: - - eb085b3dbaf8 - a58f7eb0df2c + - eb085b3dbaf8 + - 6ab1a261520a + - 3bd420ec162d - c0e71cb2bd1b + - d00e15139065 - ca90d17ff51b - - 6ab1a261520a - - 2f7702fd0a4c - 5b85006245f3 - e4a053d67e24 + - 2f7702fd0a4c - 7fbec959cf2b - - 3bd420ec162d - - d00e15139065 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 cdaf5276a..a5ca3c648 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 277dc652246e + - b18329a8ac14 - 4c177985028a - - ece627528a78 + - b574b84afc4d - 0a18ac48ac53 - - b18329a8ac14 + - ece627528a78 - f28ad96b76dc - - b574b84afc4d + - 277dc652246e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - b41107d8fe89 + - e215f71d7983 - e988563cc6e5 - - bf06d196e23d - 525f201b86c1 - - b41107d8fe89 + - bf06d196e23d - a9a28e46d54a - - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - 8da3511c9467 - bb6397b94018 - - 4fbffddde8cd - 56da27be956a - - 8da3511c9467 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - - a8157342d9a3 - 890845926d4b - b8c79e70516d - f23d67e28cc8 + - 528fb09022be + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - a69865da6f80 - 59e85306eae5 - - a95a82eb4d50 - - 25b83cbd596a - 80600735685d - - a69865da6f80 + - a95a82eb4d50 - ae304a72db7b + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d - - ed9ed1e6cca2 - 611d80c0e29d - - e0669b1854b1 - - f1897eb07081 - 83aac7741200 + - f1897eb07081 + - e0669b1854b1 + - ed9ed1e6cca2 + - 798da6bdff3d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - - a7fb9b395ddf - d426a9107a6c + - 74b61bf5bc4b - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 82f6c2f4332d - df2187f9013b - cc430977c8ff + - 82f6c2f4332d - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - ba92b59cd529 + - 1693b2126f30 - d2483487e077 + - c5aa9fca18c6 - 043f9c91f686 - 10566783d718 - - c5aa9fca18c6 - - 1693b2126f30 + - ba92b59cd529 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: - - ae4dc0c041f9 + - ff8c9e0e8a7b - 9fa3dbf06f17 - bf0728e000cd - - ff8c9e0e8a7b + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,17 +122,17 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: + - d263296cd73e - d0ea7589e95f - eac99effe86f - - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: + - 0fa397f4f40b - 4081e4faa4ab - 1c5cbf8f79ce - - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -146,8 +146,8 @@ tools: owner: galaxyp revisions: - 0d2e93e01e68 - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 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: - - d286ff4600dd - 160538a890a6 + - d286ff4600dd - e66f552a3c47 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: - - 1f39c833f65f + - 97a7f34fcb6a - e42225f8a659 - - 4d17fcdeb8ff + - 7f432d87c82c + - 837224ad1694 - 2133b0be850a + - 4d17fcdeb8ff - f522c08e900c - - 9c52362ae7bb - - 837224ad1694 + - 1f39c833f65f - 37d669de2828 - - 7f432d87c82c - - 97a7f34fcb6a + - 9c52362ae7bb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,26 +202,26 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - e63db1aa82ee - 85b8866f06d7 - - a72ac2c7cc5b - 0ed07016d668 + - e63db1aa82ee + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 767c1d761aaf - 1974224d63c2 - 990b4560ead7 + - 767c1d761aaf - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - 35cc7ca0bdc7 + - deaf035bbe9f - 99450519d727 - 4f359549383c tool_panel_section_label: Proteomics @@ -229,28 +229,28 @@ tools: - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - - 06f6826d380c - c7745841de24 + - c1343e3389ca - e79958768a2c + - 06f6826d380c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d46d64e7964d - b9d453dca8d3 - d2eac53666f0 - da986f83631b + - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - 9bf325045235 - - 944b43462104 + - 1199751329b0 - 8bd7734309f6 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -270,8 +270,8 @@ tools: - name: msstats owner: galaxyp revisions: - - 8212e342e482 - 593839e1f2c3 + - 8212e342e482 - de7593c29499 - 28434abe6c5c tool_panel_section_label: Proteomics @@ -286,10 +286,10 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 8960fb791701 - 01dbaf6a57e0 - f4be248c3d47 - 4e77b8f12cd3 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -303,38 +303,38 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 518b1730cf2a - c9eff69a7c62 - - 6ccbf9a2072c - 9cdf15d3cfc8 + - 6ccbf9a2072c - f7fef900f5b2 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - dff6c756eee5 - 9876bda3ec53 + - ca88bd28f116 - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 658494a2cb00 - 41859bbdc16e - 890025d6e426 - 1595601708ec + - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 2a93a25f0599 - - 5ad0b5bf1deb - - 9b7977080f6d - 6634cad7d797 + - 9b7977080f6d + - 5ad0b5bf1deb + - 2a93a25f0599 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -349,47 +349,47 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: + - 4af67edd5aef - 52ba9695e752 - febd569ad26f - 5ad830edc021 - - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - 27cba4c5fc42 - - 92352a475eed - 39e8fde08881 + - 92352a475eed - b2fc8da99bcc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - d3546bb9fd8e - 0efbc235f314 - 9e26f5c770f8 - - d3546bb9fd8e - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - ca1740533b59 - 3720e349ba2a + - 8a04ed1c1d1b - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - ca799a7246e7 - - a5d785af0ad8 - c427a8628cbe - - c55dddc5844a + - a5d785af0ad8 - 382cde407f81 + - ca799a7246e7 + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper @@ -397,34 +397,34 @@ tools: revisions: - b5d0905419da - 39caaa778d2e - - 8ddb7bab1138 - adca857b4884 + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 18f93351f8b6 + - 34e7afee141d - f817513840a9 - - 8d4db262964c - 1c5f31b8d632 - - 34e7afee141d + - 8d4db262964c + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - 5d9f175dff81 - 986e03d3201e - 111c3a00136d + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - 4204882495f2 + - 0e52c85f3b15 - be74a8cd7d66 - 476b5e296979 tool_panel_section_label: Proteomics @@ -433,81 +433,81 @@ tools: owner: galaxyp revisions: - a407b6790342 - - c18d8efa4474 - 2b2a7551a857 - f5ec766d80cf + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - - 021fdb80f204 - 4e66c4e73909 + - 021fdb80f204 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - bf32e0bcf554 + - ee860980edc6 - 2735db4dd8d9 - 8098330f6d91 - - ee860980edc6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - 08488066d588 - - 0ced5bc9f4dd - a2a6e9551046 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - e8f64a7dc470 - 1bf940c18d93 - c1809c05ae8c + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - 496cf619e311 - 9f505cd4428f - f861ec9fbe59 - - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring 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 + - 89254095cbf6 - 4bb198c0bd3e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - f9ed7e074900 + - f82b320ceb90 - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -523,75 +523,75 @@ tools: owner: galaxyp revisions: - bc63b4d12779 - - 4a7b96835140 - 2aebe58de46e + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - 5ae104d0da6e - - 3d8d4ada5405 - - 6b01678ec2fc - decc397c3b7e + - 6b01678ec2fc + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - dd173849c3d8 - - 5182338d5e7c - e039cc5c7aed - d6aca689dd48 + - 5182338d5e7c + - dd173849c3d8 - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - - d426affe977c - 16026cdb1330 + - d426affe977c + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - 9c70a651a53e - dd71e020e2aa + - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - 9020199dba0a + - d063e2fe4ba4 - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: + - 78c080d36945 - f036e8cf1a55 - ad2ba3a95a02 - - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: + - c8b225c69a7f - 7f6a1f27553e - fb52e95a370c - - c8b225c69a7f - 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 @@ -603,20 +603,20 @@ 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: - - 3ec27b4cee7c + - a72c48001f7c - 7fdd9119cc4f - - 1beff3ddce58 + - 3ec27b4cee7c - da885ca16cb2 - - 943a34df6047 - 3634c90301af - - a72c48001f7c + - 1beff3ddce58 + - 943a34df6047 - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -677,10 +677,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 - - a371252a2cf6 - 265c35540faa + - a371252a2cf6 - 1a5690a5eedc + - 12692567c7f9 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 bf015d3f9..52697721b 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 597c0650c..3540cf884 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,45 +2,45 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 289b7d6b69a4 - 110a346daf36 + - 2f1d464ebfd2 - e345aadf914f - 42201b90e3f4 + - 289b7d6b69a4 - cd5f98911089 - - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - 8501601a118d - - 0cd2df8af811 - - 42d9087b4789 - c207119ba5f6 - 0345dbaaa79b + - 0cd2df8af811 - fcce77c09289 + - 42d9087b4789 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - 04db7fd6b238 - - 33486216eec0 - - ad5ab22ffe24 - 89eb29319bf4 + - 33486216eec0 - 421c33b8bf17 - 405a212b32ab + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 - - 7b72fde3d27e + - 7370bb65bad4 - f6e91108b7b1 + - eb784fa07f80 - 1d839ead7ad3 - fa51dc5e8386 - - 7370bb65bad4 + - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -57,64 +57,64 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 564c33e5c3e3 - - e2db212d64ad - - a5969aa9347e - 7b881f5f5ad5 - b242deb58952 + - e2db212d64ad + - a5969aa9347e + - 564c33e5c3e3 - 887cf585cafc tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: + - b4bab607eb05 - 9a171f9a450b - bd5ff77e2036 - e897c74a48bb - 8cff84759bf6 - - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - adc7a7610d4f - - 4f65e343ecdf + - 33f0793edf93 - 887e0991eb24 - 5e10f396979e - - 33f0793edf93 + - 4f65e343ecdf + - 6dafad990086 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c5d7050e4ad7 - 4e280b27a831 + - c5d7050e4ad7 - 17d39bf0a63a - - 43e3eeb2e0ec - 97575d01f06b + - 43e3eeb2e0ec - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - cd034465d4a4 - - d9bf483266a1 - - 9586f08634c0 + - a819ec3b362d - 0b8c84a7fdb5 + - d9bf483266a1 - 09b8edb56d80 - - a819ec3b362d + - 9586f08634c0 + - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - a4b4bd84f69e - - 69842dd5aa48 - 2645575d1bf2 - bf0e43ab0416 + - 69842dd5aa48 - 95351dd0fd3f - a9c34a289493 tool_panel_section_label: RAD-seq @@ -122,11 +122,11 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - d1fda11e602f - 912f904a6e1e - - 8a35a3bc6752 - d033e1ccb386 + - cfb504394ae1 + - 8a35a3bc6752 - bb0475c884ff 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 @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 2564a13e0..d3e2e9727 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,26 +2,26 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 7acb00fc980a - - cf01dd6c6b1f - 2d4e3aff9dc7 - 31f8063eedea + - 7acb00fc980a + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - 125d20cb23d7 - 7a5a2d28c539 + - 703a2cb3fb38 - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 01ccd366690d + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -89,16 +89,16 @@ tools: - name: cufflinks owner: devteam revisions: - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - - 86285ddd4512 - 6a6717a5f421 + - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -129,30 +129,30 @@ tools: - name: describe_samples owner: iuc revisions: - - 8f0181aacb7a - - 3b36efd62b3e - 0693ccd171c4 - e3b16fd7dd08 + - 3b36efd62b3e + - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - d027d1f4984e - - 8fe98f7094de + - cd9874cb9019 - 9a882d108833 - - 6a3a025714d3 - 0696db066a5b - - cd9874cb9019 + - 6a3a025714d3 + - 8fe98f7094de - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 9a7c5b6d8f1e - df929f257179 - b47c006d90c5 + - 9a7c5b6d8f1e - 62adf13b86ea - 2872c633f07e tool_panel_section_label: RNA-seq @@ -160,25 +160,25 @@ tools: - name: edger owner: iuc revisions: - - df0c8d0a5992 - - 6e53e565fc6a - - f2843df56434 - - ae2aad0a6d50 - - 9bdff28ae1b1 + - 0cb907a2a810 - 070900306913 - - 555659de7321 - 3d89af8a44f0 + - 6e53e565fc6a - 5bf899c13979 - - 0cb907a2a810 - - a8305cf0c951 + - f2843df56434 + - df0c8d0a5992 - 334ce9b1bac5 + - 9bdff28ae1b1 + - a8305cf0c951 + - 555659de7321 + - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -190,17 +190,17 @@ tools: - name: featurecounts owner: iuc revisions: + - 7db9d3ea71c9 - f9d49f5cb597 - - 38b6d12edc68 - - 6f66ae7c5f7a - - f3a5f075498f - - a56fbe2d6ba7 - 90d16db017d7 - - af814359d244 - ea04b737afa0 - - a37612abf7f9 + - f3a5f075498f - e6a2a912677a - - 7db9d3ea71c9 + - 6f66ae7c5f7a + - a56fbe2d6ba7 + - a37612abf7f9 + - af814359d244 + - 38b6d12edc68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -224,8 +224,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - f99dd58de04f + - 3c97c841a443 - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -238,12 +238,12 @@ tools: - name: hisat2 owner: iuc revisions: + - 6c19daec423d + - f4af63aaf57a + - a86e80d3c09c - d4b55e2beb12 - 3fb01a8c902d - 6ab42baa56e9 - - a86e80d3c09c - - 6c19daec423d - - f4af63aaf57a - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -251,8 +251,8 @@ tools: owner: lparsons revisions: - 67b0b160903a - - 4418229c501e - 916cb26bd9d3 + - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -264,8 +264,8 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - 5ae5c312d718 + - 87c11c05d238 - 01247aaf0a10 - 1c75aa5de15e - ce5d418183c5 @@ -275,22 +275,22 @@ tools: owner: iuc revisions: - 10c98fab6c5a + - 40985510cd98 - 4f9c4e6566e5 - c971db6f0fe5 - - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 0921444c832d - e827f9aae031 - - 708348a17fa1 - - 32511f586472 - 58c35179ebf0 + - 0921444c832d + - 32511f586472 + - 708348a17fa1 + - d6f5fa4ee473 - 119b069fc845 - 97e06a4c7c75 - - d6f5fa4ee473 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -327,8 +327,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -346,21 +346,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 7ed2edc1337f - - 4014de1b6daf - - c7c55b694974 - - 4074fc1940e2 - b0f2be869d6d + - 4074fc1940e2 - 5ec75f5dae3c - - 3ea5a2a63fa2 + - 4df95e2d7f61 - 980d2a2e1180 - - 0a563fd2f22e - - 99b17b74a8cd - - 79de45b5069b + - 7ed2edc1337f - e132e7d02a3e - - c772497b2c32 - - 4df95e2d7f61 - b9e04854e2bb + - 99b17b74a8cd + - c7c55b694974 + - c772497b2c32 + - 3ea5a2a63fa2 + - 0a563fd2f22e + - 4014de1b6daf + - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -372,36 +372,36 @@ tools: - name: salmon owner: bgruening revisions: - - 49121db48873 - - cc05793bb896 - - f4d5237a84f6 - - ebab418107f5 - - 53e9709776a0 - e3d32471da11 + - ebab418107f5 - 2c0ca397d302 - 15cd64d7c58b + - cc05793bb896 + - 49121db48873 + - f4d5237a84f6 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - c0fd285eb553 - - fab6ff46e019 - 56242ff81c84 + - c0fd285eb553 - 8c28affc7c48 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cbf488da3b2c - - 1ebd14235b92 - - ae618321f34a + - 76d290331481 + - 258d696dbd7e + - cef79931dda5 - dd4df992d93d - 914cfcba0ec8 - - cef79931dda5 - - 258d696dbd7e - - 76d290331481 + - ae618321f34a + - 1ebd14235b92 + - cbf488da3b2c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -431,44 +431,44 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a + - d0d4cef4f967 - ffd1300599a1 - c6334cb383ff - - d0d4cef4f967 + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - bcc5f03f1900 - d6a479fd4281 - ba3720d7e68b - - bcc5f03f1900 - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 56162e446004 - 478f36effca1 - 2fb4ee002432 + - 56162e446004 - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - 3f4094b6a565 - 9ff3765e7172 + - 3f4094b6a565 - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c - 870ac06dff8e - be3f26533209 + - 34a018cbee9c - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -476,18 +476,18 @@ tools: owner: iuc revisions: - 5192f657f305 - - c5fbddcac63a - 33406f5a445c - - 05ab8d5e04a2 + - c5fbddcac63a - 65e7dea767ea + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - 1fdb25a8384d - a35cba31d904 - 6f0fb35b799c - - 1fdb25a8384d - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -495,27 +495,27 @@ tools: owner: iuc revisions: - c2c039e421af - - 7c7fbf13aadd - 964b7efe2639 + - 7c7fbf13aadd - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - eafea3083352 + - 1d689e4e1caf - 047c22569787 + - eafea3083352 - 24e94d84adc9 - - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: + - 3a4ac03d1266 - 1812dbc5bb7b - 04bb8bb7c198 - 9871104ea630 - - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -533,15 +533,15 @@ tools: - name: trinity owner: iuc revisions: - - 8f1c3df4dd49 - - d2bc35f3d1c5 - 48636f857c4b - - d84caa5a98ad - - c9cfec002f71 - - 32b86cd8eb50 - - db1f362cca3e + - d2bc35f3d1c5 - cee61b3fcf78 + - 32b86cd8eb50 + - 8f1c3df4dd49 - 9fa24d5aac68 + - d84caa5a98ad + - db1f362cca3e + - c9cfec002f71 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 636b5a8af..5c8b52871 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 - - 1a052c827e88 - 473382134e56 + - 1a052c827e88 + - 080fd5739bb4 + - 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 2ac5e8651..2f2989d3a 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -3,17 +3,17 @@ tools: owner: devteam revisions: - 10184eaa85fc - - 88eedb4abea0 - 3c661e57a88f + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - - 1dfd95ee241e - 993b19f20c76 - cb20f99fd45b + - 1dfd95ee241e + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -25,8 +25,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -75,17 +75,17 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - - e7fd6754d093 - - 19ece8afbaab - 30a201c9c310 + - 19ece8afbaab + - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -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 @@ -130,10 +130,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: + - 6856f8a01905 - 46c6639921f1 - 9149ad20699a - 12749212f61b - - 6856f8a01905 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -141,8 +141,8 @@ tools: revisions: - 26b4f9f98aca - 06dc50b7b711 - - 33208952b99d - 92ec40abcdcf + - 33208952b99d 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: - - 66e23b11feae + - a8d69aee190e + - b906586a6596 - 720217c23995 + - 66e23b11feae - b3d99709fe1a - - b906586a6596 - - a8d69aee190e 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 - - 22970df7a40e - cc61ade70eb8 - fe34990e5ce7 + - db17d5321bad + - 22970df7a40e + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7a6034296ae9 - - 88b8c2916784 - fa5d3e61e429 - - 811fc2d75ad4 - 7def34e6cf4d + - 88b8c2916784 + - 811fc2d75ad4 + - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -204,37 +204,37 @@ tools: - name: samtools_merge owner: iuc revisions: - - 65a38e8c8e2a - - 740ce0a18f0d - - cae2794d2deb - b40e2d865d52 + - cae2794d2deb + - 740ce0a18f0d + - 65a38e8c8e2a - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - - 9da0311ab1dd - 8da515fbc1bf - - 329deb17a9f7 - b61f5d6a7f25 + - 583abf29fc8e + - 329deb17a9f7 + - 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 + - bb8cfc6f6e0c - db000c6007a0 - 30388d878f81 - - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -246,38 +246,38 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - 344fc91e1bfd - b8beef827165 - a4a10c7924d1 - - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: + - d54a4df48867 - e613c1ad4c4c - - cab3f8d35989 - 6c2c1836728b - - d54a4df48867 + - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - bd850490c7f1 - - 818030fa6bbf + - bcedabb53ddf - 135c85f4cfaf - b7f7826ef1cd - 5d9ae78f34d3 - - bcedabb53ddf + - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 541082d03bef - - 3a0efe14891f - 5a08c09b9311 - 1cc79f49b8d5 + - 3a0efe14891f + - 541082d03bef - 145f6d74ff5e - 24c5d43cb545 tool_panel_section_label: SAM/BAM @@ -285,15 +285,15 @@ tools: - name: samtools_view owner: iuc revisions: - - 0dbf49c414ae - - b72793637686 - - 5826298f6a73 - - c370440f901e - - bf328cec6a42 - - 2dce91e11ca7 + - b01db2684fa5 - 6be888be75f9 + - b72793637686 + - 0dbf49c414ae - 350bbc5c2ffd + - bf328cec6a42 + - c370440f901e + - 5826298f6a73 - 32dc5f781059 - - b01db2684fa5 + - 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 4fa25de12..9d74eb127 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: + - ea5e944f447d + - a62c4a11a67d - d147d6455873 - - 4aab5ae907b6 - 6f6537780379 - - 5cb6146337d8 - - ea5e944f447d + - 4aab5ae907b6 - 59bb6d34fca6 - - a62c4a11a67d + - 5cb6146337d8 - 480d9e9d156b 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 383a5abe4..0035dea5e 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,100 +8,100 @@ tools: - name: alevin owner: bgruening revisions: + - ecb9ea6269ee + - e4c01dcece8b - e32b215b7c04 - c9944a2600f1 - f2000bc73102 - - e4c01dcece8b - - ecb9ea6269ee tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: + - c0b037b12765 - 707023fa62fe - cfaf5a405371 - - c0b037b12765 - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - fb9e030ffae4 - - 32e547223c9e - - 00712416fdaa - - 55e35e9203cf + - d330b3082107 - cfc3f5a57dc6 + - 00712416fdaa + - fb9e030ffae4 - 93dd15e13e6a - - d330b3082107 + - 55e35e9203cf + - 32e547223c9e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - 0bf7fddf90c7 - - ee98d611afc6 + - 39e945f0b2c1 + - 688357ad5e61 - 6f0d0c784f09 - - b9fac48532eb + - ee98d611afc6 - 038e32885fec - - 688357ad5e61 + - b9fac48532eb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - d4af736e7b83 - 3d748954434b + - 7e8c677a7b71 + - d4af736e7b83 - 9bd945a03d7b - 43cb7b5a6fe7 - ed4996a16f7f - - 7e8c677a7b71 - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - 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 - 0e70b2dfe4be - - 02b1fe7aed76 - 769d815e4b0d + - 4fff5a293013 + - 02b1fe7aed76 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - a90f8efe08b4 - - 344c2af50552 - aa4a6f0916b4 - c29e7bb492bf + - a90f8efe08b4 + - 344c2af50552 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - 050cf43887d3 - b13d3e4c48e1 - - c32347702e12 - 5b7c81b35b89 - - 050cf43887d3 + - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 239193b96d72 - 1d77986f9ddc - - ae969fdb8442 - 02fc39c8610d + - 239193b96d72 + - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -137,10 +137,10 @@ tools: - name: dropletutils owner: iuc revisions: - - cfe1e6c28d95 - - cdf4443d5625 - a9caad671439 + - cfe1e6c28d95 - 8855361fcfc5 + - cdf4443d5625 - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -185,15 +185,15 @@ tools: - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - 163fd744e235 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 013e53ccc7ac - f47ac4a0b337 + - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol @@ -206,8 +206,8 @@ tools: - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 45a386d18509 - 640e0e45518a + - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel @@ -241,8 +241,8 @@ tools: - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - c72fa6cb8817 - 8a11d70b6cd8 + - c72fa6cb8817 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices @@ -262,8 +262,8 @@ tools: - 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 @@ -297,8 +297,8 @@ tools: - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - 972dcccb5bbc + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops @@ -318,8 +318,8 @@ 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 @@ -339,15 +339,15 @@ tools: - 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 owner: bgruening revisions: - - dd9988943f53 - ea5d67ec94ab + - dd9988943f53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -360,8 +360,8 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -374,8 +374,8 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -400,25 +400,25 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - f36828ebdc54 - 27fe5cd1729c + - f36828ebdc54 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - eeab712b0b99 + - 4b0adaa31c95 + - 0f1aaff9b22d - 59be31ac9dc3 - e98619de2776 - - 0f1aaff9b22d - - 4b0adaa31c95 + - eeab712b0b99 - 7784821452ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -432,8 +432,8 @@ tools: owner: bgruening revisions: - 282819d09a4f - - 2cfd0db49bbc - 7ffaa0968da3 + - 2cfd0db49bbc 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: - - 7705cc75ac18 - 8c64a2da3869 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -465,20 +465,20 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b + - c4f39bf4a068 + - 0bff0ee0683a - 7e014059a88d + - a4b734cd253b - f911a64454fb - - 0bff0ee0683a - - c4f39bf4a068 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - b83fbc90161e - - 43c146e25a43 - 7608d5faee41 + - d45f092caf24 + - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -501,10 +501,10 @@ tools: owner: iuc revisions: - 72979cac22b2 - - 2af7c5086a96 - - 44b935f2271b - e93b008c637a + - 2af7c5086a96 - c92d0f9338c5 + - 44b935f2271b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -522,92 +522,92 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - aaa5da8e73a9 - - 6f83f8fd381f - - 6acb08931836 + - b2df381a6004 - f9353ee6a0d4 + - 6acb08931836 + - 77b91b9bdf52 - 38db3fef7aad - - b2df381a6004 - 4d8f983cd751 - - 77b91b9bdf52 + - aaa5da8e73a9 + - 6f83f8fd381f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 72a6bebab2a5 - - d636ce5cde16 + - a97abb8cd15b - 277313130da5 - - a03ff8633507 - b409c2486353 - - 3c86f71498bc - - a97abb8cd15b + - d636ce5cde16 - 8cb783c81905 + - a03ff8633507 + - 3c86f71498bc + - 72a6bebab2a5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 6bd82ed14acd - - c0a80a16560f - - 5e9171dc8244 - - c5d3684f7c4c - - 3081ff5c84a3 - 18262103fa61 + - 6bd82ed14acd - d1cd8c147809 - 5c3ebe2adc77 + - 3081ff5c84a3 - f54f0f0598ad + - c5d3684f7c4c - 6c145a6868cc + - 5e9171dc8244 + - c0a80a16560f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 94c19fb1281c + - 7b9fafe32c86 - c9cb76cf8d6c + - 56c0d4acef02 - d844935c906c - - 7b9fafe32c86 - 9f354c7c8c92 - a407e7f8bdc1 - 3bcd5445cd7a - - 56c0d4acef02 - ab55fe8030b6 + - 94c19fb1281c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: + - 6f5349dd5c49 + - aa0c474463c2 + - f7446fd8d5e7 - 1072ce66b426 - 9b0cdb8cf6be + - 95777145cb92 + - 6adf98e782f3 - 7647e5cd1b8b - 0185bd174ea0 - - 6f5349dd5c49 - - aa0c474463c2 - - 6adf98e782f3 - - 95777145cb92 - - f7446fd8d5e7 - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - 458e8f43a775 - a39040ae0a38 - - d18e7a6e5cd4 + - 9fb627495ec2 - 215733a383f2 + - c65fce500915 + - f2f6c703da06 - 73ab2ac53d06 - - 458e8f43a775 - - 9fb627495ec2 + - d18e7a6e5cd4 - bf2017df9837 - - f2f6c703da06 - - c65fce500915 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 @@ -615,8 +615,8 @@ tools: owner: iuc revisions: - 652923ce664f - - 7a365ec81b52 - b7ea9f09c02f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -885,15 +885,15 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - afb90d3485df - 8f8bef61fd0b + - afb90d3485df tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 88192fe25375 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting @@ -906,8 +906,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -919,8 +919,8 @@ 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 2741c67ea..c6eea94a3 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,25 +32,25 @@ tools: - name: datamash_ops owner: iuc revisions: + - 562f3c677828 + - 2f3c6f2dcf39 - 746e8e4bf929 - 419027d822d6 - - 562f3c677828 - 4c07ddedc198 - - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -70,8 +70,8 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - 7a15159140d1 + - cb1c59d69557 - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,21 +114,21 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 4c4ec859c31a - - aef56d0e7a61 - 7442b94d6a1e + - b1eda492f063 - 840f29aad145 + - aef56d0e7a61 + - 4c4ec859c31a - 9c3e1d3235c8 - - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 + - 9fda0b82f419 - 30d21a6041f6 - 375bbd555f4a - - 9fda0b82f419 + - d0352e8b4c10 - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -136,21 +136,21 @@ tools: owner: bgruening revisions: - cd02bf168d23 - - 8b1b2b91f8d0 - 4cc980df6265 - 7ae443e6217d - 2c58b83c9bad + - 8b1b2b91f8d0 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 1dd433d2c92c + - ad7e0b4291ee - bb9fc9d46ea4 - e10e776f2109 - - ad7e0b4291ee - - 7dd3fb35904f + - 1dd433d2c92c - 4bbaf77573ef + - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index dead6f029..ff317a5e3 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: - - be25c075ed54 - 464b9305180e - - 9cd341095afd - 6595517c2dd8 - - 13b6f0007d9e - aff5135563c6 - - 02026300aa45 - 6e8d94597139 + - 13b6f0007d9e + - 9cd341095afd + - 02026300aa45 + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -80,9 +80,9 @@ tools: revisions: - 90f657745fea - 9cc411a62277 - - 557ec8d7087d - 34d29339abab - 37cde8134c6a + - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -114,21 +114,21 @@ tools: owner: iuc revisions: - cf4397560712 - - 33d61c89fb8d - 2e8f945f7285 - - 3a6b78c39dca - - 83069b38aa85 + - 33d61c89fb8d + - cf34c344508d - 623f3eb7aa48 + - 83069b38aa85 - 1ea4e668bf73 - - cf34c344508d + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 503bcd6ebe4b - - ae8c4b2488e7 - 399da6b5ec21 + - ae8c4b2488e7 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -140,10 +140,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 - - c4d18aa4ec4a - f768f6183386 + - c4d18aa4ec4a - b722161a845a + - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -156,14 +156,14 @@ tools: - name: text_processing owner: bgruening revisions: - - a6f147a050a2 - 12615d397df7 - - fbf99087e067 - ddf54b12c295 - - f46f0e4f75c4 - - 86755160afbf - - 74a8bef53a00 - d698c222f354 + - a6f147a050a2 - 9ff72e942410 + - 74a8bef53a00 + - fbf99087e067 + - 86755160afbf + - f46f0e4f75c4 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 2e110d3cf..6d6bb1c62 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: - - 85c57cc9b558 - 82fb5e3bb93e - 0d18a3ba2d1c + - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -34,56 +34,56 @@ tools: - name: freebayes owner: devteam revisions: - - 57def2d7c093 - a5937157062f - - ef2c525bd8cd - 04fa42777df9 + - 57def2d7c093 + - ef2c525bd8cd - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - e61c9ac190ad - - 09d6e4693887 - 791f73caa0c8 + - 09d6e4693887 - 435b157bed6d + - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: + - 03627f24605f - 3b4b2121842f + - 4805fe3d8fda + - 65432c3abf6c + - e1461b5c52a0 - dfadc322b065 - 074d44697036 - - e1461b5c52a0 - - 03627f24605f - - 65432c3abf6c - - 4805fe3d8fda tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - 701d134358ad - - 7dfca164d2e3 - 9cb929f21cfa + - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 971e07ca4456 - 426d707dfc47 - - f4473557ffc7 - c27549b9aa1f + - f4473557ffc7 + - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - dbd9f2db9ed8 + - cdaab621d454 - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -103,8 +103,8 @@ tools: - name: snippy owner: iuc revisions: - - fa016f1eea1a - d220115f882b + - fa016f1eea1a - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -141,21 +141,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 - 40f0591deda0 - - 3b1e7c170b10 + - ee4a90760848 - e7aff4a85df5 + - 3b1e7c170b10 - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 4934c0ac6197 - - 42818629ec4c + - adc0645b945c - 9793bc5d741b + - 4934c0ac6197 - 02d81b994ef5 - - adc0645b945c + - 42818629ec4c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index c082231e1..ac6b4a3d1 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ 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owner: nml revisions: - - 18aad692772a - 9def47f3c1e4 + - 18aad692772a tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu