From 358f9fb70265be5933b4d623c353039dc5f3ab8f Mon Sep 17 00:00:00 2001 From: admin Date: Thu, 19 Sep 2024 00:13:01 +0000 Subject: [PATCH] Jenkins install build 1624. --- automated_tool_installation_log.tsv | 1 + requests/rseqc.yml | 6 - staging.gvl.org.au/annotation.yml | 118 +++---- staging.gvl.org.au/assembly.yml | 256 +++++++-------- staging.gvl.org.au/bacterial_typing.yml | 12 +- staging.gvl.org.au/bb_tools.yml | 10 +- staging.gvl.org.au/bed.yml | 14 +- staging.gvl.org.au/blast.yml | 16 +- staging.gvl.org.au/chemicaltoolbox.yml | 62 ++-- staging.gvl.org.au/chip_seq.yml | 8 +- staging.gvl.org.au/collection_operations.yml | 14 +- staging.gvl.org.au/convert_formats.yml | 40 +-- staging.gvl.org.au/deeptools.yml | 128 ++++---- staging.gvl.org.au/dna_metabarcoding.yml | 12 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 8 +- staging.gvl.org.au/fastafastq.yml | 94 +++--- staging.gvl.org.au/fastq_quality_control.yml | 38 +-- staging.gvl.org.au/filter_and_sort.yml | 6 +- staging.gvl.org.au/gemini_tools.yml | 26 +- staging.gvl.org.au/genome_editing.yml | 2 +- staging.gvl.org.au/get_data.yml | 40 +-- staging.gvl.org.au/graphdisplay_data.yml | 62 ++-- staging.gvl.org.au/hca_single_cell.yml | 36 +-- staging.gvl.org.au/hicexplorer.yml | 24 +- staging.gvl.org.au/imaging.yml | 64 ++-- staging.gvl.org.au/ivar.yml | 74 ++--- .../join_subtract_and_group.yml | 10 +- staging.gvl.org.au/machine_learning.yml | 46 +-- staging.gvl.org.au/mapping.yml | 58 ++-- staging.gvl.org.au/metabolomics.yml | 26 +- staging.gvl.org.au/metagenomic_analysis.yml | 152 ++++----- staging.gvl.org.au/mothur.yml | 6 +- staging.gvl.org.au/multiple_alignments.yml | 62 ++-- staging.gvl.org.au/nanopore.yml | 50 +-- staging.gvl.org.au/none.yml | 58 ++-- staging.gvl.org.au/phylogenetics.yml | 100 +++--- staging.gvl.org.au/picard.yml | 12 +- staging.gvl.org.au/proteomic_ai.yml | 12 +- staging.gvl.org.au/proteomics.yml | 192 ++++++------ staging.gvl.org.au/qiime_2.yml | 2 +- staging.gvl.org.au/rad_seq.yml | 74 ++--- staging.gvl.org.au/rna_seq.yml | 184 +++++------ staging.gvl.org.au/rseqc.yml | 1 + staging.gvl.org.au/sambam.yml | 76 ++--- staging.gvl.org.au/send_data.yml | 10 +- staging.gvl.org.au/single_cell.yml | 180 +++++------ staging.gvl.org.au/statistics.yml | 22 +- staging.gvl.org.au/text_manipulation.yml | 38 +-- staging.gvl.org.au/variant_calling.yml | 34 +- staging.gvl.org.au/vcfbcf.yml | 262 ++++++++-------- usegalaxy.org.au/annotation.yml | 118 +++---- usegalaxy.org.au/assembly.yml | 250 +++++++-------- usegalaxy.org.au/bacterial_typing.yml | 12 +- usegalaxy.org.au/bb_tools.yml | 6 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 14 +- usegalaxy.org.au/chemicaltoolbox.yml | 64 ++-- usegalaxy.org.au/chip_seq.yml | 12 +- usegalaxy.org.au/collection_operations.yml | 14 +- usegalaxy.org.au/convert_formats.yml | 42 +-- usegalaxy.org.au/deeptools.yml | 128 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 10 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 8 +- usegalaxy.org.au/fastafastq.yml | 102 +++--- usegalaxy.org.au/fastq_quality_control.yml | 36 +-- .../fetch_alignmentssequences.yml | 2 +- usegalaxy.org.au/filter_and_sort.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 24 +- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 42 +-- usegalaxy.org.au/graphdisplay_data.yml | 66 ++-- usegalaxy.org.au/hca_single_cell.yml | 40 +-- usegalaxy.org.au/hicexplorer.yml | 20 +- usegalaxy.org.au/imaging.yml | 70 ++--- usegalaxy.org.au/ivar.yml | 72 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 8 +- usegalaxy.org.au/machine_learning.yml | 50 +-- usegalaxy.org.au/mapping.yml | 52 ++-- usegalaxy.org.au/metabolomics.yml | 22 +- usegalaxy.org.au/metagenomic_analysis.yml | 138 ++++----- usegalaxy.org.au/mothur.yml | 6 +- usegalaxy.org.au/multiple_alignments.yml | 54 ++-- usegalaxy.org.au/nanopore.yml | 46 +-- usegalaxy.org.au/none.yml | 62 ++-- usegalaxy.org.au/phylogenetics.yml | 90 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 12 +- usegalaxy.org.au/proteomics.yml | 214 ++++++------- usegalaxy.org.au/rad_seq.yml | 64 ++-- usegalaxy.org.au/rna_seq.yml | 154 ++++----- usegalaxy.org.au/rseqc.yml | 1 + usegalaxy.org.au/sambam.yml | 68 ++-- usegalaxy.org.au/send_data.yml | 10 +- usegalaxy.org.au/single_cell.yml | 174 +++++------ usegalaxy.org.au/statistics.yml | 28 +- usegalaxy.org.au/text_manipulation.yml | 46 +-- usegalaxy.org.au/variant_calling.yml | 36 ++- usegalaxy.org.au/vcfbcf.yml | 292 +++++++++--------- usegalaxy.org.au/viral_tools.yml | 2 +- 101 files changed, 2827 insertions(+), 2830 deletions(-) delete mode 100644 requests/rseqc.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 8e4664403..c5eee51ea 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7801,3 +7801,4 @@ Update 210 18/09/24 16:13:12 scanpy_plot False Installed iuc 2dfb2227a16c 2dfb22 Update 210 18/09/24 16:37:11 scanpy_remove_confounders False Installed iuc b70219da4a96 b70219da4a96 6/6 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt Install 1620 19/09/24 08:55:15 artic_minion True Installed iuc 468b90c41cde 468b90c41cde Variant Calling toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1620/install_log.txt Install 1622 19/09/24 09:14:09 data_manager_primer_scheme_bedfiles True Installed iuc dd451e45681c dd451e45681c 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1622/install_log.txt +Install 1624 19/09/24 10:12:40 rseqc False Installed nilesh 27e16a30667a latest 31/31 RSeQC toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1624/install_log.txt diff --git a/requests/rseqc.yml b/requests/rseqc.yml deleted file mode 100644 index afb2b9890..000000000 --- a/requests/rseqc.yml +++ /dev/null @@ -1,6 +0,0 @@ -tools: -- name: rseqc - owner: nilesh - tool_panel_section_label: RSeQC - 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 d7b67aee8..e31371679 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,9 +2,9 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - - 3f3e247c053d - 4efdca267d51 + - 3f3e247c053d + - 78c75f134c16 - 6e9aea89e388 - c2ef298da409 tool_panel_section_label: Annotation @@ -12,8 +12,8 @@ tools: - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -33,23 +33,23 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 133f36c29579 - fe3ca740a485 - - cd2480f35935 - - 4f2967b27e67 - - 3e1f6f6d557e - - b5d8e5475247 - - 1aae04680c4b - f29602ae449e - - a79ee60b6926 - 44018dd6b447 + - a79ee60b6926 + - b5d8e5475247 + - 1aae04680c4b + - 4f2967b27e67 + - 133f36c29579 + - 3e1f6f6d557e + - cd2480f35935 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 - 7be22100e5e1 + - dc027fa56d55 - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 28433faa6e42 - ca6d970d931c - 09855551d713 + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - d77802fe76f7 - 728dacaf08a9 + - da5f1924bb2e - 92eee5f31117 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 @@ -101,8 +101,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -114,9 +114,9 @@ tools: - name: cpat owner: bgruening revisions: + - 8e9e228c54c4 - 1ac12c0cc7a0 - 7ccc6234b54e - - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper @@ -148,60 +148,60 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - - 582fd74dc2a1 - 9f2455341fac - - 9c15ca7e764e + - 14f588312c56 + - 3bbe70fef6df - 756376aeb1ae + - 9c15ca7e764e - b6b5cd37f2a2 - - 14f588312c56 + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 8e1ace8f77c6 - - 0ffe5be70caf - - 30fb23d4c31c - a230ea445788 - - 73428a792541 - 1691af4a0d17 - 989f7c061f35 + - 0ffe5be70caf + - 73428a792541 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: + - e94187d661df - 563a19373357 - - 57c6718cbfcc - 5a5ae61da69c - - 0418d28136de - - 30f08d74024f + - 57c6718cbfcc - 494f0bb4a993 - - e94187d661df + - 30f08d74024f + - 0418d28136de tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - - 1bc5a03faf2e - 7abc5f6dd595 - - d6c7106b7b2e + - f31125bb85ea - f77d7b685bb3 - - 4b96ced19f75 - 2bba2ff070d9 + - 1bc5a03faf2e + - 4b96ced19f75 + - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - b3cf4684e9c7 + - d77fdcca400e - fed64e676186 - 54961e026fe4 - 52af33194019 - 520e30695ec3 - - b3cf4684e9c7 - - d77fdcca400e - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -214,9 +214,9 @@ tools: - name: gff_to_prot owner: iuc revisions: + - 07d7991bf205 - 79261884facd - 2aea122fbd25 - - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -228,10 +228,10 @@ tools: - name: goseq owner: iuc revisions: - - 43798b4caee0 + - 602de62d995b - ef2ad746b589 - 8b3e3657034e - - 602de62d995b + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -255,8 +255,8 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan @@ -282,25 +282,25 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: + - d46d803ca6cc - 3c1a01127868 - 370c210d9541 - - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - e95d52d295d7 - 624606f7c996 - - c8ac28e8ac44 + - e95d52d295d7 - b815ec682418 + - c8ac28e8ac44 - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -338,10 +338,10 @@ tools: owner: crs4 revisions: - a17498c603ec + - bf68eb663bc3 - 8a22554cdde2 - eaee459f3d69 - d643e3b03500 - - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -353,15 +353,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -379,22 +379,22 @@ tools: - name: snpeff owner: iuc revisions: - - 68693743661e - - 5c7b70713fb5 - 8f92c2b26e6d - - 5b80f544c67f - 268d162b9c49 + - cfcf33df7fc0 - 5a29ab10dba6 + - 5c7b70713fb5 + - 68693743661e + - 5b80f544c67f - 9473cd297a76 - - cfcf33df7fc0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - - 09d6806c609e - 5fab4f81391d + - 09d6806c609e + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -406,8 +406,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -419,17 +419,17 @@ tools: - name: tbprofiler owner: iuc revisions: + - 45083d070fb8 + - ba6f87115e13 + - ac8250086ac3 - 4839e590cb26 - - e1a9d6fd258d + - d03af1c7002c - 37213cf56392 - 200c378d85f3 - - 037a11682176 - - ba6f87115e13 - - d03af1c7002c - - 809dfc93d593 + - e1a9d6fd258d - 51dd22484644 - - 45083d070fb8 - - ac8250086ac3 + - 809dfc93d593 + - 037a11682176 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index dccbebc93..fede2ab3e 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,33 +2,33 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 - - 841084c5fc46 - 0e93176640ac + - 7547fcab5d19 + - 0124fce4654a + - 841084c5fc46 + - 890b794c997d - 553bfe8bd0b5 - - a929ce596a34 + - 8f1b150a2487 - fa5259cc561b - - 890b794c997d - - 0124fce4654a - - 7547fcab5d19 + - a929ce596a34 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - 94fe43e75ddc + - b9e31c5c01c7 - ddddce450736 - - 067592b6b312 - b2860df42e16 - - b9e31c5c01c7 + - 067592b6b312 - 21e491ad532a - - 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 @@ -36,46 +36,46 @@ tools: revisions: - 22286dab5aa1 - a7f16f24e9a1 - - faee8629b460 - 3371c5bdc17a - 5258e18bbe23 + - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - 8c2167481e72 + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 41030a6c03b7 - - 602fb8e63aa7 - 2babe6d5c561 - - 1e62c28ba91d - - e824f5d958d0 - - bb935709506a + - 46ae58b1d792 + - 602fb8e63aa7 - f18f0b887c31 + - e824f5d958d0 - 94170eee0ad8 - - 46ae58b1d792 + - 1440ae06552f + - bb935709506a - 0d243f458b53 - - e4bd1e99bacf - - 4048d82f0c88 - cf13a1e03e5b - - 1440ae06552f + - 4048d82f0c88 + - ea8146ee148f + - e4bd1e99bacf + - 41030a6c03b7 + - 1e62c28ba91d - 2dd755c1c6ff - 5ecdeca79a0d - - ea8146ee148f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 86f150c8019d - - 5732f959936a - c5b7390290b1 + - 5732f959936a + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -87,41 +87,41 @@ tools: - name: flye owner: bgruening revisions: - - 8d4f03b5fe9d - - 3e4f8642c77e - - e27815e82dd4 - - 291923e6f276 - 276f5d8712d5 - 3ee0ef312022 - - cb8dfd28c16f + - 291923e6f276 + - 8d4f03b5fe9d - 1ce9b1d72ec3 + - cb8dfd28c16f + - e27815e82dd4 + - 3e4f8642c77e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - b2f674562a18 - - 3169a38c2656 - - 01210c4e9144 - 460fad600dce + - 01210c4e9144 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - 7348b69e5109 - 06bcf65179fb - ba88bc5a6446 + - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - 3ef480892a9f - - 690c2caa367e - 5127a713de83 - 3fba9c77550a + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -133,23 +133,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - 284a1cb82b61 - - ec9e21e9c71b - - 60024a528cbd - - 3f7be05a1597 - - 71740308d412 - - df25d4fb79b7 - - 6505bd37670d - - 41cea2aa2dce + - 5bec28269d95 - f3c89da3af16 - - 2061fb3b81b4 + - 0ee0c3089254 + - 3f7be05a1597 - da9d8bf98802 + - 6505bd37670d + - 284a1cb82b61 - 366a11d316a7 - - 5f625c63b8bc - 045c7c3d8e59 - 9ef6920c3089 - - 0ee0c3089254 - - 5bec28269d95 + - df25d4fb79b7 + - 71740308d412 + - 60024a528cbd + - 2061fb3b81b4 + - 5f625c63b8bc + - 41cea2aa2dce + - ec9e21e9c71b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -167,43 +167,43 @@ tools: - name: megahit owner: iuc revisions: + - de387b2b2803 - 14ddfc8ffb93 - 7518ee87b53d - a96f3ad4e0d8 - - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - d7edbc9c3a07 + - 39edec572bae - f8113c25bc6b - 09c589057ee8 - - 39edec572bae - - eb7b00ec347d - 9d79beb19ac3 + - eb7b00ec347d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - 29dabd8db6f2 - - 51c2360aa807 - eadfd71dde37 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - f369ef5f210b + - 2ecf5a570907 - fd128c111ab0 + - 3ca2d2a9068c - 606b09cc9860 - - 2ecf5a570907 - - e731ea24e48d - f338e9942b27 - - f369ef5f210b - - 99ecfdafc64f - eb7a370f6588 - - 3ca2d2a9068c + - 99ecfdafc64f + - e731ea24e48d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -215,11 +215,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d - - a7b889b90140 - - 8b6d0d85252b - b799a615995d + - a7b889b90140 - 73a3846701e1 + - 8b6d0d85252b + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -237,9 +237,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 64a1c751d99b - 15200570e926 + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -251,11 +251,11 @@ tools: - name: pretext_map owner: iuc revisions: - - d256a51a656b - - 02831bf9e95f - - dfb8a4497339 - bbe19ef04a74 + - dfb8a4497339 - 2b16ba799da9 + - d256a51a656b + - 02831bf9e95f - 79b48f02db49 - 8fef980d48b5 tool_panel_section_label: Assembly @@ -263,8 +263,8 @@ tools: - name: purge_dups owner: iuc revisions: - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -272,25 +272,25 @@ tools: owner: iuc revisions: - 6fcbee531de6 - - 675488238c96 - - 875d0f36d66f - - 342a1d1fed7b - 59db8ea8c845 - - 3061c8b029e5 - - 7594365c546b + - 675488238c96 - 72472698a2df + - 3061c8b029e5 + - 342a1d1fed7b - ebb0dcdb621a + - 875d0f36d66f + - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 78c533842eeb - aa39b19ca11e - cd06929b224b - - a199cd7ac344 - - d865b62f501c - 39bed8de8017 + - d865b62f501c + - 78c533842eeb + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -308,30 +308,30 @@ tools: - name: raven owner: iuc revisions: - - 2b2a352488fa - - 5c55448d0f33 - f11b994b7eb2 - f8564b2d7f63 - - 3edba9afc9bc - 33b7d8481a76 + - 2b2a352488fa + - 3edba9afc9bc + - 5c55448d0f33 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - e122f9101584 + - ef69617ecb42 - 378e55aeeb25 + - 5fc94b3a4704 - 53c2bc8c2ae3 - 28189050e437 - - ef69617ecb42 - - 5fc94b3a4704 + - e122f9101584 - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -344,69 +344,69 @@ tools: - name: shovill owner: iuc revisions: - - 196a599ec43d - - 865119fcb694 - 83ead2be47b2 - - d9f6a00b6db7 + - 865119fcb694 - ad80238462c1 - - ee17a294d3a3 + - d9f6a00b6db7 - f698c7604b3b + - 196a599ec43d + - ee17a294d3a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - 5e0825476fb7 - - 015283de3004 - 24e471d13fe9 + - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - 1bb12736175c - - 7490b213baa9 - - 1fc82fe7ebef - - 051fd2db8a27 - - 604782a8a53a - 904bf932cf78 + - 604782a8a53a - c33a476f4001 + - 7490b213baa9 + - 051fd2db8a27 + - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - ad8b536d1caa - - 655fa188c3cc + - 9678993ca5bd - fee85957cebe + - 655fa188c3cc + - ad8b536d1caa + - 808b3a0a6716 - 34305b013402 - - 9678993ca5bd - d6e617c4e338 - - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 6b5a5842531e + - 037f9927c4ff + - 8d4b90bf9caf - b8002c3f7141 - - 7e27faaad80e - 21da31ed41a1 - e5a3b75a271f - - 8d4b90bf9caf - - 037f9927c4ff + - 6b5a5842531e + - 7e27faaad80e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 5b26685e5d3b - - 86f66ab58e14 + - 7922870efcca - 328aa71f0f3c - 9de69775f512 - - 7922870efcca - f1532cb33c75 + - 86f66ab58e14 - 2a10645aeadd + - 5b26685e5d3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades @@ -414,119 +414,119 @@ tools: revisions: - 1708851f8804 - e41dcb0e913b - - 8cc856b935ee - 85fb02c43042 - 340bc17f49cf + - 8cc856b935ee - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: + - de1260f8a300 - b65a43f70b99 - - d159735a6a9f - - 6357b127161e - b3490b036c5a + - d159735a6a9f - d5fb354f745d + - 6357b127161e - 249f6a28c751 - - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - d5887ace0dd4 - - d2d1df21dfb9 - - a90db5dbaaf3 - - 7897763d14ec - - 9006e5836729 - b7829778729f + - 7897763d14ec + - a90db5dbaaf3 + - d2d1df21dfb9 + - 33368fec3b70 - dd7ad84f3943 + - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - - 189e837009c9 - ed2425b9fd27 - 6f4c8ad6ea01 + - 505a9833ab5d - 8f631679571f - ced385aa976d + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 19bdfd1e6fe3 - - f31d376ce725 - - e59bee4565b3 - - 356afed970b4 - 9ded6109434a - d40ed4eb0c0e + - f31d376ce725 + - 356afed970b4 + - 19bdfd1e6fe3 + - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - af40e971a8cc - - b23249f81bc4 - - 4688ae3b49b5 - - 80a17897564d - 6dd935e4984b + - 4688ae3b49b5 + - b23249f81bc4 + - af40e971a8cc - ebd801e712bc + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - 937ea677d437 + - b5e35a2ca4f3 - 59bd28f6265d + - cb1e3db43020 - bb11fefb23a3 - b64696992ee9 - - cb1e3db43020 - - b5e35a2ca4f3 - - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 2628f6790eda - - 383bb5ad32e2 - cb4768eeca3b - - 6bfab4a4a988 - - 6015aa0303f2 - 05bd7504fdb2 + - 6015aa0303f2 + - 6bfab4a4a988 + - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - e92675014ac9 + - 3e44ef016b45 - 0a3a602cd1e3 + - 9e3e80cc4ad4 + - 6e26c9afd301 - 8f9f06995f98 - - 3e44ef016b45 - e022dff952df - - 9e3e80cc4ad4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 920677cd220f - - 5da9a0e2fb2d - 08256557922f - 8d09f8be269e + - 920677cd220f + - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 4a53b89fa703 - - 0e2b4e3f9ca1 - 37d88f41c810 + - 0e2b4e3f9ca1 - 82398ba86ba7 - d81360ea69d8 tool_panel_section_label: Assembly diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 5f9d10918..bf5a89dbf 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: - - 392f100eebcd - - 4768f7f8e93f - - bfd290fe1588 - 1ae00120dd24 + - bfd290fe1588 + - 4768f7f8e93f + - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 31812e7a1315 - ded48b36f3b7 - - 1f5641a52664 - 8e8dc9a1e3e5 + - 1f5641a52664 + - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 24a7a95867b0 - - 17fcac7ddf54 - 5c8ff92e38a9 + - 17fcac7ddf54 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 d8ce7566b..5159ccbd5 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: - - d1f62024a08b - - 0840ba83860c - 1c427e24fb79 - - a9c9d768b751 - - 204a131e47db - - 7beb76ffbc0f - 159b04e36791 + - 7beb76ffbc0f + - 0840ba83860c + - 204a131e47db + - d1f62024a08b + - a9c9d768b751 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 780a0af53..5fe95d1a6 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 + - 87ee588b3d45 - a68aa6c1204a - - 589e7e57fd6d - - e19bebe96cd2 - - a1a923cd89e8 + - a8eabd2838f6 - ce3c7f062223 - 64e2edfe7a2c - - 0a5c785ac6db - 07e8b80f278c + - 589e7e57fd6d + - a1a923cd89e8 + - e19bebe96cd2 + - 0a5c785ac6db - b28e0cfa7ba1 - - 87ee588b3d45 - - a8eabd2838f6 - - dde39ba9c031 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 ad99ab6cd..9a15f2467 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - 54f751e413f4 - - f921014aba5a - 62c9df8382c2 + - f921014aba5a + - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - cbf3f518b668 - - 5edc472ec434 + - a52d2d93e595 - e25d3acf6e68 - d999e774072a - - 0e3cf9594bb7 - - 6f386c5dc4fb + - 5edc472ec434 - 2889433c7ae1 + - 6f386c5dc4fb + - 0e3cf9594bb7 + - cbf3f518b668 - acf4e47b734c - - a52d2d93e595 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus @@ -43,8 +43,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 59c079ea5..6674c5386 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,12 +8,12 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - - f4230f116196 + - c8cdde00b105 - 710301bc46fa + - 6ca543ec1bf8 - da6bd1975a71 + - f4230f116196 - 095ad4d096d1 - - c8cdde00b105 - 27ee142314a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,8 +105,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -124,39 +124,39 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - bfb65cb551d8 - - 79cfd9ead848 - - 0fac8e2afc13 - 3b8a9d5ced85 + - 0fac8e2afc13 + - 88076940fa94 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - f5d979cb4b54 - b46d4b4d995c - - 55918daa5651 + - eb6564a60136 - 715cd0e87781 + - 55918daa5651 - d532b7e5f64b - - f5d979cb4b54 - - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - - fdf2cc80adb5 - 5579659312e6 + - fdf2cc80adb5 - 97872d87ba80 + - d2f955aea23a - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - 319a28774da9 + - bc31d02be922 - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,34 +164,34 @@ tools: owner: chemteam revisions: - 4da9ee404eab - - 2c349b027a01 - ed736e6eee39 - - cac1886249a2 - 070e3ecc3fda + - cac1886249a2 + - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 525ca7c8065f - - da8753545526 - 73008ef1f487 + - 525ca7c8065f + - 2e219a2d9327 + - 807aa4c9293d - f197e34c33a9 - - d1f803b5943c - c0c9a5024177 - - 807aa4c9293d - - 2e219a2d9327 + - da8753545526 + - d1f803b5943c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 - 27ea4e1a3f95 - - 61094e01eff9 - - 7568ae18908a - - 1809414a9454 - 2c8ed1b52bf7 + - 1809414a9454 + - c4fbab8e03c5 + - 7568ae18908a + - 61094e01eff9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -203,18 +203,18 @@ tools: - name: md_converter owner: chemteam revisions: - - d7ec25187599 - ba83f0923369 - - 79e8ab8f1e81 - - 730ef07b90ae + - d7ec25187599 - ccfbd956a2d3 + - 730ef07b90ae + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -262,9 +262,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e6011617c748 - b59c91adeac1 - 1400d1977e7b + - e6011617c748 - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -277,8 +277,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -333,8 +333,8 @@ tools: owner: bgruening revisions: - 85fad59f8168 - - d4c67ced6abc - 9b48456a96fe + - d4c67ced6abc - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 38730b4a1..333a94633 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - fa56d93f7980 - - 163688bb8f73 - c97a786e8fb5 + - 163688bb8f73 - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,16 +23,16 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: + - 424aefbd7777 - 86e2413cf3f8 - 495a4173006f - - 424aefbd7777 - 640d3af5d833 - f5d67c722d67 tool_panel_section_label: ChiP-seq @@ -53,8 +53,8 @@ tools: - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 4a14714649b4 + - 5c2cc3b58c7d - 74c9214cc8e6 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 3cb288d85..626933523 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 25136a2b0cfe + - 33151a38533a - 90981f86000f + - 25136a2b0cfe - 830961c48e42 - - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - - baabc30154cd - 2dae863c8f42 - 6cbe2f30c2d7 + - 0046692724f9 + - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index b8a780029..ccee0bf1a 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: - - 3b6f97e7094c + - a3b86937ead6 + - 6ef0b5664c69 - 4a6ee918c13a - e3cbd2287f63 - - 0b3c3ad92827 - - 367b1ed91207 - - f3a19509108a - 5e1240a87bcb - - 6ef0b5664c69 - ab9350a8ab4d - - a3b86937ead6 + - 367b1ed91207 + - 3b6f97e7094c + - f3a19509108a + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e177a8ea0bf1 - - bd46669113b9 - - 72ed72122deb - d4d4e9febf5c - - 54ccb7e1f49a - 584008e574b2 + - 72ed72122deb + - 1b5fc03380d4 + - e177a8ea0bf1 + - 54ccb7e1f49a - 091bb5922a82 - - 33c99804a32f - 501c21cce614 - e525f9ffb9ac - - 1b5fc03380d4 + - 33c99804a32f + - bd46669113b9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,23 +59,23 @@ 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: + - 8979c288aefb - 77b41c89d856 - 186b8d913e6c - - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -87,8 +87,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -100,8 +100,8 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - 4dea02886337 + - 3e436657dcd0 - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -148,11 +148,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 26c6706bfb07 - b9b385097f13 - 19e45916daf9 - - 92ac8e086317 - 63769c4217a7 + - 26c6706bfb07 + - 92ac8e086317 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 1be746316..4572683dd 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,35 +2,35 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 268e91e540ee - - c929a006727f - 5f6d123679f4 - - de72ba3ed6f2 - - a1ca9bccc7f2 - e821645ef8fc + - c929a006727f - 29451af70c52 + - de72ba3ed6f2 + - a1ca9bccc7f2 + - 268e91e540ee tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 7a7fd0f5f15d - - 5d11599b8a7d - - bb1e4f63e0e6 - - 0e143b4c3987 - - 0e49b109abc2 - 2d2cf5c1ea8a + - 0e49b109abc2 - 12af64f93288 + - 5d11599b8a7d + - 0e143b4c3987 + - 7a7fd0f5f15d + - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 7c1beb6d6eca + - dc059492a995 - c06951d10364 - 1d848bc4585f - - dc059492a995 - 81b1e3e1fc6c + - 7c1beb6d6eca - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,24 +38,24 @@ tools: owner: bgruening revisions: - 3d211717a775 - - a67ac707496a - - 07418a30ed01 - - 93eb012d9eed - bfff7454b59a - 71aa86af6762 - 26e7304d6737 + - a67ac707496a + - 07418a30ed01 + - 93eb012d9eed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - b8858746dc1f - - 29fcfd36e90a + - 56d5b797ce84 + - dd0b7398bb96 - 26983857c91a + - 29fcfd36e90a - 5be24eba848d - - dd0b7398bb96 + - b8858746dc1f - 2bc10a9ca58b - - 56d5b797ce84 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations @@ -63,144 +63,144 @@ tools: revisions: - e6d0bff01239 - ee3a1b0f45f1 - - 7ef978dc1b8a - - 72bfafe3330b - 7e6bcd2e5128 + - 72bfafe3330b - c3e012dfe21f + - 7ef978dc1b8a - 9384cd033f30 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - 514fa53b5efb + - d9a637e83828 - 167788df3b46 - 9470f29702f8 - - a60c359ec43c - - b73e213add0c - - d9a637e83828 - fb9cf9c97ec4 + - b73e213add0c + - a60c359ec43c - fd1275e01605 - - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 5bffaa8354a1 - - e479c7ca5570 - - 86febdcc4283 - - a02cfa31e9cb - 2c37ce318bc3 - - ca0616bb2cdf + - 86febdcc4283 + - e479c7ca5570 - c34d11ea4ba6 + - ca0616bb2cdf + - 5bffaa8354a1 + - a02cfa31e9cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 - - 78f405266706 - - 2d466b530754 - - 192ef85c0b0b - 004aea905d4d - 1fcb7adc39b8 + - 01fb6a7654e6 + - 192ef85c0b0b - 69a8621ca2f0 + - 2d466b530754 + - 78f405266706 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 + - 137c4beed34b + - 3c9f0c486cca - d580d6acd1df + - db940c262830 + - 9ecba5e225a6 - 2f9e4843f480 - d9ce4897dbb2 - 459cfa861f0b - - db940c262830 - - 137c4beed34b - - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: + - 2c66e43f1c86 - bad3ca889618 - fd408d755394 - - 32e451def88c - - 2c66e43f1c86 - - f264afa9fa6f - - bd7db9e2f2cb - fbe773640707 + - bd7db9e2f2cb + - f264afa9fa6f + - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 9368fbc49c8b - - 56bce3c82278 + - 3b9d990a0a0e - 231994413f89 - 7fda5607e777 - - 4e12ea27f788 - - 3b9d990a0a0e + - 56bce3c82278 - 7e361d147872 + - 9368fbc49c8b + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - b1779366c8e9 - - 4431f39ede55 - - 94ca68515826 - c03c3384cd81 - e65d16fb2724 - - ce4ce3316f74 - d9114ef1c8a5 + - 4431f39ede55 + - b1779366c8e9 + - 94ca68515826 + - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - b88ebb3672a1 - - d57251071381 - - 2da482e408b8 - f8fc4e5aff9d + - d57251071381 + - b88ebb3672a1 - 23f7c5f1fdaf - - 793665fff0f8 - 4ed32329e0ed + - 793665fff0f8 + - 2da482e408b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - a7849312d328 + - e4c7985d4585 - ba6efa77fb79 + - 010e58e9d822 - 512155688d98 - - c60570fa602f - 25d830337d31 - - 010e58e9d822 - - a7849312d328 - - e4c7985d4585 + - c60570fa602f - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - c899e0ccff8c + - 00d869ea03a1 + - 443d9a9d6d11 + - aa200e4f3939 - 69264da0ce77 - 4d678170d29b - - aa200e4f3939 - 38e3f226248b - - 443d9a9d6d11 - - 00d869ea03a1 + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - d806504e96d9 - - c361b12d207a - 6662b1a8d326 - - a2d70c4fd406 + - c361b12d207a - 10301d137111 - aac8444d6681 + - d806504e96d9 + - a2d70c4fd406 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 2a084e5ca..c8e604665 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -30,8 +30,8 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -44,28 +44,28 @@ tools: - 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: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 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 owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index f664232e7..fe227f636 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 832c20329690 + - ce385837c160 - 63dd26468588 + - 832c20329690 - dba489bfcd62 - - 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 a44770ab0..01b09e704 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 29bdbc353f20 - - 62f5fab76dfb + - 6da3972210ee - cf1322aeb137 + - 62f5fab76dfb - d82648ad25a3 - - 6da3972210ee + - 29bdbc353f20 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 e72d6e337..0c859841e 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 - - 093678460093 - - 44e2cc14f75b - de6cebe3c043 - b1c926deaa2d - - 5915ea1ec9b1 + - 135b80fb1ac2 + - fe74900d6dc7 + - 49370cb85f0f + - 64172f1c1202 - c053d4cad713 - - 8665bcc8b847 + - 4e5056fefd88 - c4b82dce8335 - - 64172f1c1202 - - 49370cb85f0f - - fe74900d6dc7 + - 5915ea1ec9b1 + - 093678460093 + - 48f587c13075 - c5e2e5902201 - - 8c0175e03cee - - 135b80fb1ac2 - - 660cffd8d92a - - 4e5056fefd88 + - 8665bcc8b847 - 288f97432497 + - 44e2cc14f75b + - 5eb7e84243f2 + - 8c0175e03cee - e4691e1589d3 - - 48f587c13075 + - 660cffd8d92a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -40,8 +40,8 @@ tools: owner: devteam revisions: - 8889eb864cef - - 9db07fd39f85 - f666895cbebd + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -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: + - 859422bcb689 - 9457a20156db - 516b97a23d7e - - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -94,16 +94,16 @@ tools: - 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 owner: devteam revisions: - f81d4362b6c1 - - f773e98b26cf - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -116,9 +116,9 @@ tools: owner: iuc revisions: - 9c620a950d3a + - 56022eb50bbd - 0dbb995c7d35 - cd0874854f51 - - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -130,11 +130,11 @@ tools: - name: fastp owner: iuc revisions: - - c59d48774d03 - 65b93b623c77 - - dbf9c561ef29 - - d60c3f704da0 - 1d8fe9bc4cb0 + - d60c3f704da0 + - dbf9c561ef29 + - c59d48774d03 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -160,22 +160,22 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation 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: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -195,16 +195,16 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - 09a2199cd356 + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - 249c8393f2d4 - - 35e38452bb3f - e39cc71d3ed6 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -216,9 +216,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - - 045f0e1043f7 - 54053ea6c77e + - 045f0e1043f7 + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -250,10 +250,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 - 529bccd5e4a1 - - d5e9e83cd3d8 + - 567d5b3c52b1 - 09070cacefd8 + - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -265,9 +265,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: + - 4bedca26c133 - 0b7ec11b3c7c - 8abdedf55101 - - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -281,8 +281,8 @@ tools: revisions: - cb1e251cac37 - 90858c306551 - - bdf1ce174e39 - 736b8f6ee456 + - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -294,8 +294,8 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -310,8 +310,8 @@ tools: revisions: - 02f8a17a4ebd - 3599f5451ee2 - - f984bb114520 - b29d37ca9e41 + - f984bb114520 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 - - 177f0621c266 - 0c2907307ba4 + - 177f0621c266 + - e246088b6e34 - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -340,8 +340,8 @@ tools: revisions: - 547e8d00f11c - 61b4cedc8934 - - 73194cdd4f57 - 377ac2829eac + - 73194cdd4f57 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: - - f69501361cec - - 2f804526f5fd - 037f0acc7830 - b4c6f054210a + - f69501361cec + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -380,22 +380,22 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - fdc21382376d - 61eb4cfc7313 + - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -440,11 +440,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - e654095ab143 - - b557acca0b56 - a535cf1e5da4 + - e654095ab143 - 8250ea3a1501 + - b557acca0b56 + - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -465,9 +465,9 @@ tools: - f3759eec3018 - 6a675c3aa610 - 9fa7803d1c51 + - 27ac32a22ad2 - 828dba98cdb4 - 7accf7407811 - - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index c3528a832..7d89a165b 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,82 +3,82 @@ tools: owner: devteam revisions: - ce9cd02d5b88 - - 7b4468117008 - - 64e9a6afdd0c - e41385662e5e + - 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: - - 3d0c7bdf12f5 - - f2e8552cf1d0 - - 5ec9f6bceaee - - ff9530579d1f - - 2b0c9d9fc6ca - 2c64fded1286 + - ff9530579d1f + - 3d0c7bdf12f5 - 9da02be9c6cc + - 2b0c9d9fc6ca + - 5ec9f6bceaee - e7b2202befea + - f2e8552cf1d0 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - ad116ae3f4d9 - 18a51655db17 + - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - - 7306ec78632a - 59003d0543cd + - 7306ec78632a + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 1f296803dfa3 - 8880fb74ef56 + - 1f296803dfa3 - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - b2f1f75d49c4 + - 9a913cdee30e - abfd8a6544d7 - - f7985e0479b9 - - 5e33b465d8d5 - bf675f34b056 - 3d93dd18d9f8 - - b2f1f75d49c4 - - f7e2f1eb3a16 + - f7985e0479b9 - 1c2db0054039 - - 9a913cdee30e + - 5e33b465d8d5 + - f7e2f1eb3a16 - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 949f01671246 - 084bbd8ba7b8 - cd7e644cae1d - - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index 54bbfa7ed..d934ded82 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - - 141612f8c3e3 - 85ef5f5a0562 + - 141612f8c3e3 + - 83a19df00eab tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 7d6baea4c..bdeb54091 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,23 +2,23 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - - 0c8f7322f8fc - 8f53b238a360 + - 0c8f7322f8fc + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: - - 45296e47d565 - b2c25142267e - cf61daf064fe + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -101,8 +101,8 @@ tools: - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -115,8 +115,8 @@ tools: - name: gemini_qc owner: iuc revisions: - - 86e46972e183 - 9e83673fa6d2 + - 86e46972e183 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query @@ -130,15 +130,15 @@ tools: - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -151,8 +151,8 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index aade5505c..18d33de94 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -23,8 +23,8 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index dd68d1708..0f7c1e180 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -3,8 +3,8 @@ tools: owner: galaxyp revisions: - 983bf725dfc2 - - e9df53a75f3c - c1b437242fee + - e9df53a75f3c - b39347891609 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,45 +25,45 @@ tools: - name: sra_tools owner: iuc revisions: - - aad3885b3216 - - 516a54ddf218 - - 5e6237d58b0c - - 653e89d73fc4 - - 6591f049cf7e - - 83c7d564b128 - - c441583adae5 - - 6ea73833cf67 + - 1ec814014652 - 9a776b080193 - - 4df8de2d0e48 - - 69ebb7f46e45 - - 8848455c0270 + - e407b9da183a + - 653e89d73fc4 + - f8054ea1c365 - 4317d3cb6cba - - ba931a59dd59 - - e08a7ad4378b - - 1790dcf3c32d - 7068f48d0ef9 - - 1ec814014652 + - 6ea73833cf67 + - ba931a59dd59 + - 516a54ddf218 + - 83c7d564b128 - f5ea3ce9b9b0 + - e08a7ad4378b + - 8848455c0270 + - 5e6237d58b0c + - 69ebb7f46e45 + - 4df8de2d0e48 + - 6591f049cf7e + - c441583adae5 - 734abc7ac21d - - f8054ea1c365 - - e407b9da183a + - 1790dcf3c32d + - aad3885b3216 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 21a560af5913 + - 75b3b3d0adbf - 9aaa46d45472 - 34758ab8aaa4 - - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 468c71dac78a - af5eccf83605 - 054483e27a35 + - 468c71dac78a - bfdc6a7ffd3a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 0f30d2b11..ce6fb6078 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: - - 7f13dc906cb9 - - 290a11559985 - - ae9994cf526f - 4b519282a05b - - 740057a5126d + - 290a11559985 - a64dc31ab7f2 + - 7f13dc906cb9 + - df7356989ac1 - c4bde687c846 + - ae9994cf526f + - 740057a5126d - fd59d783248a - - df7356989ac1 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 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,21 +48,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 3b37b1b1c3a7 - - 374e9062d874 - 53460afd5115 - - '566197475670' + - 3b37b1b1c3a7 - ca7cb0eaad62 + - '566197475670' + - 374e9062d874 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - - 10515715c940 - - 391a4cc45fea - d3a9e32672ec + - da4c086cff5b - 3d059e9c2fba + - 391a4cc45fea + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -81,9 +81,9 @@ tools: owner: iuc revisions: - 1acf88921176 - - d0fc8b746d57 - 5fe1dc76176e - 299307abd804 + - d0fc8b746d57 - e3a675da7fd0 - 3b12bf9b4b87 tool_panel_section_label: Graph/Display Data @@ -110,15 +110,15 @@ 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 owner: devteam revisions: - - cdb9e89e2970 - 6f134426c2b0 + - cdb9e89e2970 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse2 @@ -130,17 +130,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 - - 2bb2e07a7a21 - 112eb40ba6cf + - 17359b808b01 + - 6cd09d7b5f37 - 667e17248bfe + - 1cfc579079a6 + - 2bb2e07a7a21 - a6e57ff585c0 - - 17359b808b01 + - 4542035c1075 + - ca2def38369c - fd5dbf0f732e - - 1cfc579079a6 - 836d1aa3e89a - - ca2def38369c - - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -158,8 +158,8 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - fe154a7af404 + - f1691de443a7 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -172,17 +172,17 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f - 62e3a4e8c54c - f234e2e59d76 - 85da91bbdbfb + - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -195,8 +195,8 @@ tools: owner: iuc revisions: - 7c9417381ad5 - - 44c66e8d21e6 - 6c571966cfb9 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -208,21 +208,21 @@ tools: - name: pygenometracks owner: iuc revisions: - - 36b848d5f3ec - - 326a3db8d9d1 - 14e7c35f3d00 - - 2824d77cd8f8 - 4ac4e7083b7e + - 326a3db8d9d1 + - 36b848d5f3ec + - 360df4999907 - 7dd841a32245 + - 2824d77cd8f8 - a1abfa420d9d - - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 73b8cb5bddcd + - 44608d0193ed - 83c573f2e73c - 2f557f6abbfb tool_panel_section_label: Graph/Display Data @@ -236,7 +236,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 79f257581..71c6e28cf 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,29 +21,29 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - - 23d838d1569d - cc64914b0cf4 + - 23d838d1569d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster @@ -63,22 +63,22 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony @@ -91,9 +91,9 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 94697510d55f - 9a2f72d7dbd2 - ff6decc0f432 - - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -106,22 +106,22 @@ 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 owner: ebi-gxa revisions: - - 7d5c97823f8b - 1be0fc4d8654 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -134,29 +134,29 @@ tools: - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc 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 owner: ebi-gxa revisions: - - d18ed15697bb - 0bab2ae44e7a + - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -169,8 +169,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -183,15 +183,15 @@ 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 diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 9a419442c..2d57a4763 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,51 +2,51 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 921a2da49a0c - - ed2cca6b5de4 - a4c13ddcc8ee - 29f66c353bcb + - ed2cca6b5de4 + - 921a2da49a0c - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - ec4b948dc6f0 - - 755df866ad0c - - 5746d61f0a91 - d404277cc87a - 78fb5e286609 + - 5746d61f0a91 + - ec4b948dc6f0 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 9e357a8b2ec3 - 03dd3c16ae4e - - 4d511437b1e5 - 977dc15add20 + - 4d511437b1e5 - 11fa44ee0603 - - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 0ba4f56a3613 - 3b5b54ed6392 - c3e5e2cf12b7 - - 41dbf4d162a2 - - 0ba4f56a3613 - 77919cc3618e + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e - 9939786dd9c9 - - 5308ca68ef3d - - 7babd8a46fe0 - 12d51d7be66f + - 7babd8a46fe0 + - b63363075c2e + - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 368b3f520..456916b01 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,11 +2,11 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - - 699a5e9146b3 + - 7db4fc31dbee - 81f0cbca04a7 - 8bccb36e055a - - 7db4fc31dbee + - 3df9f0a4bf34 + - 699a5e9146b3 - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -14,16 +14,16 @@ tools: owner: imgteam revisions: - 2436a8807ad1 - - 5bc8cdc17fd0 - 5791a7f65275 + - 5bc8cdc17fd0 - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - 6ad1d3cfdea1 + - e576b73a2e2f - 9d47aabda459 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,42 +38,42 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: + - dba87c4b32d3 - f70b215d155c - d51310ab328a - - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - fcadded98e61 - - 85edbb7a436b - - b07f4839ca77 - 10eed33aa9b2 + - b07f4839ca77 + - 85edbb7a436b - f3360fbeda64 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - - b58447a2eed2 - 664232d2a3f7 + - b58447a2eed2 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - eb6c08714244 - - 0e4dccaafef5 - e917a2424690 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -102,72 +102,72 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: + - 5d28ac336861 - 6a7da2e5f696 - 2484086dee41 - - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - bace5a93a97c - 11f177b1a59e + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - - f8fa0f6718a3 - f24c370e5ea4 + - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - ad271f78a87a - 31d195bedf6d - 3245681b2f6d - - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - ff1a86a87364 - - 6100a22bf4f2 - c09dcda1143f + - 6100a22bf4f2 + - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - 3a05117669cf - - 667a513e67e4 - b178453ea8d1 + - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - 91e03287f285 + - 20dbb1f7ec7b - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -182,24 +182,24 @@ tools: - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - - d3890df07463 - 6f4715b8540a + - d3890df07463 + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - e52c75a28c4b - 980aed9e8fd5 - 407925835dd9 - - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - acf3aa487283 + - 79e10d12d90a - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -207,8 +207,8 @@ tools: owner: bgruening revisions: - 80b200ae516b - - 035a58c7f54a - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -220,8 +220,8 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -229,8 +229,8 @@ tools: owner: bgruening revisions: - 33f4fa1413fb - - 27edbb90ab2b - 4ecf93628f97 + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -263,7 +263,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index 688a864ee..dab3e08b8 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: + - e4ee04da1c19 - 40737febe339 - - a38934e303b9 + - 1069f6db0a0e - f362150bef41 - e319b5b65879 - - e4ee04da1c19 + - 3a72fede57ce - d6e72da3ec35 + - a38934e303b9 - 78bbd17d0703 - - 1069f6db0a0e - 3e4f434a69c6 - - 3a72fede57ce tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - 2b95d5c04908 - 0135f1d487a0 - - 9537184d421f - - 72ddd32392cd - - 618297d23022 + - 7fe36019c073 - fcbeda41d0ac - - 2b95d5c04908 - - c88553ec696e - 8f8df367470d + - 72ddd32392cd + - 618297d23022 - f91cfb73d369 - - 7fe36019c073 + - c88553ec696e + - 9537184d421f tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - fafb3d685fa9 - - d7e79eb3bcb3 - 2cf4a1cafc16 + - d7e79eb3bcb3 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 94df24c6bc00 - - ee2beb764a7b - - 3d18f8c3c0f6 - 8c05afb547fa - - a1c2aecd7a0d - - 9eaadf03e0df + - 43aac8d29685 + - 7f1cfa4c0e32 + - 3d18f8c3c0f6 - 5dc33613c288 - - 6a1515bb0687 + - 94df24c6bc00 - 28a6f1908fcc - - bd2a7d1316b9 + - 6a1515bb0687 + - 9eaadf03e0df - 8d36959b000d - - 43aac8d29685 - ee29337f905c - - 7f1cfa4c0e32 + - ee2beb764a7b + - bd2a7d1316b9 + - a1c2aecd7a0d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - a250929be21b - - 86a20ae274fc - - c092052ed673 + - 9f978da6528a - db536ad45f28 + - 5d6ed46cc101 + - c092052ed673 - 364f4ffec275 + - 86a20ae274fc + - cb903c9dc33d - d37ede8589b2 - - 5d6ed46cc101 - - bcaa0d571ce2 - - 9f978da6528a - 8858fa037a15 - - e3bb03cf207a - - cb903c9dc33d + - a250929be21b + - bcaa0d571ce2 - 5671e1d3d5ee + - e3bb03cf207a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 584beffa972b - - ed28dd32141c - - 49236b03e4fd - - abbc8041e8ec - 38b91a3190cd - - 3b6a16d82c1b + - 584beffa972b + - e1a015876aa9 + - 12d66d0d05ac - c5c9f02b6167 + - 230b05597996 + - 49236b03e4fd - 194e3ceee923 - - 12d66d0d05ac - - e1a015876aa9 + - 3b6a16d82c1b + - abbc8041e8ec - f95f403841ad - - 230b05597996 + - ed28dd32141c 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 c1ecd3ff5..d3d5710a7 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - - 0f1724dd59d2 - 17e3b698dd52 - f198773344e4 + - 0f1724dd59d2 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a - - a513e3fbb4c5 - ba0c40780ecf - - 22c2a1ac7ae3 + - a513e3fbb4c5 + - 374cb875d38a - ac092723240d + - 22c2a1ac7ae3 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 bd6604571..f41957d68 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,9 +2,9 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 522137aaa9c4 - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config @@ -19,82 +19,82 @@ tools: owner: bgruening revisions: - 2af1346e68c9 - - f1b9a42d6809 - e1317b5502fa - - b6ef6d0cb6b7 + - f1b9a42d6809 - 818f9b69d8a0 + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: + - 05143043ca13 - 8334dc98c48e + - 1588f9076e32 - c80db5d6fd8c - 947c2eacccb8 - - 05143043ca13 - - 1588f9076e32 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 25b46af53232 - 29e4122c90de - - 9991c4ddde14 + - 25b46af53232 - 83228baae3c5 + - 1552b8cb4a94 + - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 - 53616c8b0865 - - 841a6cc5fc58 - - 060ca94ac049 - - f3dfa4bdf87e - 1a53edc4b438 + - f3dfa4bdf87e + - 060ca94ac049 + - 841a6cc5fc58 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 2fc89dcd41c8 - - d4808d5b83da - - 91c4e3331208 - - dc4b5fd604a6 - 40f4447733b2 + - dc4b5fd604a6 - 927586a18553 + - d4808d5b83da + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - - 7626ea9c2e1b - - 25ab6b4e376e - 301e07345c93 - - e5a5ad882f1f + - 25ab6b4e376e - 36e8d6d5d01b + - 7626ea9c2e1b + - e5a5ad882f1f + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 02d2be90dedb - 4ed102b922cb + - 02d2be90dedb - b7c3e9a3b954 - - 0630258dcf35 - f9639b488779 + - 0630258dcf35 - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 61634a87efc7 - - caeb57858702 - ec69cbe34b73 + - 61634a87efc7 - 14180f9c831e + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index beb89cb5f..c476ece0c 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,16 +2,16 @@ tools: - name: bowtie2 owner: devteam revisions: + - cd659e8cc5fa - 937aa69e715f - - 749c918495f7 - - a6d65b0c67af - - 03e9b2fbc005 - - 3ba8d4563129 + - d5ceb9f3c25b - 017aba02828d - - 17062a0decb7 + - a6d65b0c67af - 0d4acadabb04 - - cd659e8cc5fa - - d5ceb9f3c25b + - 17062a0decb7 + - 3ba8d4563129 + - 03e9b2fbc005 + - 749c918495f7 - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 2477830927ec - - e188dc7a68e6 - - 3fe632431b68 + - dfd8b7f78c37 - 64f11cf59c6e + - e188dc7a68e6 + - 2477830927ec - 53646aaaafef - - dfd8b7f78c37 + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: + - 3e1ea2facca6 - 60afcc2c1d05 - - e7f19d6a9af8 - 2ff111fac1d7 - 37b497aa133f - - 3e1ea2facca6 + - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 037c6e54df11 - - 77b2770508f6 - - 8c6cd2650d1f - - 3f4d6399997b - f54f5baedfdd + - b3eab4b67562 - 5cc34c3f440d - - 09b53c1d4ab1 + - 77b2770508f6 + - 3f4d6399997b - be1d967337e4 - - b3eab4b67562 - - c0c2d0941de8 - - 11a0d50a54e6 - - 6b1e195506a3 + - 8c6cd2650d1f - 53c0b7a1a0c3 + - 6b1e195506a3 + - 09b53c1d4ab1 + - 11a0d50a54e6 + - 037c6e54df11 + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - 42ce70172b72 + - 5ef7ec16b04f - 1cd2511a396e + - 79b885ce78d7 - 9ee34ba73ebf - - b8f5f6e87f5c - 178bdbdb6d24 - - 45795f582ae9 - 13022c3d3076 + - 45795f582ae9 + - b8f5f6e87f5c + - 00fbfac99d39 - e403d27e8f24 - ec9cbd6b9a49 - - 42ce70172b72 - - 79b885ce78d7 - - 5ef7ec16b04f - - 00fbfac99d39 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 6017294bb..e7f3d2097 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -114,8 +114,8 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 9e3c83d2afc3 - 1b09315a3f87 + - 9e3c83d2afc3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -141,8 +141,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - 1d74ae228df3 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -166,8 +166,8 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7627b40601f6 - 9ff95a1a2705 + - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split @@ -241,38 +241,38 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 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: - - 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 - 134be5abb208 + - dfebc82ba1f0 - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -280,23 +280,23 @@ tools: owner: recetox revisions: - 9064aecc78a7 - - 51332c2520c7 - 02c772a49998 + - 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 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - 17a48d0a80f4 - dd7bbc2b99d1 + - 17a48d0a80f4 - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -311,9 +311,9 @@ tools: - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ea0758b41473 - d90187b0f247 - ffbabefbd2e2 + - ea0758b41473 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -325,8 +325,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 80b4ca5ec..602027d9f 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,9 +8,9 @@ tools: - name: cat_bins owner: iuc revisions: - - 0e63d03c8790 - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -41,51 +41,51 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 63f86089423e - - 76d3d2b10738 - 7c2100246a2f - 5b5a7af9fbb4 - 65db807336bc + - 63f86089423e + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - - 96336c6a2bb7 - 1c35dadbe76f - 00f5005840fa + - 84fd33a60b35 - 18a502a9d287 + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - addaf9d22850 + - f732237754fc + - a9f4a217dcd6 - e8fba04706d3 - 34e55239e68b - - a9f4a217dcd6 - - f732237754fc + - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 5fe3edf19b9c - - 04c15826a0b8 - 75403243703a - 0776d824d896 + - 5fe3edf19b9c + - 04c15826a0b8 - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - - e96bbb9e24ea + - 1c9b3bcd4261 - 75c8945b0da2 + - 43c99742158b - 8470de786d47 - - 1c9b3bcd4261 + - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs @@ -93,48 +93,48 @@ tools: revisions: - 306a40d4bb8f - 35176674168c + - 1d75bd0595e2 - 84743da21318 - 5c865a382933 - - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - 555ccac8a4c5 + - 32c9ea835770 - ac72310b038a - 8daf4564ccda - 78faebd0879c - - 32c9ea835770 - - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - cae017b76acb - d60df8727f59 - f947b4bb5107 - - 7b8cb2b02978 - a58e4a43f49c + - cae017b76acb + - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 1bc3657cd694 - 7f3b59dee073 + - 04144473e59e - 073608a50ac3 - - 1bc3657cd694 - 7136e9ab70db - - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - 9058d8943303 - - 0a1224c4b781 - d943081510da + - 0a1224c4b781 + - 19299bb1c6af - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -148,27 +148,27 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - c4db8c4de66f - - b907a3c0434f - - f8f56dd6449f - dbf1798c0dcc - 65d52c693b8e + - b907a3c0434f + - f8f56dd6449f + - a68b985913ab + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level 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 @@ -180,25 +180,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 + - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - - c6676a890f50 - b084117133af + - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: + - 9704f1a3b32d - 7f208f1eb64f - cad93abecac9 - - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -235,29 +235,29 @@ tools: owner: iuc revisions: - 79706f10d680 - - c409a495841f - 31c6d107e7a5 - 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 - d24841f5c3d2 - - 71ea608ddfa3 + - 094ad9c068af + - 172920f67a84 - 714d5a28cc5c + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - - 12fb63b5f63f - - 4137b492233e - d7e9a3c41657 + - 4137b492233e - a4d7148ccee4 + - a293a742194f + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -269,12 +269,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - 75bedfb2078b - 6fcb8ac37a3e - - cf87759761eb - - 97f7bb0851e7 - 64bc7acc22a9 - e2c71b852aba - - 75bedfb2078b + - cf87759761eb + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -293,19 +293,19 @@ tools: owner: iuc revisions: - 080ea153677c - - 5e5a999ffaa9 - - 2d35528d2141 - c82508e76ad1 - 4033827c76b8 + - 2d35528d2141 + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - - fc6c328c292f - 95bf7479d53c - 6b7622dda516 + - 2cd76b089570 + - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -372,8 +372,8 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 - 20e2f64aa1fe + - cdee7158adf3 - 4a9da2b6c2e3 - 328c607150ff tool_panel_section_label: Metagenomic Analysis @@ -381,8 +381,8 @@ tools: - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -394,15 +394,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -421,8 +421,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -490,22 +490,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 3cc4a60615c0 + - 327d9f4cc95f - e073891b2afc + - 3cc4a60615c0 - 27250f92a01a - - 327d9f4cc95f - - 2cff76cf35c6 - - 4fd3b5d8706b - 7f5d7b0e9884 + - 2cff76cf35c6 - 0270541aaf46 + - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb - eb50e7eca3dc + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -571,31 +571,31 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: + - 1a037928504c + - fd69c607b43f + - ff8f55893e7d - 1a6cdf55390f + - 6dee4abadccb + - a16313517e55 - 2131d7dca455 + - b89b0765695d - 289b3807e80c - - fd69c607b43f - - 6dee4abadccb - - a92a632c4d9b - ef65b083bd0c - - b89b0765695d - - 1a037928504c - - ff8f55893e7d - - a16313517e55 + - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -634,15 +634,15 @@ 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 @@ -655,8 +655,8 @@ tools: - 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 @@ -668,8 +668,8 @@ 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 @@ -730,13 +730,13 @@ tools: - name: staramr owner: nml revisions: + - 3b22de20bd4b + - 4b9a8031ab74 + - 2fd4d4c9c5c2 - aeaa20b96ef2 - 141afacabcfa - be818ae858e4 - 4d83eccf5f81 - - 3b22de20bd4b - - 4b9a8031ab74 - - 2fd4d4c9c5c2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -766,8 +766,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - - 9495df9dd6ef - b3c7199d8786 + - 9495df9dd6ef + - 576963db5f1b 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 be3ccea53..350bb5efe 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -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: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 75d9afd66..90ce845cf 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -3,38 +3,38 @@ tools: owner: galaxy-australia revisions: - 48c13389050d + - 098506c54016 + - bdfbaf0c10aa + - a74dbfee5a86 - cd07731e4434 - - 80f03df2e2ce + - 9baa871cb1d1 - 6ae5a7b5a0a2 - - 94b8c6013083 - - 9eeb13a92d79 - - a74dbfee5a86 + - 2263989660f5 - 9422c5a87ee2 - 8b67dd48fec1 - - 9baa871cb1d1 - - 2263989660f5 - - bdfbaf0c10aa - - 098506c54016 + - 94b8c6013083 + - 80f03df2e2ce + - 9eeb13a92d79 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 4a60927aaca5 - - '764845535798' - c44f824c051a - - f0af8936ed41 - - fc2e49f91e52 + - c18157c68134 - aaa0d6a8b808 - - bc3831dd65c1 - - f14193ec1f50 - - d7ce0ec78e51 - 2e093badc689 + - 4a60927aaca5 + - f14193ec1f50 + - fc2e49f91e52 + - '764845535798' + - d390fe1567dc - be78f13134e2 - - 3ff17bad4006 + - bc3831dd65c1 - 5abf2c2249aa - - c18157c68134 - - d390fe1567dc + - d7ce0ec78e51 + - 3ff17bad4006 + - f0af8936ed41 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,8 +53,8 @@ tools: - name: clustalw owner: devteam revisions: - - 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 - - bf28a8cff401 + - 6f28e90db932 - f1a5908ea2cb - - c5908940967d - 15974dd17515 - - 6f28e90db932 + - bf28a8cff401 + - c5908940967d - f0d493f8f84f - 8e649f27aa0d + - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - e8fdceffea4c - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 + - e8fdceffea4c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: + - c9685bc0407c - 60698466facd - 5561a1193611 - - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: + - 48823c9635a4 - bcd65de9725b - 57f042937ba7 - - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - fb43e8887350 + - 4fc0cb2ac8ae - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - - 636b049e6141 - 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 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index a8b90a482..53134a3e8 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,9 +8,9 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: + - 28928576e1ea - 7c47b3c9e493 - 18a8d140ec6f - - 28928576e1ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado @@ -29,21 +29,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - fc8804320156 - - a7228a7ea146 - - 0e9e7fcdd543 - - 72b5e9dda577 - 79e9a869f40e + - 72b5e9dda577 + - 0e9e7fcdd543 + - a7228a7ea146 + - cb34f00cc10f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - 18505fe2bdb1 - db25ec99c3ea - d6cddc06aeae - fa11aa8103b2 - - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -55,15 +55,15 @@ tools: - name: medaka_variant owner: iuc revisions: + - 2bf63b38ee9b - eb746fa6f514 - - 43815fa60f3a - - 19f3b583a9b3 - 0f5f4a208660 + - cc36773a3681 + - 19f3b583a9b3 - edf6d4003fad - - 222669c4afb6 - ec699520444c - - 2bf63b38ee9b - - cc36773a3681 + - 43815fa60f3a + - 222669c4afb6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -82,60 +82,60 @@ tools: - name: nanoplot owner: iuc revisions: - - 7b379e98b9a9 - - a3c4fe6f49ab - - a38bdcec9e4c - 0f1c34698076 - - edbb6c5028f5 - - 645159bcee2d + - a38bdcec9e4c - a02b8b3f5a0c + - 645159bcee2d + - edbb6c5028f5 + - a3c4fe6f49ab + - 7b379e98b9a9 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 owner: bgruening revisions: - - a8d4be409446 - 90a922f32523 + - a8d4be409446 - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - 4857d5bcce52 - d376944466bf - 449e9aeded2d - - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - bec636361cfd + - a3afc5f0a96c - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 93d623d9979c - 543cbeef3949 + - 93d623d9979c - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 28d7819c312f - 1d835c691480 + - 28d7819c312f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -147,8 +147,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -173,15 +173,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 832e38210..3a043bc0f 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -59,11 +59,11 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 97b1b5ad1cda - d74850cf4e42 - - baceff842902 - - adfd6bf710bd - 3e73c97f025d + - 97b1b5ad1cda + - adfd6bf710bd + - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -83,18 +83,18 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - e4b4837f06f5 - - edacc4bcd3cb - - ed1518ce2237 - 2f27f3b86827 - 1e34d2e3d285 + - edacc4bcd3cb + - e4b4837f06f5 + - ed1518ce2237 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 @@ -114,22 +114,22 @@ tools: owner: iuc revisions: - 38ccd4589990 - - 48a42ca61006 - 5711fc06a63e + - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -142,8 +142,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -162,17 +162,17 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: + - b4b2b284230a - 27a6a256cd23 - 5bcf0e24f42c - 172815da3d41 - - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer owner: iuc revisions: - - 10232d2b5062 - df84aaed4769 + - 10232d2b5062 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_hisat2_index_builder @@ -192,15 +192,15 @@ tools: owner: iuc revisions: - 87febc68b45b - - 19bbd19b74b3 - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -225,36 +225,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 + - 5fe20c915fa6 + - 2c61c30a57e7 - 4ba60cb14cb0 + - 9c43baa60906 - d8dc037e3c13 - - 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: + - aec831b54a5b - 0db22932bc39 - 9d09724f2bf1 - - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 6e24e79d3d69 - 29c738066906 - - ed7a967cb11b - df30a2f1db55 + - ed7a967cb11b + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -272,9 +272,9 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 1865e693d8b2 - 3e4d45aca422 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -293,8 +293,8 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - 64deddb6a8ec + - d63c1442407f - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -302,8 +302,8 @@ tools: owner: devteam revisions: - 625fd9476402 - - 94a50db37d1a - 9946bc39c834 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1067,8 +1067,8 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - a22969b08177 - c362398df83b + - a22969b08177 - e4b7d1507a75 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1081,11 +1081,11 @@ tools: - name: salsa owner: iuc revisions: + - 58a870ef434c - ab5b7f6b7198 + - ba7b0f11e470 - 9a22227bb6d0 - f77f7a7f3b83 - - 58a870ef434c - - ba7b0f11e470 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index e5bbd086c..2f1ce5221 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 3b8b5bde0bd9 - - 81e66674859e - - d7c7ef3353fe - - 8834daeb9892 - - '841557158611' - - 6a457678efcb - - b89cac5156ec - - f73435dc282b - - 26de3a7b1cb9 - 3f59ebfbfe3d - d033ffc1c161 - - cce7b18495e4 + - 8834daeb9892 + - c78f3d7dd1db + - f73435dc282b - f04a1264e2a2 + - 81e66674859e - 5a7c56a5cc08 - - 107d3ba7024a + - 26de3a7b1cb9 + - '841557158611' - a6619171428e - - c78f3d7dd1db + - d7c7ef3353fe + - cce7b18495e4 + - 3b8b5bde0bd9 + - 107d3ba7024a + - 6a457678efcb + - b89cac5156ec tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - b0af57c1a968 + - 4755f52427c4 + - 6a726db04d4b - df47d4845b62 - - aa8cc71438cf + - a185b079b095 - 6283babe736e - - e75442c7f4da - - 5b777002c2de - - 4755f52427c4 - - 659517798cc4 - - 6223845127ea - - 5fcd1ece3a6e - 02b8758214b0 - - 6a726db04d4b + - 3b96e92e8ec3 - 88c4aa435ded - - a185b079b095 - 7a2092844346 - - 3b96e92e8ec3 + - 5fcd1ece3a6e + - aa8cc71438cf + - 5b777002c2de + - b0af57c1a968 + - 6223845127ea + - e75442c7f4da + - 659517798cc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 111bd54f6bc4 + - f97743d52b87 + - d1c340a5664b - 0878b7fd5260 - b8476e82ac20 - - d1c340a5664b - - f97743d52b87 - 24d024316465 - - 70acec670c30 - 524d31add34a + - 111bd54f6bc4 + - 70acec670c30 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: + - 9e10ba792be2 + - feb40665d7cd - 4f6349228462 - daddf188c13f - - feb40665d7cd - - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,26 +110,26 @@ tools: - name: pangolin owner: iuc revisions: - - 03ed9524dcd1 - - ca337cce3888 - - b6abccb1f25b + - 83a69484cb87 + - 36912871ccdc - b7e297c2ede6 - - 3a43c3982401 - - 437e28791761 - - 7bb8726be37c - - ca0d8cf80567 - - 42a174224817 - - abf6dbe8c9d7 - - 81804a978fc0 + - b6abccb1f25b + - a2099fb98cdb - 8ad84c5753ea - - 2fa9d4f1b48f - 2f1019071464 - - a2099fb98cdb + - 2fa9d4f1b48f + - abf6dbe8c9d7 + - 42a174224817 + - ca337cce3888 + - 437e28791761 - 9d61d3fa046c - 5f8727ff21e7 + - 03ed9524dcd1 + - 3a43c3982401 + - ca0d8cf80567 + - 7bb8726be37c + - 81804a978fc0 - 14ae456b8cc5 - - 36912871ccdc - - 83a69484cb87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - - 73a469f7dc96 - - b1e68bbe4cef - - ba29b5e2a4be - ea30d3089354 + - ba29b5e2a4be + - 73a469f7dc96 - 29ff6a849eac + - a4b71be30c3c + - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 9b2b122d0415 - 91887494eb97 - e88a7de55d6e - - dbe2b2204555 - 15ac71df11a0 - 809e42326fc2 - f1ccc8a6eb05 + - dbe2b2204555 + - 9b2b122d0415 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 92f2abe88..840e08027 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 - - 881d7645d1bf - - 3f254c5ced1d - 7d34178f2812 - - 1aac2a13842a - - f9242e01365a - - a1f0b3f4b781 - fc288950c3b7 + - f9242e01365a - f6ced08779c4 + - 3f254c5ced1d + - 881d7645d1bf + - 1aac2a13842a + - b502c227b5e6 + - a1f0b3f4b781 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 219cbac6c..56abcb563 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: + - 7fbec959cf2b + - 5b85006245f3 - e4a053d67e24 - - c0e71cb2bd1b + - d00e15139065 + - 3bd420ec162d - eb085b3dbaf8 + - c0e71cb2bd1b - ca90d17ff51b - - a58f7eb0df2c - 2f7702fd0a4c - - 5b85006245f3 - - 3bd420ec162d - 6ab1a261520a - - d00e15139065 - - 7fbec959cf2b + - a58f7eb0df2c tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index a296927aa..c20f55759 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,65 +2,65 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 4c177985028a - - 277dc652246e - 0a18ac48ac53 + - f28ad96b76dc + - b574b84afc4d - ece627528a78 + - 277dc652246e + - 4c177985028a - b18329a8ac14 - - b574b84afc4d - - f28ad96b76dc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - bf06d196e23d - - b41107d8fe89 - - e988563cc6e5 - a9a28e46d54a - - e215f71d7983 + - e988563cc6e5 + - b41107d8fe89 - 525f201b86c1 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - 8da3511c9467 - 56da27be956a - bb6397b94018 + - 4fbffddde8cd + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - b8c79e70516d - 528fb09022be - a8157342d9a3 - - 890845926d4b - - b8c79e70516d - f23d67e28cc8 + - 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 - a69865da6f80 - a95a82eb4d50 + - 25b83cbd596a + - 59e85306eae5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - f1897eb07081 - ed9ed1e6cca2 - - e0669b1854b1 + - f1897eb07081 - 611d80c0e29d - - 83aac7741200 - 798da6bdff3d + - e0669b1854b1 + - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report @@ -68,28 +68,28 @@ tools: revisions: - a7fb9b395ddf - 74b61bf5bc4b - - 5a35e3a8d013 - d426a9107a6c + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - 91f0f5922011 - df2187f9013b - - 82f6c2f4332d - cc430977c8ff - - 91f0f5922011 + - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - c5aa9fca18c6 - - 1693b2126f30 + - ba92b59cd529 - 10566783d718 + - c5aa9fca18c6 - 043f9c91f686 - - ba92b59cd529 - d2483487e077 + - 1693b2126f30 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 + - ff8c9e0e8a7b - ae4dc0c041f9 - 9fa3dbf06f17 - - ff8c9e0e8a7b - - bf0728e000cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,8 +129,8 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 4081e4faa4ab + - 1c5cbf8f79ce - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -144,9 +144,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - ce1a157a41bd - d6a4dfdad269 - 0d2e93e01e68 + - ce1a157a41bd 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: + - d286ff4600dd - e66f552a3c47 - 160538a890a6 - - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -181,15 +181,15 @@ tools: owner: galaxyp revisions: - 4d17fcdeb8ff + - 1f39c833f65f - 2133b0be850a - f522c08e900c - - 837224ad1694 - 7f432d87c82c - 9c52362ae7bb - - e42225f8a659 - - 1f39c833f65f - - 37d669de2828 - 97a7f34fcb6a + - 37d669de2828 + - e42225f8a659 + - 837224ad1694 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,8 +201,8 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - e63db1aa82ee + - a72ac2c7cc5b - 0ed07016d668 - 85b8866f06d7 tool_panel_section_label: Proteomics @@ -210,53 +210,53 @@ tools: - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - 352b37c66d97 - 767c1d761aaf - 1974224d63c2 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 35cc7ca0bdc7 - deaf035bbe9f - 99450519d727 - 4f359549383c + - 35cc7ca0bdc7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - c1343e3389ca - - e79958768a2c - 06f6826d380c + - e79958768a2c - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 + - d46d64e7964d - da986f83631b - d2eac53666f0 - - d46d64e7964d + - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - 1199751329b0 - - 944b43462104 - 8bd7734309f6 + - 944b43462104 - 9bf325045235 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 @@ -269,71 +269,71 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - - de7593c29499 - 8212e342e482 + - 28434abe6c5c - 593839e1f2c3 + - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - f4be248c3d47 - - 4e77b8f12cd3 + - 01dbaf6a57e0 - 8960fb791701 + - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - 370141bc0da3 - - 25529df60a81 - 06cca574e337 + - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - c9eff69a7c62 + - 518b1730cf2a - f7fef900f5b2 + - c9eff69a7c62 - 6ccbf9a2072c - 9cdf15d3cfc8 - - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - dff6c756eee5 - - 5e948629bc73 - 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: - - 5ad0b5bf1deb - 6634cad7d797 - 2a93a25f0599 - 9b7977080f6d + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -341,63 +341,63 @@ tools: revisions: - d6878d27f051 - 05d5e1ddc985 - - fe4e4587d265 - 0bb5056cb775 + - fe4e4587d265 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: + - 5ad830edc021 - 52ba9695e752 - - 4af67edd5aef - febd569ad26f - - 5ad830edc021 + - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: + - 39e8fde08881 + - 27cba4c5fc42 - 92352a475eed - b2fc8da99bcc - - 27cba4c5fc42 - - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - - 9e26f5c770f8 - d3546bb9fd8e + - 9e26f5c770f8 - d413dc49d650 + - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b + - 3720e349ba2a - ca1740533b59 + - 8a04ed1c1d1b - c28f13cab67a - - 3720e349ba2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - ca799a7246e7 + - c55dddc5844a + - a5d785af0ad8 - c427a8628cbe - 382cde407f81 - - a5d785af0ad8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - b5d0905419da - - adca857b4884 - 39caaa778d2e + - b5d0905419da - 8ddb7bab1138 + - adca857b4884 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger @@ -406,8 +406,8 @@ tools: - 8d4db262964c - f817513840a9 - 34e7afee141d - - 1c5f31b8d632 - 18f93351f8b6 + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability @@ -415,24 +415,24 @@ tools: revisions: - c69f69d7867a - 5d9f175dff81 - - 986e03d3201e - 111c3a00136d + - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - 4204882495f2 - be74a8cd7d66 + - 0e52c85f3b15 - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter @@ -440,23 +440,23 @@ tools: revisions: - c18d8efa4474 - a407b6790342 - - 2b2a7551a857 - f5ec766d80cf + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - d0304fb829c0 - - 021fdb80f204 - 4e66c4e73909 + - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - 2735db4dd8d9 + - ee860980edc6 - 8098330f6d91 - bf32e0bcf554 tool_panel_section_label: Proteomics @@ -472,56 +472,56 @@ tools: - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - c1809c05ae8c - - 1bf940c18d93 - e8f64a7dc470 + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 496cf619e311 - 9f505cd4428f - f861ec9fbe59 + - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - c99d5004b74f - d4396637b9f5 - 0bddef8d144e + - c99d5004b74f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 89254095cbf6 - 8b814eafce2c - 4bb198c0bd3e - - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 - f82b320ceb90 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - d31426ef20f6 + - 6e8cc5ed2a9b - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -536,28 +536,28 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e + - decc397c3b7e - 3d8d4ada5405 - 6b01678ec2fc - - decc397c3b7e + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - 5182338d5e7c + - dd173849c3d8 - d6aca689dd48 - 539a3a4dcc9e - - dd173849c3d8 + - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: + - d426affe977c - 16026cdb1330 - 8a45fd5a608a - - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -571,24 +571,24 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - 1b03536aa3c9 - - 9020199dba0a - d063e2fe4ba4 + - 9020199dba0a + - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - f036e8cf1a55 - - 78c080d36945 - ad2ba3a95a02 + - 78c080d36945 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - 7f6a1f27553e + - c8b225c69a7f - 5c2a97a234d6 - fb52e95a370c tool_panel_section_label: Proteomics @@ -596,8 +596,8 @@ tools: - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -609,19 +609,19 @@ 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: - - 07ff622ec007 - - 1beff3ddce58 - - 3634c90301af - 3ec27b4cee7c - da885ca16cb2 + - 07ff622ec007 + - 3634c90301af - a72c48001f7c + - 1beff3ddce58 - 943a34df6047 - 7fdd9119cc4f tool_panel_section_label: Proteomics @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 + - a371252a2cf6 - 265c35540faa - 1a5690a5eedc - - a371252a2cf6 + - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/staging.gvl.org.au/qiime_2.yml +++ b/staging.gvl.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index f35be777c..72a5b8ebd 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 42201b90e3f4 - - 2f1d464ebfd2 - - 289b7d6b69a4 - e345aadf914f + - 289b7d6b69a4 - 110a346daf36 + - 2f1d464ebfd2 - cd5f98911089 + - 42201b90e3f4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 8501601a118d - - 0cd2df8af811 + - 42d9087b4789 - fcce77c09289 + - 0cd2df8af811 - c207119ba5f6 - - 42d9087b4789 - 0345dbaaa79b + - 8501601a118d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - 33486216eec0 - - 405a212b32ab - - ad5ab22ffe24 - - 89eb29319bf4 - 04db7fd6b238 + - ad5ab22ffe24 - 421c33b8bf17 + - 33486216eec0 + - 89eb29319bf4 + - 405a212b32ab tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - 1d839ead7ad3 - - f6e91108b7b1 - fa51dc5e8386 - - 7b72fde3d27e - 7370bb65bad4 - eb784fa07f80 + - 7b72fde3d27e + - f6e91108b7b1 + - 1d839ead7ad3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - 3d70c2996730 - a3e86cd9cac7 + - d30e36c48c93 - 8a55d29c8fcf - c9b77ced9a78 + - 3d70c2996730 - 1544278c272e - - d30e36c48c93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: + - 7b881f5f5ad5 + - b242deb58952 - a5969aa9347e + - e2db212d64ad - 564c33e5c3e3 - - b242deb58952 - 887cf585cafc - - e2db212d64ad - - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,10 +104,10 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - 9a171f9a450b - - 8cff84759bf6 - bd5ff77e2036 + - 8cff84759bf6 + - e897c74a48bb - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: + - adc7a7610d4f + - 33f0793edf93 - 5e10f396979e - 6dafad990086 - 4f65e343ecdf - - 33f0793edf93 - 887e0991eb24 - - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - c5d7050e4ad7 - - 4e280b27a831 + - 43e3eeb2e0ec - c287418eb288 - 17d39bf0a63a + - c5d7050e4ad7 + - 4e280b27a831 - 97575d01f06b - - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - d9bf483266a1 - - cd034465d4a4 + - 9586f08634c0 - a819ec3b362d - - 09b8edb56d80 - 0b8c84a7fdb5 - - 9586f08634c0 + - 09b8edb56d80 + - d9bf483266a1 + - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - bf0e43ab0416 - - a4b4bd84f69e - 95351dd0fd3f + - bf0e43ab0416 - 69842dd5aa48 - - a9c34a289493 - 2645575d1bf2 + - a9c34a289493 + - a4b4bd84f69e 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: - - 912f904a6e1e - - bb0475c884ff - - d033e1ccb386 - 8a35a3bc6752 - - d1fda11e602f + - d033e1ccb386 + - bb0475c884ff - cfb504394ae1 + - 912f904a6e1e + - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 6fc5c5028..be4f23192 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,24 +2,24 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - - 2d4e3aff9dc7 - 31f8063eedea + - 2d4e3aff9dc7 + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 32e542c2a773 - 703a2cb3fb38 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -75,16 +75,16 @@ tools: - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - - 86285ddd4512 - cf747d1bd79a + - 86285ddd4512 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -121,10 +121,10 @@ tools: - name: describe_samples owner: iuc revisions: + - 8f0181aacb7a - 3b36efd62b3e - 0693ccd171c4 - e3b16fd7dd08 - - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -136,13 +136,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 8fe98f7094de + - 6a3a025714d3 + - 9a882d108833 - 0696db066a5b - - d027d1f4984e - - cd9874cb9019 - 24a09ca67621 - - 9a882d108833 - - 6a3a025714d3 + - cd9874cb9019 + - d027d1f4984e + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -155,10 +155,10 @@ tools: owner: iuc revisions: - df929f257179 - - 2872c633f07e - 62adf13b86ea - - b47c006d90c5 - 9a7c5b6d8f1e + - b47c006d90c5 + - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -170,18 +170,18 @@ tools: - name: edger owner: iuc revisions: - - 9bdff28ae1b1 + - df0c8d0a5992 - 070900306913 - - a8305cf0c951 + - f2843df56434 + - ae2aad0a6d50 + - 3d89af8a44f0 + - 5bf899c13979 + - 9bdff28ae1b1 - 6e53e565fc6a - - 555659de7321 - 334ce9b1bac5 - - df0c8d0a5992 - - 3d89af8a44f0 + - a8305cf0c951 - 0cb907a2a810 - - ae2aad0a6d50 - - 5bf899c13979 - - f2843df56434 + - 555659de7321 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -193,8 +193,8 @@ tools: - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -212,17 +212,17 @@ tools: - name: featurecounts owner: iuc revisions: - - af814359d244 - f9d49f5cb597 + - af814359d244 + - ea04b737afa0 + - a37612abf7f9 - 6f66ae7c5f7a - e6a2a912677a - - a37612abf7f9 - - f3a5f075498f - - a56fbe2d6ba7 - - 7db9d3ea71c9 - - ea04b737afa0 - 90d16db017d7 + - f3a5f075498f - 38b6d12edc68 + - 7db9d3ea71c9 + - a56fbe2d6ba7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -272,13 +272,13 @@ tools: - name: hisat2 owner: iuc revisions: - - a86e80d3c09c - - 3fb01a8c902d - - 6ab42baa56e9 - - d4b55e2beb12 - - 6c19daec423d - f4af63aaf57a + - 6ab42baa56e9 - 26371a1df031 + - 6c19daec423d + - a86e80d3c09c + - d4b55e2beb12 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -296,9 +296,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 4418229c501e - 67b0b160903a - 916cb26bd9d3 + - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -316,11 +316,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: + - ce5d418183c5 - 87c11c05d238 - 5ae5c312d718 - - ce5d418183c5 - - 01247aaf0a10 - 1c75aa5de15e + - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -332,9 +332,9 @@ tools: - name: kallisto_quant owner: iuc revisions: + - 10c98fab6c5a - 4f9c4e6566e5 - c971db6f0fe5 - - 10c98fab6c5a - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -347,13 +347,13 @@ tools: - name: limma_voom owner: iuc revisions: - - 119b069fc845 - - 32511f586472 - - d6f5fa4ee473 - - 0921444c832d - - e827f9aae031 - 97e06a4c7c75 - 58c35179ebf0 + - 0921444c832d + - e827f9aae031 + - 119b069fc845 + - d6f5fa4ee473 + - 32511f586472 - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -403,8 +403,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -422,21 +422,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - b9e04854e2bb - - c772497b2c32 - - b0f2be869d6d + - 79de45b5069b + - 3ea5a2a63fa2 + - 0a563fd2f22e + - 4014de1b6daf - 7ed2edc1337f - - 4074fc1940e2 + - c772497b2c32 - 980d2a2e1180 - - 4df95e2d7f61 - - 3ea5a2a63fa2 - - c7c55b694974 - - 79de45b5069b - 99b17b74a8cd - - 0a563fd2f22e + - 4074fc1940e2 + - 4df95e2d7f61 + - b0f2be869d6d - e132e7d02a3e - 5ec75f5dae3c - - 4014de1b6daf + - b9e04854e2bb + - c7c55b694974 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -460,14 +460,14 @@ tools: - name: salmon owner: bgruening revisions: - - 2c0ca397d302 - - 49121db48873 - - ebab418107f5 - - 53e9709776a0 - - 15cd64d7c58b - f4d5237a84f6 + - ebab418107f5 - cc05793bb896 + - 2c0ca397d302 + - 53e9709776a0 - e3d32471da11 + - 15cd64d7c58b + - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -479,23 +479,23 @@ tools: - name: seurat owner: iuc revisions: - - fab6ff46e019 - 8c28affc7c48 - - 56242ff81c84 - c0fd285eb553 + - 56242ff81c84 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cbf488da3b2c + - 76d290331481 - ae618321f34a - - 258d696dbd7e + - cbf488da3b2c - cef79931dda5 - - dd4df992d93d - 914cfcba0ec8 + - dd4df992d93d - 1ebd14235b92 - - 76d290331481 + - 258d696dbd7e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -531,10 +531,10 @@ tools: - name: transdecoder owner: iuc revisions: + - 0db979fead3a + - c6334cb383ff - d0d4cef4f967 - ffd1300599a1 - - c6334cb383ff - - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -547,9 +547,9 @@ tools: owner: iuc revisions: - 74217fbfba4d - - ba3720d7e68b - - d6a479fd4281 - bcc5f03f1900 + - d6a479fd4281 + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -561,10 +561,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - - 56162e446004 - c2b82a94493e + - 478f36effca1 - 2fb4ee002432 + - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -576,9 +576,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - 9ff3765e7172 - fab23c3b5258 - 3f4094b6a565 - - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -591,8 +591,8 @@ tools: owner: iuc revisions: - 34a018cbee9c - - 870ac06dff8e - 4687ecf0eb2d + - 870ac06dff8e - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -605,11 +605,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 05ab8d5e04a2 - 65e7dea767ea + - 33406f5a445c - c5fbddcac63a - 5192f657f305 - - 05ab8d5e04a2 - - 33406f5a445c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -621,10 +621,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - a35cba31d904 - - 6f0fb35b799c - - e406ac71165d - 1fdb25a8384d + - e406ac71165d + - 6f0fb35b799c + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -636,10 +636,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 7c7fbf13aadd - - 37a1129c89d2 - c2c039e421af + - 7c7fbf13aadd - 964b7efe2639 + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -651,10 +651,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 24e94d84adc9 + - 047c22569787 - 1d689e4e1caf + - 24e94d84adc9 - eafea3083352 - - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -666,9 +666,9 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 04bb8bb7c198 - 3a4ac03d1266 + - 04bb8bb7c198 + - 1812dbc5bb7b - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -693,15 +693,15 @@ tools: - name: trinity owner: iuc revisions: - - c9cfec002f71 - - db1f362cca3e - - 32b86cd8eb50 - - 8f1c3df4dd49 - - 48636f857c4b - 9fa24d5aac68 + - 32b86cd8eb50 - d84caa5a98ad + - 48636f857c4b - d2bc35f3d1c5 + - db1f362cca3e - cee61b3fcf78 + - 8f1c3df4dd49 + - c9cfec002f71 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -713,10 +713,10 @@ tools: - name: trinotate owner: iuc revisions: + - 9e61bc67866f - 2b093007fab9 - 6fd16fad465d - 4383070d29ed - - 9e61bc67866f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index b2c45c52e..9eed3b471 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -4,6 +4,7 @@ tools: revisions: - 1a052c827e88 - 080fd5739bb4 + - 27e16a30667a - 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 9a9bdb0b1..71ab45a9c 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: + - 3c661e57a88f - 88eedb4abea0 - 10184eaa85fc - - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - - cb20f99fd45b - 1dfd95ee241e - 993b19f20c76 + - cb20f99fd45b + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -37,8 +37,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - - e7fd6754d093 - - 19ece8afbaab - 30a201c9c310 + - 19ece8afbaab + - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -149,9 +149,9 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - dc6ff68ea5e8 - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a + - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -164,9 +164,9 @@ tools: owner: devteam revisions: - 46c6639921f1 + - 12749212f61b - 6856f8a01905 - 9149ad20699a - - 12749212f61b 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 - - 06dc50b7b711 - 26b4f9f98aca + - 06dc50b7b711 - 33208952b99d + - 92ec40abcdcf 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: - - b3d99709fe1a - - b906586a6596 - 66e23b11feae - - 720217c23995 - a8d69aee190e + - 720217c23995 + - b3d99709fe1a + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -228,11 +228,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c - cc61ade70eb8 - - db17d5321bad + - fefd89ab563c - 22970df7a40e - fe34990e5ce7 + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 88b8c2916784 - fa5d3e61e429 - 7a6034296ae9 - - 811fc2d75ad4 - 7def34e6cf4d + - 811fc2d75ad4 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -267,19 +267,19 @@ tools: - name: samtools_merge owner: iuc revisions: - - 740ce0a18f0d - - cae2794d2deb - b40e2d865d52 - 36677f429310 - 65a38e8c8e2a + - 740ce0a18f0d + - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - 583abf29fc8e - - 9da0311ab1dd - 329deb17a9f7 + - 9da0311ab1dd - fa7ad9b89f4a - b61f5d6a7f25 tool_panel_section_label: SAM/BAM @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - db000c6007a0 - - 85e38b31e8b3 - 30388d878f81 + - 85e38b31e8b3 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - b8beef827165 - 344fc91e1bfd + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,8 +341,8 @@ tools: - name: samtools_sort owner: devteam revisions: - - d54a4df48867 - cab3f8d35989 + - d54a4df48867 - 6c2c1836728b - e613c1ad4c4c tool_panel_section_label: SAM/BAM @@ -357,11 +357,11 @@ tools: owner: devteam revisions: - 135c85f4cfaf + - bcedabb53ddf - 5d9ae78f34d3 + - bd850490c7f1 - 818030fa6bbf - b7f7826ef1cd - - bd850490c7f1 - - bcedabb53ddf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 1cc79f49b8d5 - - 5a08c09b9311 - 3a0efe14891f - - 541082d03bef - - 24c5d43cb545 + - 5a08c09b9311 + - 1cc79f49b8d5 - 145f6d74ff5e + - 24c5d43cb545 + - 541082d03bef tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - 0dbf49c414ae - bf328cec6a42 + - b72793637686 + - 0dbf49c414ae + - b01db2684fa5 + - 2dce91e11ca7 - 350bbc5c2ffd - 32dc5f781059 + - 5826298f6a73 - c370440f901e - - 2dce91e11ca7 - 6be888be75f9 - - b72793637686 - - 5826298f6a73 - - b01db2684fa5 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 9b6e1227e..3af328961 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: + - 480d9e9d156b + - 59bb6d34fca6 - d147d6455873 - - a62c4a11a67d - - 5cb6146337d8 + - ea5e944f447d - 6f6537780379 - - 59bb6d34fca6 - - 480d9e9d156b + - a62c4a11a67d - 4aab5ae907b6 - - ea5e944f447d + - 5cb6146337d8 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 587d144af..19ea14f38 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,32 +8,32 @@ tools: - name: alevin owner: bgruening revisions: - - ecb9ea6269ee - f2000bc73102 - - c9944a2600f1 - - e32b215b7c04 - e4c01dcece8b + - e32b215b7c04 + - c9944a2600f1 + - ecb9ea6269ee tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - c0b037b12765 - - 707023fa62fe - cfaf5a405371 + - 707023fa62fe + - c0b037b12765 - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - d330b3082107 - - fb9e030ffae4 + - 55e35e9203cf - 00712416fdaa - 93dd15e13e6a - - cfc3f5a57dc6 - - 55e35e9203cf - 32e547223c9e + - cfc3f5a57dc6 + - d330b3082107 + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - 038e32885fec - - 0bf7fddf90c7 + - ee98d611afc6 + - 39e945f0b2c1 + - b9fac48532eb - 688357ad5e61 + - 0bf7fddf90c7 - 6f0d0c784f09 - - b9fac48532eb - - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -65,10 +65,10 @@ tools: revisions: - b85871dd69f9 - 43cb7b5a6fe7 - - 9bd945a03d7b - - 7e8c677a7b71 - d4af736e7b83 - ed4996a16f7f + - 7e8c677a7b71 + - 9bd945a03d7b - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -81,45 +81,45 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - fe75d2414dc0 - - 2e8022f1923c - a4774b7b2e85 + - 2e8022f1923c + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: + - 769d815e4b0d - 02b1fe7aed76 - 0e70b2dfe4be - 4fff5a293013 - - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - c29e7bb492bf - - a90f8efe08b4 - - 344c2af50552 - aa4a6f0916b4 + - 344c2af50552 + - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - 5b7c81b35b89 - c32347702e12 - b13d3e4c48e1 + - 050cf43887d3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - ae969fdb8442 + - 239193b96d72 - 1d77986f9ddc + - ae969fdb8442 - 02fc39c8610d - - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -155,11 +155,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 - - cdf4443d5625 - - cfe1e6c28d95 - 8855361fcfc5 + - cfe1e6c28d95 + - cdf4443d5625 - a9caad671439 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -195,36 +195,36 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 57aeaf6b237d - 9d42a6133690 + - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - 163fd744e235 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - f47ac4a0b337 - 013e53ccc7ac + - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - a63e9713c39d - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -258,8 +258,8 @@ tools: - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - f0216498a666 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions @@ -286,8 +286,8 @@ 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 @@ -335,15 +335,15 @@ tools: - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - c261b6b05ee3 + - 55b013e59018 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains @@ -363,22 +363,22 @@ tools: - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - dd9988943f53 - ea5d67ec94ab + - dd9988943f53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - 11f39d7f6c64 + - 6326cd29c1c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl @@ -405,8 +405,8 @@ tools: - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 - 36dfa2825a59 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -424,8 +424,8 @@ 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 @@ -438,12 +438,12 @@ tools: - name: modify_loom owner: iuc revisions: - - 4b0adaa31c95 - 59be31ac9dc3 - 0f1aaff9b22d - - e98619de2776 + - 4b0adaa31c95 - 7784821452ac - eeab712b0b99 + - e98619de2776 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -455,16 +455,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 7ffaa0968da3 - 2cfd0db49bbc - 282819d09a4f - - 7ffaa0968da3 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 @@ -489,11 +489,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b - - f911a64454fb - 0bff0ee0683a - - c4f39bf4a068 + - f911a64454fb - 7e014059a88d + - c4f39bf4a068 + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -505,10 +505,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 + - b83fbc90161e - 43c146e25a43 - 7608d5faee41 - - b83fbc90161e + - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -520,9 +520,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: + - 2b0d3e2f402a - 37a47c4fd84d - f3eb2291da05 - - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -534,9 +534,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - df8e4e54d367 - 69018f285aa3 - a6821f856a1e - - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -548,10 +548,10 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - e93b008c637a - - 44b935f2271b - 72979cac22b2 + - 44b935f2271b + - c92d0f9338c5 - 2af7c5086a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -576,15 +576,15 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - f9353ee6a0d4 - - b2df381a6004 - - 6acb08931836 - - 6f83f8fd381f - edec35114f72 - - 77b91b9bdf52 - 178242b82297 - - 4d8f983cd751 + - f9353ee6a0d4 - aaa5da8e73a9 + - 6acb08931836 + - 4d8f983cd751 + - 77b91b9bdf52 + - 6f83f8fd381f + - b2df381a6004 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -597,13 +597,13 @@ tools: owner: iuc revisions: - 713a0c65b1fe - - b409c2486353 - 277313130da5 - - 3c86f71498bc + - 72a6bebab2a5 + - d636ce5cde16 + - b409c2486353 - a97abb8cd15b - a03ff8633507 - - d636ce5cde16 - - 72a6bebab2a5 + - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -615,16 +615,16 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - c0a80a16560f - - c5d3684f7c4c - - 18262103fa61 - - cc0deb593fc8 - f54f0f0598ad - - 6bd82ed14acd + - c0a80a16560f - 5e9171dc8244 - - 6c145a6868cc + - 6bd82ed14acd + - cc0deb593fc8 + - 18262103fa61 - 3081ff5c84a3 - 5c3ebe2adc77 + - c5d3684f7c4c + - 6c145a6868cc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -636,15 +636,15 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 5dada6f76047 - 3bcd5445cd7a - - 9f354c7c8c92 - - ab55fe8030b6 - - a407e7f8bdc1 - - 7b9fafe32c86 - - c9cb76cf8d6c - d844935c906c + - c9cb76cf8d6c + - a407e7f8bdc1 - 94c19fb1281c + - 9f354c7c8c92 + - 7b9fafe32c86 + - 5dada6f76047 + - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -656,16 +656,16 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 2dfb2227a16c - f7446fd8d5e7 - - 1072ce66b426 - 6adf98e782f3 - - 7647e5cd1b8b + - 6f5349dd5c49 - 9b0cdb8cf6be + - 95777145cb92 - aa0c474463c2 + - 2dfb2227a16c - dbbe1ea8ecb1 - - 6f5349dd5c49 - - 95777145cb92 + - 7647e5cd1b8b + - 1072ce66b426 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -677,15 +677,15 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - 458e8f43a775 - - 215733a383f2 - d18e7a6e5cd4 + - 73ab2ac53d06 - c65fce500915 + - bf2017df9837 - f2f6c703da06 - a39040ae0a38 - - 73ab2ac53d06 - - bf2017df9837 - b70219da4a96 + - 215733a383f2 + - 458e8f43a775 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -731,9 +731,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: + - 2e41b35b5bdd - 81e5bdff4853 - ef4c80837bc5 - - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -751,9 +751,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - - 9e5c0bb18d08 - 46fc6751d746 + - 9e5c0bb18d08 + - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1000,22 +1000,22 @@ 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 owner: iuc revisions: - - fecf9664c885 - 370d45e0d1a8 + - fecf9664c885 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index df329cac8..8503bd9d0 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -34,9 +34,9 @@ tools: revisions: - 419027d822d6 - 2f3c6f2dcf39 + - 746e8e4bf929 - 4c07ddedc198 - 562f3c677828 - - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 4c4ec859c31a - aef56d0e7a61 + - 4c4ec859c31a - 9c3e1d3235c8 - 840f29aad145 - - 7442b94d6a1e - b1eda492f063 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - 9fda0b82f419 - 375bbd555f4a - - 07843f917990 - 30d21a6041f6 - - 9fda0b82f419 - d0352e8b4c10 + - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad + - 7ae443e6217d - cd02bf168d23 - - 4cc980df6265 - 8b1b2b91f8d0 - - 7ae443e6217d + - 4cc980df6265 + - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: + - ad7e0b4291ee - 1dd433d2c92c + - 7dd3fb35904f + - e10e776f2109 - bb9fc9d46ea4 - 4bbaf77573ef - - e10e776f2109 - - ad7e0b4291ee - - 7dd3fb35904f 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 51c44d039..39bb18152 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -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: - - 13b6f0007d9e - 6595517c2dd8 + - 626658afe4cb - aff5135563c6 + - 9cd341095afd - 6e8d94597139 - - 626658afe4cb - be25c075ed54 + - 13b6f0007d9e - 464b9305180e - - 9cd341095afd - 02026300aa45 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - - 90f657745fea - 34d29339abab - - 557ec8d7087d - 37cde8134c6a + - 557ec8d7087d + - 9cc411a62277 + - 90f657745fea tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - f2aac0c5c60d + - dd40b1e9eebe - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 623f3eb7aa48 - - 83069b38aa85 - - 33d61c89fb8d - cf4397560712 - - cf34c344508d - - 3a6b78c39dca - 1ea4e668bf73 + - 3a6b78c39dca + - cf34c344508d + - 83069b38aa85 - 2e8f945f7285 + - 33d61c89fb8d + - 623f3eb7aa48 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - 503bcd6ebe4b - ae8c4b2488e7 - 399da6b5ec21 - - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a + - f768f6183386 - c4d18aa4ec4a + - b722161a845a - bce29ec10b78 - - f768f6183386 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -160,11 +160,11 @@ tools: revisions: - 12615d397df7 - a6f147a050a2 - - 86755160afbf - fbf99087e067 + - f46f0e4f75c4 + - 86755160afbf - 0a8c6b61f0f4 - 74a8bef53a00 - - f46f0e4f75c4 - 9ff72e942410 - d698c222f354 - ddf54b12c295 diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index 579105cca..c004a7ca6 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -15,8 +15,8 @@ tools: owner: iuc revisions: - 0d18a3ba2d1c - - 85c57cc9b558 - 82fb5e3bb93e + - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -35,48 +35,48 @@ tools: owner: devteam revisions: - 57def2d7c093 - - 156b60c1530f - a5937157062f - 04fa42777df9 + - 156b60c1530f - ef2c525bd8cd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - e61c9ac190ad - 435b157bed6d - - 791f73caa0c8 + - e61c9ac190ad - 09d6e4693887 + - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 074d44697036 - - 4805fe3d8fda - 03627f24605f - - 65432c3abf6c - - e1461b5c52a0 - dfadc322b065 - 3b4b2121842f + - 4805fe3d8fda + - 65432c3abf6c + - e1461b5c52a0 + - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 9cb929f21cfa - 7dfca164d2e3 - 701d134358ad - - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - 971e07ca4456 - - 426d707dfc47 - f4473557ffc7 - c27549b9aa1f + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -102,11 +102,11 @@ tools: - name: snippy owner: iuc revisions: + - c9a8ef2aa380 - d220115f882b + - fa016f1eea1a - 5bbf9eada9c2 - 9bccc8404a3c - - fa016f1eea1a - - c9a8ef2aa380 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -148,21 +148,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 + - 3b1e7c170b10 - 32f14a2723ec + - ee4a90760848 - 40f0591deda0 - - 3b1e7c170b10 - e7aff4a85df5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 02d81b994ef5 - - 9793bc5d741b - - 42818629ec4c - 4934c0ac6197 - adc0645b945c + - 42818629ec4c + - 02d81b994ef5 + - 9793bc5d741b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index f495d5598..eba784044 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: + - b7ea370b8f5d - 265fe0f9ea64 - - ebe5fc018e72 - 8a2e296c07ef + - 95815a0bb307 + - ebe5fc018e72 - 2c372041ed8c - 6a88248893c4 - - 95815a0bb307 - e075b1be5abb - - b7ea370b8f5d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 544cb432072b + - 22637b1a55bf - c37b684e7f4e - - 0fba2c15b40d - b03984136ce4 - - 1001172b5089 - 21687e35f066 - - 22637b1a55bf + - 544cb432072b + - 0fba2c15b40d + - 1001172b5089 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 143796b504eb + - 8408bffd5616 + - ccb83bf54de0 - 8627b2b383b4 + - 0238f68ad641 + - 3a7084316a6e + - bf1f4994f104 - 01d6b7d6365e - 8ca3647c90fd - - bf1f4994f104 - - 3a7084316a6e - - 0238f68ad641 - - 8408bffd5616 - - ccb83bf54de0 + - 143796b504eb 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: - d144af39073a - - 03e0645395d2 - - f430a1ec7ee4 - 62ca6da715bf - 6b6c992d3a14 - - 9b5abbf50d23 - - 81426b3cf18b - abd489215f73 + - f430a1ec7ee4 + - 81426b3cf18b + - 9b5abbf50d23 + - 03e0645395d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - 1171446da5db - - 8aa352093d73 - 2363ef414c9b - 1829900b5dcd + - 1171446da5db - d37e313a41be - - d3081540d175 + - 8aa352093d73 - e522022137f6 - 95c6f3f4c77f + - d3081540d175 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 012656fd329f + - b14ff40958cb + - d58d2e8c7a57 - 9b29129fb491 - - 348cd212dbad - 92c0aff8b53e - - d58d2e8c7a57 - - b14ff40958cb - - 1137ce8efc1e - 09f37afb3621 + - 348cd212dbad + - 012656fd329f + - 1137ce8efc1e 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: - - ecc9192912b8 - - 7291189e98b4 - - 55c0e906c14c + - 1f2183a23823 - cfd81f17580b - 367ba501b6eb - - 1f2183a23823 - de68c11034f6 + - ecc9192912b8 + - 55c0e906c14c + - 7291189e98b4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: - - d237eaef451f - - e6f4badbe6f3 - - 6c790a091c7c - - ae68ceb4cca3 - - 039ea3f1dea9 - 7cbf3c66d4ad - 64a8f7dae3ad + - 6c790a091c7c + - e6f4badbe6f3 + - 039ea3f1dea9 + - d237eaef451f + - ae68ceb4cca3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -153,13 +153,13 @@ tools: owner: iuc revisions: - e7452697afd9 + - cdb7b4927742 - 6ea7170a016d - - 33bd9301568c - 46fcafba49ec - - cdb7b4927742 - - 5d6653c989cb - 963a3635b2e1 + - 33bd9301568c - 277719af4dd7 + - 5d6653c989cb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: + - a1213a0b7b66 + - 91c1e57d5c7f + - 7b4454382d39 - a29a2f40b665 + - 501bfb078342 - 5a321fab1fe4 - b7f0f59baa7e - 26d97cdd5410 - - a1213a0b7b66 - - 501bfb078342 - - 7b4454382d39 - - 91c1e57d5c7f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 5f27e814a119 + - 768d04526638 - d7d1663559e9 - - 15da1ddcfeff + - 5f27e814a119 - 81e4014fa809 - - 97d19c008d15 - - 39bca000353d - - 768d04526638 - - 709dd8291b83 + - 15da1ddcfeff - c803c34361e0 + - 709dd8291b83 + - 39bca000353d + - 97d19c008d15 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: + - b1eba148b35b + - 5b006286a458 + - 7ba36babba2d + - b931e65638b8 - 85ee7e6c4204 - 86296490704e - - 5b006286a458 - - b1eba148b35b - b84fda8ebef0 - 2215287d5cc9 - - b931e65638b8 - - 7ba36babba2d 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: + - 4e1d23e5c691 - cf06b44624c7 - - 5660b21a0dbd - 0a5dcc9a8ec2 - f506df85c652 - - 31ea13dfe5e6 + - 37757ffb4c5f - 9c711df3258d - - 4e1d23e5c691 - ce9396ddcb2b - - 37757ffb4c5f - 56556e1267de + - 5660b21a0dbd + - 31ea13dfe5e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -251,12 +251,12 @@ tools: owner: iuc revisions: - 1ca7418e46ee - - 021693fdadaa - - 6deb4d549bc9 - 48291658fdf6 - - 271965b55437 - a404f786a94c - 19905c025d2a + - 021693fdadaa + - 271965b55437 + - 6deb4d549bc9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,13 +268,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: + - 71c78e0eea52 + - 3f6fadf8b8ff - 69d8b7567281 - f7879f1e77f9 - - c450406f722b - - 3f6fadf8b8ff - 97e8145d7e30 - - 71c78e0eea52 - 5ad5d4243987 + - c450406f722b - dadbd61dc4cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 6cf13a657cf6 - - d31a2e310a52 - 79f7a1acc2cd - 2514e684f8a3 - - cc7f9a4e186b + - d31a2e310a52 - 0fe007201caf - 283911fe7e1a + - 6cf13a657cf6 - 52f9e4a660e3 + - cc7f9a4e186b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 230e424bde67 - - 6963a6841d22 - - 026a989b7cee - 0a62420cb9cd + - 026a989b7cee + - 6963a6841d22 + - a12844ca467a - 1411bef27a75 - - 80e6e399ccd0 - 75ddd081f608 - - a12844ca467a + - 230e424bde67 + - 80e6e399ccd0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -328,11 +328,11 @@ tools: - b10d1510fa84 - bca7ce81688f - 5808f77b2bb6 - - ba20340426fe - 450a265f92e8 + - e493702b19eb - 444e6a756c35 + - ba20340426fe - 5acfca5a76af - - e493702b19eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 68fec03a63b7 + - c43399f161f4 + - 12152af85697 + - 157ffcdd3fa7 - 4d236c696844 - d52b8947b269 - dd72ff87cfd0 - - c43399f161f4 - f2482aa4862e - - 157ffcdd3fa7 - - 12152af85697 + - 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: - - 6f8e223f78f3 - - cbe39e530cbf + - 0e5d11004815 - 8f2fc0ab30fb - 75becf493cd3 - - 0e5d11004815 - - 8dbce095986c + - cbe39e530cbf - 29ba253e2e05 + - 6f8e223f78f3 + - 8dbce095986c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,13 +381,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 8f5962c43868 - - e0a856def0b0 + - 9708e3086f32 + - a8630d4fbaf8 - 3ff5654b4e7d - a367a15c6de5 - - 9708e3086f32 + - 8f5962c43868 + - e0a856def0b0 - f544f71adb73 - - a8630d4fbaf8 - 88bb477f45f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 6ce175385dd9 - - 96d0145c041a + - 31c096c6b156 + - 4ed46189d6c6 - 5c9729d54721 - 34dc0bbc7e93 - - 31c096c6b156 + - 6ce175385dd9 + - 96d0145c041a - 8b260d252ff4 - - 4ed46189d6c6 - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 11af7fce71cf - - 09f5e45a8212 - - 2c4941386820 + - 40daf124be88 + - 681bdf1e22ff - 46eb13bc2c73 + - 11af7fce71cf - a730269af659 + - 2c4941386820 - a1aad8b559c6 - - 681bdf1e22ff - - 40daf124be88 + - 09f5e45a8212 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: + - 0594ea1417c8 + - 8cb121b6a1d2 - 882b2e649602 - - 3897eaadfbff - b74b8cbfc1f1 + - f272b8ba0983 - 6cbb9c47795c - - 0594ea1417c8 - - 743cd1472aeb - 12038f59c0f4 - - 8cb121b6a1d2 - - f272b8ba0983 + - 3897eaadfbff + - 743cd1472aeb 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: - - 238f78e38a8b - - adee7e8b746f + - dba06328556a - eccb508bb678 + - 238f78e38a8b - 18cf9de1cf73 - cced6715f926 - a9826db86d9a - - dba06328556a + - adee7e8b746f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - 9f36041495a3 - - e53501abf992 - - f64e7ca2efd2 - - e0ad88dec40d - 31a1b89eab9b - - 3ce32adc55b2 - fdec14f69010 + - 3ce32adc55b2 + - e53501abf992 - c9935c9e8a24 + - f64e7ca2efd2 + - 9f36041495a3 + - e0ad88dec40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,13 +495,13 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - d43eb39b989e + - fd3539749127 - 79489d5685dd + - 4db0695a6fc7 + - d43eb39b989e - 3b7b1fe7b937 - - fd3539749127 - 2331ddcbd5aa - b7be725976b6 - - 4db0695a6fc7 - d68c43202172 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 5296d26b0373 - - 1a989b4110da - - 58091e1be01b - - 6a636d58dfc2 - - 78cd8b69da4c - b0d39ef600a7 + - 1a989b4110da - 1ccf0e7fb4f6 + - 78cd8b69da4c + - 6a636d58dfc2 + - 5296d26b0373 + - 58091e1be01b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: - - e8af591435d1 - - '388983871932' - baa8823f8073 - - 4d3ce9dc1525 - - 591cc8518033 - - b641062a2587 - bf8325a07ce7 + - '388983871932' + - e8af591435d1 - b17394940c7a + - 591cc8518033 + - 4d3ce9dc1525 + - b641062a2587 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - 3a233c8eb814 - - 38d75661c235 - d1f8f55f564d - - e6b5cbbf449b - - 59fa8742285e - 3ca3de4e5291 - - c2ab91a0d506 + - 38d75661c235 - 1a2ef636f48e + - 59fa8742285e + - e6b5cbbf449b + - 3a233c8eb814 + - c2ab91a0d506 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -598,22 +598,22 @@ tools: - name: vcfannotategenotypes owner: devteam revisions: - - 84959112d9a6 - 70bc6ced57f7 + - 84959112d9a6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -640,15 +640,15 @@ tools: - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - fa24bf0598f4 + - eae7c08ebb6f - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -697,15 +697,15 @@ tools: - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples @@ -749,7 +749,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 723b17d52..42e8f2c1f 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - - 4efdca267d51 - 3f3e247c053d - 78c75f134c16 - c2ef298da409 + - 6e9aea89e388 + - 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 @@ -26,8 +26,8 @@ tools: - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval @@ -41,55 +41,55 @@ tools: owner: iuc revisions: - cd2480f35935 + - 44018dd6b447 - 3e1f6f6d557e + - f29602ae449e - 133f36c29579 + - fe3ca740a485 + - a79ee60b6926 - 1aae04680c4b - - f29602ae449e - - 44018dd6b447 - b5d8e5475247 - 4f2967b27e67 - - a79ee60b6926 - - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: + - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - ca6d970d931c - - 09855551d713 - 28433faa6e42 + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - 92eee5f31117 - - 728dacaf08a9 + - da5f1924bb2e - d77802fe76f7 + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -101,8 +101,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -114,9 +114,9 @@ tools: - name: cpat owner: bgruening revisions: + - 1ac12c0cc7a0 - 8e9e228c54c4 - 7ccc6234b54e - - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper @@ -149,60 +149,60 @@ tools: owner: iuc revisions: - 9f2455341fac + - 9c15ca7e764e + - b6b5cd37f2a2 - 14f588312c56 + - 756376aeb1ae - 582fd74dc2a1 - - 9c15ca7e764e - 3bbe70fef6df - - 756376aeb1ae - - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 73428a792541 - - 8e1ace8f77c6 - - a230ea445788 - 1691af4a0d17 - - 30fb23d4c31c - - 0ffe5be70caf - 989f7c061f35 + - 0ffe5be70caf + - 8e1ace8f77c6 + - 30fb23d4c31c + - 73428a792541 + - a230ea445788 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c - 57c6718cbfcc + - e94187d661df + - 0418d28136de - 30f08d74024f - 563a19373357 - 494f0bb4a993 - - e94187d661df - - 0418d28136de + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - - f77d7b685bb3 - - 4b96ced19f75 - 2bba2ff070d9 - - d6c7106b7b2e - 1bc5a03faf2e + - 4b96ced19f75 + - f77d7b685bb3 + - f31125bb85ea + - d6c7106b7b2e - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 520e30695ec3 - 54961e026fe4 - - 52af33194019 - fed64e676186 - - 520e30695ec3 - - d77fdcca400e - - d3af38b9c7e1 - b3cf4684e9c7 + - d3af38b9c7e1 + - 52af33194019 + - 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: + - 2aea122fbd25 - 79261884facd - 07d7991bf205 - - 2aea122fbd25 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: - - 8b3e3657034e - - 43798b4caee0 - 602de62d995b - ef2ad746b589 + - 43798b4caee0 + - 8b3e3657034e 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: - - 74810db257cc - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -290,17 +290,17 @@ tools: owner: iuc revisions: - 370c210d9541 - - d46d803ca6cc - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 + - c8ac28e8ac44 - e95d52d295d7 - b815ec682418 - - c8ac28e8ac44 + - 624606f7c996 - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -343,9 +343,9 @@ tools: - name: prokka owner: crs4 revisions: + - bf68eb663bc3 - d643e3b03500 - a17498c603ec - - bf68eb663bc3 - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -358,8 +358,8 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler @@ -385,13 +385,13 @@ tools: owner: iuc revisions: - 68693743661e - - cfcf33df7fc0 - - 9473cd297a76 - 268d162b9c49 - - 8f92c2b26e6d - - 5c7b70713fb5 - 5a29ab10dba6 + - cfcf33df7fc0 + - 5c7b70713fb5 - 5b80f544c67f + - 8f92c2b26e6d + - 9473cd297a76 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -405,8 +405,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -418,17 +418,17 @@ tools: - name: tbprofiler owner: iuc revisions: - - 51dd22484644 - e1a9d6fd258d - - d03af1c7002c - - ac8250086ac3 - - 45083d070fb8 - - 4839e590cb26 - ba6f87115e13 - - 809dfc93d593 - 37213cf56392 - - 200c378d85f3 - 037a11682176 + - ac8250086ac3 + - 51dd22484644 + - d03af1c7002c + - 4839e590cb26 + - 200c378d85f3 + - 45083d070fb8 + - 809dfc93d593 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 0972cce99..6ef41a80a 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,12 +2,12 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 + - 0124fce4654a - 7547fcab5d19 + - 8f1b150a2487 - a929ce596a34 - - 841084c5fc46 - 0e93176640ac - - 0124fce4654a + - 841084c5fc46 - fa5259cc561b - 553bfe8bd0b5 - 890b794c997d @@ -16,11 +16,11 @@ tools: - name: bandage owner: iuc revisions: - - b9e31c5c01c7 + - 94fe43e75ddc - 067592b6b312 - - ddddce450736 - b2860df42e16 - - 94fe43e75ddc + - b9e31c5c01c7 + - ddddce450736 - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,47 +34,47 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - a7f16f24e9a1 - 5258e18bbe23 - - 3371c5bdc17a - faee8629b460 + - 3371c5bdc17a + - 22286dab5aa1 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: - - 1440ae06552f - - 41030a6c03b7 - - 4048d82f0c88 - - ea8146ee148f - - 2dd755c1c6ff - - 602fb8e63aa7 + - 0d243f458b53 + - e824f5d958d0 + - 5ecdeca79a0d - 46ae58b1d792 + - 94170eee0ad8 + - e4bd1e99bacf + - 2dd755c1c6ff + - ea8146ee148f - 1e62c28ba91d - - 5ecdeca79a0d - bb935709506a - - 94170eee0ad8 + - 4048d82f0c88 - 2babe6d5c561 - - 0d243f458b53 + - 41030a6c03b7 + - 1440ae06552f - cf13a1e03e5b - - e824f5d958d0 - - e4bd1e99bacf + - 602fb8e63aa7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - - 86f150c8019d - c5b7390290b1 + - 86f150c8019d + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -86,41 +86,41 @@ tools: - name: flye owner: bgruening revisions: - - 3e4f8642c77e + - e27815e82dd4 - 276f5d8712d5 - 1ce9b1d72ec3 - - 8d4f03b5fe9d - - 291923e6f276 - 3ee0ef312022 - cb8dfd28c16f - - e27815e82dd4 + - 291923e6f276 + - 8d4f03b5fe9d + - 3e4f8642c77e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - 460fad600dce - - 01210c4e9144 - 3169a38c2656 - b2f674562a18 + - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb + - 7348b69e5109 - ba88bc5a6446 + - 06bcf65179fb - 8b330a577046 - - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 690c2caa367e - 5127a713de83 - - 3ef480892a9f - 3fba9c77550a - - 690c2caa367e + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -132,23 +132,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - da9d8bf98802 - - 0ee0c3089254 - 366a11d316a7 - - 9ef6920c3089 - - df25d4fb79b7 + - f3c89da3af16 + - 71740308d412 + - da9d8bf98802 - 284a1cb82b61 - - 5f625c63b8bc - - ec9e21e9c71b - 045c7c3d8e59 - - 41cea2aa2dce - - 5bec28269d95 - - 71740308d412 - - 6505bd37670d + - df25d4fb79b7 + - 0ee0c3089254 - 60024a528cbd - - 3f7be05a1597 - - f3c89da3af16 - 2061fb3b81b4 + - 5bec28269d95 + - 41cea2aa2dce + - ec9e21e9c71b + - 9ef6920c3089 + - 5f625c63b8bc + - 3f7be05a1597 + - 6505bd37670d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -172,19 +172,19 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - - 7518ee87b53d - de387b2b2803 - 14ddfc8ffb93 + - 7518ee87b53d + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - 09c589057ee8 - - 39edec572bae - - eb7b00ec347d - 9d79beb19ac3 + - eb7b00ec347d + - 39edec572bae - f8113c25bc6b - d7edbc9c3a07 tool_panel_section_label: Assembly @@ -192,23 +192,23 @@ tools: - name: meryl owner: iuc revisions: - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 99ecfdafc64f + - 606b09cc9860 + - fd128c111ab0 - 3ca2d2a9068c + - f338e9942b27 - f369ef5f210b - - fd128c111ab0 - - 606b09cc9860 - e731ea24e48d - eb7a370f6588 - - f338e9942b27 - 2ecf5a570907 + - 99ecfdafc64f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -222,9 +222,9 @@ tools: revisions: - b799a615995d - a7b889b90140 + - 8b6d0d85252b - 8dee0218ac7d - 73a3846701e1 - - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -242,9 +242,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 15200570e926 - 7c2f5268d01c - 64a1c751d99b + - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -257,45 +257,45 @@ tools: owner: iuc revisions: - 79b48f02db49 + - d256a51a656b - dfb8a4497339 + - 2b16ba799da9 - 8fef980d48b5 - 02831bf9e95f - bbe19ef04a74 - - d256a51a656b - - 2b16ba799da9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - a315c25dc813 - - e9bd16ba5ebd - 76d4cbefff85 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - 6fcbee531de6 - - 7594365c546b + - ebb0dcdb621a - 675488238c96 - - 3061c8b029e5 - - 59db8ea8c845 - - 875d0f36d66f - 342a1d1fed7b - - ebb0dcdb621a + - 59db8ea8c845 - 72472698a2df + - 7594365c546b + - 875d0f36d66f + - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - aa39b19ca11e - - 78c533842eeb - d865b62f501c - - cd06929b224b - - a199cd7ac344 - 39bed8de8017 + - a199cd7ac344 + - cd06929b224b + - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -307,12 +307,12 @@ tools: - name: raven owner: iuc revisions: + - 2b2a352488fa - f11b994b7eb2 - - 5c55448d0f33 - - 3edba9afc9bc - f8564b2d7f63 - - 2b2a352488fa + - 3edba9afc9bc - 33b7d8481a76 + - 5c55448d0f33 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -325,13 +325,13 @@ tools: - name: rnaspades owner: iuc revisions: + - 378e55aeeb25 + - 5fc94b3a4704 - e122f9101584 + - 28189050e437 - 1d06c8b38e77 - - ef69617ecb42 - - 5fc94b3a4704 - 53c2bc8c2ae3 - - 28189050e437 - - 378e55aeeb25 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -343,136 +343,136 @@ tools: - name: shovill owner: iuc revisions: + - ee17a294d3a3 + - 196a599ec43d - 865119fcb694 - d9f6a00b6db7 - f698c7604b3b - - ee17a294d3a3 - 83ead2be47b2 - - 196a599ec43d - ad80238462c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - - 24e471d13fe9 - 015283de3004 + - 24e471d13fe9 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 904bf932cf78 - 1fc82fe7ebef - - 051fd2db8a27 - - 7490b213baa9 + - 1bb12736175c - 604782a8a53a - c33a476f4001 - - 1bb12736175c + - 904bf932cf78 + - 7490b213baa9 + - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 34305b013402 - - 9678993ca5bd - - 808b3a0a6716 - ad8b536d1caa - 655fa188c3cc - fee85957cebe + - 808b3a0a6716 + - 34305b013402 - d6e617c4e338 + - 9678993ca5bd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 21da31ed41a1 - - 6b5a5842531e - - 8d4b90bf9caf - - 037f9927c4ff - b8002c3f7141 - 7e27faaad80e + - 8d4b90bf9caf + - 21da31ed41a1 - e5a3b75a271f + - 6b5a5842531e + - 037f9927c4ff tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - f1532cb33c75 - - 328aa71f0f3c - - 7922870efcca - - 5b26685e5d3b - 86f66ab58e14 - - 2a10645aeadd + - 328aa71f0f3c - 9de69775f512 + - 2a10645aeadd + - f1532cb33c75 + - 5b26685e5d3b + - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 85fb02c43042 - 6aad515a5270 - 8cc856b935ee - - 340bc17f49cf - e41dcb0e913b + - 85fb02c43042 - 1708851f8804 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 6357b127161e + - de1260f8a300 - b3490b036c5a - - d159735a6a9f - b65a43f70b99 - - 249f6a28c751 - d5fb354f745d - - de1260f8a300 + - d159735a6a9f + - 6357b127161e + - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - 7897763d14ec - - a90db5dbaaf3 - - 9006e5836729 - - d2d1df21dfb9 - - b7829778729f + - 33368fec3b70 - dd7ad84f3943 + - b7829778729f + - d2d1df21dfb9 - d5887ace0dd4 + - 9006e5836729 + - a90db5dbaaf3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ed2425b9fd27 - - 189e837009c9 + - 8f631679571f - 505a9833ab5d - 6f4c8ad6ea01 - - 8f631679571f + - 189e837009c9 - ced385aa976d + - ed2425b9fd27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 356afed970b4 - - e59bee4565b3 - d40ed4eb0c0e - - 19bdfd1e6fe3 - f31d376ce725 + - e59bee4565b3 + - 19bdfd1e6fe3 - 9ded6109434a + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 80a17897564d - 6dd935e4984b - - ebd801e712bc - 4688ae3b49b5 - - 80a17897564d + - ebd801e712bc - af40e971a8cc - b23249f81bc4 tool_panel_section_label: Assembly @@ -480,44 +480,44 @@ tools: - name: trycycler_reconcile_msa owner: iuc revisions: + - cb1e3db43020 + - 937ea677d437 + - bb11fefb23a3 - b64696992ee9 - b5e35a2ca4f3 - - bb11fefb23a3 - 59bd28f6265d - - cb1e3db43020 - - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - cb4768eeca3b + - 6015aa0303f2 - 383bb5ad32e2 - - 2628f6790eda - 6bfab4a4a988 - - 6015aa0303f2 - 05bd7504fdb2 - - cb4768eeca3b + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - - e92675014ac9 - e022dff952df - - 0a3a602cd1e3 + - e92675014ac9 - 9e3e80cc4ad4 - - 8f9f06995f98 - 3e44ef016b45 + - 0a3a602cd1e3 + - 8f9f06995f98 + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 8d09f8be269e - - 5da9a0e2fb2d - 920677cd220f + - 5da9a0e2fb2d + - 8d09f8be269e + - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser @@ -538,7 +538,7 @@ tools: owner: iuc revisions: - 39495e107274 - - ff4031bfaa22 - 425e63adcc5d + - 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 476fe7b08..4ba720af1 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,26 +2,26 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 + - 4768f7f8e93f - 392f100eebcd + - 1ae00120dd24 - bfd290fe1588 - - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: + - 31812e7a1315 - 1f5641a52664 - - ded48b36f3b7 - 8e8dc9a1e3e5 - - 31812e7a1315 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - - 24a7a95867b0 - 5c8ff92e38a9 + - 24a7a95867b0 + - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 4bbf63d2c..0bc26f295 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: + - 0840ba83860c - a9c9d768b751 - - 159b04e36791 - 1c427e24fb79 + - 159b04e36791 - 7beb76ffbc0f - - d1f62024a08b - - 0840ba83860c - 204a131e47db + - d1f62024a08b 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 a760b9940..4d29c2797 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - b28e0cfa7ba1 - - a8eabd2838f6 + - dde39ba9c031 - 87ee588b3d45 + - 589e7e57fd6d + - e19bebe96cd2 + - a8eabd2838f6 - 64e2edfe7a2c - ce3c7f062223 - - e19bebe96cd2 - - dde39ba9c031 + - a1a923cd89e8 + - 0a5c785ac6db - 07e8b80f278c - a68aa6c1204a - - 0a5c785ac6db - - a1a923cd89e8 - - 589e7e57fd6d + - 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 1890f8060..5bf87ce55 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: + - f921014aba5a - e8ac2b53f262 - - 54f751e413f4 - 62c9df8382c2 - - f921014aba5a + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - acf4e47b734c - 0e3cf9594bb7 - - 5edc472ec434 + - a52d2d93e595 + - 2889433c7ae1 - cbf3f518b668 + - acf4e47b734c - e25d3acf6e68 - - 2889433c7ae1 + - 5edc472ec434 - d999e774072a - - a52d2d93e595 - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 648ff3457..d8f43029e 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - - f4230f116196 + - c8cdde00b105 + - 710301bc46fa - 27ee142314a9 - da6bd1975a71 - - c8cdde00b105 + - f4230f116196 - 095ad4d096d1 - - 710301bc46fa + - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_rxn_maker @@ -124,73 +124,73 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - 88076940fa94 - bfb65cb551d8 - 3b8a9d5ced85 + - 79cfd9ead848 - 0fac8e2afc13 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - 715cd0e87781 - - b46d4b4d995c - 55918daa5651 - eb6564a60136 - f5d979cb4b54 - d532b7e5f64b + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - dae135dfd519 - 5579659312e6 - fdf2cc80adb5 - - d2f955aea23a - - dae135dfd519 - f26afd1b7104 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - 319a28774da9 - - bc31d02be922 - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - - ed736e6eee39 - - 2c349b027a01 - cac1886249a2 - 4da9ee404eab + - ed736e6eee39 + - 2c349b027a01 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 73008ef1f487 - - 525ca7c8065f - 807aa4c9293d - - da8753545526 - - c0c9a5024177 - - d1f803b5943c - f197e34c33a9 + - 525ca7c8065f + - c0c9a5024177 + - 73008ef1f487 - 2e219a2d9327 + - d1f803b5943c + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - - 61094e01eff9 - - 7568ae18908a - 2c8ed1b52bf7 + - 61094e01eff9 + - 1809414a9454 - 27ea4e1a3f95 + - 7568ae18908a - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -203,18 +203,18 @@ tools: - name: md_converter owner: chemteam revisions: + - ccfbd956a2d3 + - ba83f0923369 - 79e8ab8f1e81 - - d7ec25187599 - 730ef07b90ae - - ba83f0923369 - - ccfbd956a2d3 + - d7ec25187599 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -262,10 +262,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - - e6011617c748 - - 4242b4d68e9c - e2c36f62e22f + - 4242b4d68e9c + - e6011617c748 + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -277,8 +277,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -344,10 +344,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - bf99565cec1f - - 9b48456a96fe - d4c67ced6abc + - 85fad59f8168 + - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 470108db3..da344e045 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: - - 2605cbdaa7d8 - - f907216064f6 - 163688bb8f73 - fa56d93f7980 + - 2605cbdaa7d8 + - f907216064f6 - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,25 +18,25 @@ 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: - 86e2413cf3f8 - - 495a4173006f - - 640d3af5d833 - 424aefbd7777 + - 495a4173006f - f5d67c722d67 + - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 2fce659f9..865c7141b 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 830961c48e42 + - 90981f86000f - 33151a38533a - 25136a2b0cfe - - 90981f86000f + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 6cbe2f30c2d7 - 0046692724f9 - - 2dae863c8f42 - baabc30154cd - - 6cbe2f30c2d7 + - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 8754fbdba..5d2be7bb5 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - 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: - - 367b1ed91207 + - 4a6ee918c13a + - a3b86937ead6 - 0b3c3ad92827 - - 6ef0b5664c69 - 5e1240a87bcb - - e3cbd2287f63 - 3b6f97e7094c + - e3cbd2287f63 - ab9350a8ab4d - - 4a6ee918c13a + - 6ef0b5664c69 + - 367b1ed91207 - f3a19509108a - - a3b86937ead6 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 72ed72122deb - - 33c99804a32f - - 584008e574b2 - - e177a8ea0bf1 - - d4d4e9febf5c - - e525f9ffb9ac - 501c21cce614 - 54ccb7e1f49a + - e525f9ffb9ac + - 72ed72122deb + - d4d4e9febf5c + - e177a8ea0bf1 + - 091bb5922a82 - 1b5fc03380d4 + - 33c99804a32f - bd46669113b9 - - 091bb5922a82 + - 584008e574b2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -58,23 +58,23 @@ 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: - - 77b41c89d856 - 8979c288aefb - 186b8d913e6c + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -93,9 +93,9 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - - 3e436657dcd0 - 154d00cbbf2d + - 3e436657dcd0 + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -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 @@ -141,10 +141,10 @@ tools: owner: galaxyp revisions: - 63769c4217a7 - - 26c6706bfb07 - - b9b385097f13 - 19e45916daf9 - 92ac8e086317 + - 26c6706bfb07 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index e40923fdb..a3b20f907 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,70 +2,70 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - a1ca9bccc7f2 - - 29451af70c52 - de72ba3ed6f2 - 268e91e540ee - - e821645ef8fc - 5f6d123679f4 + - 29451af70c52 + - a1ca9bccc7f2 - c929a006727f + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e143b4c3987 + - bb1e4f63e0e6 + - 5d11599b8a7d - 0e49b109abc2 - 2d2cf5c1ea8a - - 12af64f93288 - - bb1e4f63e0e6 - - 0e143b4c3987 - 7a7fd0f5f15d - - 5d11599b8a7d + - 12af64f93288 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 81b1e3e1fc6c - 7c1beb6d6eca - - dc059492a995 - c06951d10364 - - 81b1e3e1fc6c - - 1d848bc4585f - 195e98217334 + - dc059492a995 + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 - - 3d211717a775 - 26e7304d6737 - - a67ac707496a - - bfff7454b59a - - 93eb012d9eed - 71aa86af6762 + - 3d211717a775 + - 93eb012d9eed + - bfff7454b59a + - a67ac707496a + - 07418a30ed01 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 26983857c91a + - b8858746dc1f + - dd0b7398bb96 + - 2bc10a9ca58b - 29fcfd36e90a - 5be24eba848d - - dd0b7398bb96 + - 26983857c91a - 56d5b797ce84 - - b8858746dc1f - - 2bc10a9ca58b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - 7ef978dc1b8a - - ee3a1b0f45f1 + - c3e012dfe21f - 72bfafe3330b + - ee3a1b0f45f1 - 7e6bcd2e5128 - - c3e012dfe21f - 9384cd033f30 - e6d0bff01239 tool_panel_section_label: DeepTools @@ -73,134 +73,134 @@ tools: - name: deeptools_compute_matrix owner: bgruening revisions: - - a60c359ec43c - - fb9cf9c97ec4 - - 9470f29702f8 - b73e213add0c + - 9470f29702f8 + - d9a637e83828 + - fb9cf9c97ec4 - fd1275e01605 - 167788df3b46 + - a60c359ec43c - 514fa53b5efb - - d9a637e83828 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - e479c7ca5570 - - ca0616bb2cdf + - 2c37ce318bc3 - 5bffaa8354a1 + - 86febdcc4283 + - e479c7ca5570 - c34d11ea4ba6 - - 2c37ce318bc3 - a02cfa31e9cb - - 86febdcc4283 + - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 78f405266706 - 004aea905d4d - - 1fcb7adc39b8 + - 69a8621ca2f0 - 2d466b530754 - - 192ef85c0b0b - 01fb6a7654e6 - - 69a8621ca2f0 + - 78f405266706 + - 192ef85c0b0b + - 1fcb7adc39b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 3c9f0c486cca - db940c262830 - 459cfa861f0b - - 3c9f0c486cca + - 137c4beed34b + - d9ce4897dbb2 + - d580d6acd1df - 2f9e4843f480 - 9ecba5e225a6 - - d580d6acd1df - - d9ce4897dbb2 - - 137c4beed34b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fbe773640707 - - 2c66e43f1c86 - - fd408d755394 - - bd7db9e2f2cb - 32e451def88c + - 2c66e43f1c86 + - fbe773640707 - bad3ca889618 - f264afa9fa6f + - fd408d755394 + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 56bce3c82278 + - 3b9d990a0a0e - 231994413f89 + - 4e12ea27f788 - 7e361d147872 - - 9368fbc49c8b - 7fda5607e777 - - 4e12ea27f788 - - 3b9d990a0a0e + - 9368fbc49c8b + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 4431f39ede55 - ce4ce3316f74 - b1779366c8e9 - - c03c3384cd81 - e65d16fb2724 - - 94ca68515826 + - c03c3384cd81 + - 4431f39ede55 - d9114ef1c8a5 + - 94ca68515826 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 2da482e408b8 - - d57251071381 + - 4ed32329e0ed + - 23f7c5f1fdaf - f8fc4e5aff9d - b88ebb3672a1 - - 23f7c5f1fdaf + - 2da482e408b8 + - d57251071381 - 793665fff0f8 - - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 - 512155688d98 - - c60570fa602f - - 25d830337d31 - - ba6efa77fb79 + - a7849312d328 - a4dfb122e52b - - 010e58e9d822 - e4c7985d4585 + - 25d830337d31 + - c60570fa602f + - 010e58e9d822 + - ba6efa77fb79 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 69264da0ce77 + - 00d869ea03a1 - 4d678170d29b + - 69264da0ce77 + - c899e0ccff8c - aa200e4f3939 - 38e3f226248b - 443d9a9d6d11 - - c899e0ccff8c - - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 10301d137111 - - d806504e96d9 - a2d70c4fd406 - - aac8444d6681 - - c361b12d207a - 6662b1a8d326 + - d806504e96d9 + - 10301d137111 + - c361b12d207a + - aac8444d6681 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 cec358c1d..f33f801e1 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,22 +9,22 @@ tools: - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 91a1ed0b486f + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - d4bea99366f9 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 931e5eb7a..2bdbfb936 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 - 832c20329690 - - 63dd26468588 - ce385837c160 - - dba489bfcd62 + - 63dd26468588 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 68f49c8e3..8471072f9 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - - 62f5fab76dfb - - d82648ad25a3 - 29bdbc353f20 + - d82648ad25a3 + - 6da3972210ee - cf1322aeb137 + - 62f5fab76dfb 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/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 34002ae63..dbe378421 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,41 +8,41 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8665bcc8b847 - - b1c926deaa2d - - 48f587c13075 - - c053d4cad713 + - 5eb7e84243f2 + - 64172f1c1202 - 4e5056fefd88 + - fe74900d6dc7 + - b1c926deaa2d + - 44e2cc14f75b - 660cffd8d92a - e4691e1589d3 - - c4b82dce8335 - - 49370cb85f0f - - 8c0175e03cee + - 48f587c13075 + - c053d4cad713 - 288f97432497 - - 5eb7e84243f2 - - fe74900d6dc7 - - 135b80fb1ac2 - - 64172f1c1202 - - de6cebe3c043 - - 44e2cc14f75b - 5915ea1ec9b1 - c5e2e5902201 + - 8665bcc8b847 + - 135b80fb1ac2 + - c4b82dce8335 + - 49370cb85f0f - 093678460093 + - 8c0175e03cee + - de6cebe3c043 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - f666895cbebd - 8889eb864cef - 9db07fd39f85 + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -60,50 +60,50 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - - 9457a20156db - 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: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - f773e98b26cf + - ec0b5076173a - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - cd0874854f51 - 0dbb995c7d35 - - 9c620a950d3a - 56022eb50bbd + - cd0874854f51 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - d60c3f704da0 - - 1d8fe9bc4cb0 - dbf9c561ef29 - - c59d48774d03 - 65b93b623c77 + - 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 @@ -123,15 +123,15 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 5b87038565bb - 7861f3b10c68 + - 5b87038565bb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -144,8 +144,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -159,8 +159,8 @@ tools: owner: devteam revisions: - e39cc71d3ed6 - - 35e38452bb3f - 249c8393f2d4 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -174,8 +174,8 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -194,60 +194,60 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - 567d5b3c52b1 + - 529bccd5e4a1 - d5e9e83cd3d8 - 09070cacefd8 - - 529bccd5e4a1 - - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 + - 90858c306551 - bdf1ce174e39 + - cb1e251cac37 - 736b8f6ee456 - - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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_renamer owner: devteam revisions: - - b29d37ca9e41 - - 3599f5451ee2 - 02f8a17a4ebd + - b29d37ca9e41 - f984bb114520 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - 177f0621c266 - - e246088b6e34 + - 6027ef51ef91 - 0c2907307ba4 + - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - 377ac2829eac + - 73194cdd4f57 - 547e8d00f11c - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ @@ -262,16 +262,16 @@ tools: owner: iuc revisions: - 2f804526f5fd + - 037f0acc7830 - b4c6f054210a - f69501361cec - - 037f0acc7830 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort @@ -284,39 +284,39 @@ tools: - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 71f649c23021 - bf04bd405d5b + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - e654095ab143 + - a535cf1e5da4 - 8250ea3a1501 - 24013bf85a6f - - a535cf1e5da4 - b557acca0b56 + - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -328,12 +328,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 - 27ac32a22ad2 - - 9fa7803d1c51 + - 828dba98cdb4 + - 6a675c3aa610 - f3759eec3018 - 7accf7407811 - - 828dba98cdb4 + - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index 2f3e42a68..a31f07476 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -3,9 +3,9 @@ tools: owner: devteam revisions: - 7b4468117008 - - 64e9a6afdd0c - e41385662e5e - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,61 +18,61 @@ tools: - name: fastqc owner: devteam revisions: - - 3d0c7bdf12f5 - - 9da02be9c6cc - - 2b0c9d9fc6ca - 2c64fded1286 - - f2e8552cf1d0 - e7b2202befea - - 5ec9f6bceaee + - f2e8552cf1d0 - ff9530579d1f + - 5ec9f6bceaee + - 3d0c7bdf12f5 + - 9da02be9c6cc + - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 - c1a33f603da2 + - 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 - 7306ec78632a + - 59003d0543cd - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 8880fb74ef56 - - 1f296803dfa3 - a72af9de6bf5 + - 1f296803dfa3 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - 5e33b465d8d5 - - c1a4b5f3b432 - - 75c93c70d094 - - abfd8a6544d7 - - 1c2db0054039 - - bf675f34b056 - - 3d93dd18d9f8 - f7e2f1eb3a16 - - b2f1f75d49c4 - 9a913cdee30e + - b2f1f75d49c4 + - 1c2db0054039 + - 3d93dd18d9f8 + - bf675f34b056 + - 75c93c70d094 + - c1a4b5f3b432 + - abfd8a6544d7 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index 0dfc5355c..c01999d90 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 9d1465d9e..1dc6b6ca8 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 1016e394b..728f20dec 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,8 +16,8 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - 0c8f7322f8fc + - 8f53b238a360 - f2f3bc622a16 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: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -79,16 +79,16 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - b2c25142267e - cf61daf064fe - 45296e47d565 + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -122,9 +122,9 @@ tools: - 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 @@ -137,15 +137,15 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -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/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 18d33de94..0fe27413f 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: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index f6fe6e919..72f846eae 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,9 +3,9 @@ tools: owner: galaxyp revisions: - c1b437242fee + - 983bf725dfc2 - e9df53a75f3c - b39347891609 - - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - e063168e0a81 - 1c58de56d587 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 734abc7ac21d - 6591f049cf7e - - 83c7d564b128 - - 8848455c0270 - - e08a7ad4378b - - 653e89d73fc4 - - 1ec814014652 - - 5e6237d58b0c - - 7068f48d0ef9 - - 4df8de2d0e48 - - f8054ea1c365 - - e407b9da183a - - 1790dcf3c32d - 9a776b080193 + - 1ec814014652 + - 8848455c0270 - 516a54ddf218 - 6ea73833cf67 - - 69ebb7f46e45 - - 4317d3cb6cba - f5ea3ce9b9b0 + - aad3885b3216 + - 4df8de2d0e48 - ba931a59dd59 + - 4317d3cb6cba + - 69ebb7f46e45 + - 5e6237d58b0c + - f8054ea1c365 + - e08a7ad4378b + - 7068f48d0ef9 + - 83c7d564b128 + - e407b9da183a - c441583adae5 - - aad3885b3216 + - 734abc7ac21d + - 1790dcf3c32d + - 653e89d73fc4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 21a560af5913 - 75b3b3d0adbf - 9aaa46d45472 + - 21a560af5913 - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 - - bfdc6a7ffd3a - - 95fb5712344f - 468c71dac78a - 054483e27a35 + - 95fb5712344f + - af5eccf83605 + - bfdc6a7ffd3a 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 068840739..3f4d2de59 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 740057a5126d - - ae9994cf526f - - c4bde687c846 - 4b519282a05b - - 7f13dc906cb9 - fd59d783248a - - df7356989ac1 - - a64dc31ab7f2 - 290a11559985 + - a64dc31ab7f2 + - 7f13dc906cb9 + - c4bde687c846 + - 740057a5126d + - df7356989ac1 + - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - f95284aa2946 - 867ab348287d + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -43,20 +43,20 @@ tools: owner: iuc revisions: - 53460afd5115 - - ca7cb0eaad62 - - 374e9062d874 - - 3b37b1b1c3a7 - '566197475670' + - 3b37b1b1c3a7 + - 374e9062d874 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 391a4cc45fea - - da4c086cff5b + - 3d059e9c2fba - d3a9e32672ec - 10515715c940 - - 3d059e9c2fba + - 391a4cc45fea + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -74,12 +74,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 3b12bf9b4b87 - - 1acf88921176 - - 5fe1dc76176e - - e3a675da7fd0 - d0fc8b746d57 + - 1acf88921176 - 299307abd804 + - e3a675da7fd0 + - 3b12bf9b4b87 + - 5fe1dc76176e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -97,15 +97,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 97e3b735ed22 - 5d6f8f0bef7c + - 97e3b735ed22 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -123,17 +123,17 @@ tools: - name: jbrowse owner: iuc revisions: - - ca2def38369c - fd5dbf0f732e - - 836d1aa3e89a - - a6e57ff585c0 - 4542035c1075 - - 667e17248bfe - 2bb2e07a7a21 - 112eb40ba6cf - - 6cd09d7b5f37 + - 667e17248bfe - 17359b808b01 - 1cfc579079a6 + - 6cd09d7b5f37 + - ca2def38369c + - 836d1aa3e89a + - a6e57ff585c0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -151,9 +151,9 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - 03c13085aecc - f1691de443a7 + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -165,10 +165,10 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: + - f234e2e59d76 - 62e3a4e8c54c - 1c5dcef5ce0f - 85da91bbdbfb - - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -201,22 +201,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - - 360df4999907 - 2824d77cd8f8 - - 36b848d5f3ec - - 14e7c35f3d00 - - 4ac4e7083b7e - a1abfa420d9d - 326a3db8d9d1 + - 14e7c35f3d00 + - 4ac4e7083b7e + - 36b848d5f3ec + - 360df4999907 + - 7dd841a32245 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - - 2f557f6abbfb - 83c573f2e73c + - 2f557f6abbfb + - 44608d0193ed - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 228f3ef43..4b362032f 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -28,29 +28,29 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 7779b9dcf040 - 22bd5861706d + - 7779b9dcf040 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 361608369dda - bf1e0bdec1db + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - - 23d838d1569d - cc64914b0cf4 + - 23d838d1569d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster 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 @@ -63,15 +63,15 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat @@ -84,30 +84,30 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 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: - - 9a2f72d7dbd2 - - 94697510d55f - ff6decc0f432 + - 94697510d55f + - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 53ce0e336840 - 70cb0596ffef + - 53ce0e336840 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: - - 3027cb62adbd - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -127,29 +127,29 @@ tools: - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc 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 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 @@ -162,36 +162,36 @@ tools: - name: scanpy_run_dpt owner: ebi-gxa revisions: - - 12f67b0c1a94 - 03921aa8b29c + - 12f67b0c1a94 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga owner: ebi-gxa revisions: - - 6d4f88995e40 - b2768cae00a1 + - 6d4f88995e40 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 0cf90e01d9f8 - 4428dba93375 + - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 9f49b3cb9..cec11d553 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,40 +2,40 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 29f66c353bcb - - 921a2da49a0c - - 9edf8894a22d - a4c13ddcc8ee + - 921a2da49a0c + - 29f66c353bcb - ed2cca6b5de4 + - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - 78fb5e286609 + - 5746d61f0a91 - ec4b948dc6f0 - 755df866ad0c - - 5746d61f0a91 - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - 11fa44ee0603 + - 4d511437b1e5 - 03dd3c16ae4e - 977dc15add20 - - 4d511437b1e5 + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - c3e5e2cf12b7 - - 0ba4f56a3613 - 77919cc3618e - 3b5b54ed6392 + - 0ba4f56a3613 + - c3e5e2cf12b7 - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu @@ -43,9 +43,9 @@ tools: owner: bgruening revisions: - b63363075c2e - - 12d51d7be66f - - 5308ca68ef3d - 9939786dd9c9 + - 5308ca68ef3d + - 12d51d7be66f - 7babd8a46fe0 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 dca505ebd..14bc8f57f 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,29 +2,29 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 699a5e9146b3 - 7db4fc31dbee - - 3df9f0a4bf34 - 81f0cbca04a7 - - 0c777d708acc - 8bccb36e055a + - 699a5e9146b3 + - 3df9f0a4bf34 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 2436a8807ad1 - - 5bc8cdc17fd0 - - 0a53256b48c6 - 5791a7f65275 + - 0a53256b48c6 + - 5bc8cdc17fd0 + - 2436a8807ad1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: + - e576b73a2e2f - 6ad1d3cfdea1 - 9d47aabda459 - - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -52,113 +52,113 @@ tools: - name: bfconvert owner: imgteam revisions: - - fcadded98e61 - 85edbb7a436b + - f3360fbeda64 + - fcadded98e61 - 10eed33aa9b2 - b07f4839ca77 - - f3360fbeda64 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - 5bf8eb50b280 - - 664232d2a3f7 - b58447a2eed2 + - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - - eb6c08714244 - e917a2424690 + - eb6c08714244 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: + - e7273daa5ae2 - 6070780813d9 - 670975e92458 - - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - df3ad3ba5c6f - - ef4aed1d34c4 - cdf8e3c57dae + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - - 2484086dee41 - 6a7da2e5f696 + - 2484086dee41 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - 11f177b1a59e - bace5a93a97c - f2ed92b011a9 - - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f24c370e5ea4 + - d0178bdcd00e - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - ad271f78a87a - 3245681b2f6d - 31d195bedf6d - - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - - 993faa34333b - 87d4d92d7487 + - 993faa34333b + - 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 + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: + - b178453ea8d1 - 667a513e67e4 - 3a05117669cf - - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity @@ -172,25 +172,25 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 91e03287f285 - a32c3f810ade - 20dbb1f7ec7b + - 91e03287f285 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 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - d3890df07463 - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -204,39 +204,39 @@ tools: - name: cp_measure_object_size_shape owner: bgruening revisions: + - 79e10d12d90a - d85f11570109 - acf3aa487283 - - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - b76841ee5560 - 80b200ae516b - 035a58c7f54a - - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - b44b081bcf37 - 91560258e972 + - b44b081bcf37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 48102a685037 - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 27edbb90ab2b - 4ecf93628f97 + - 27edbb90ab2b - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -262,9 +262,9 @@ tools: - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - 7b6d9412c7f8 - f8b4eada923c + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index ac0d66281..eaabf2453 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 3e4f434a69c6 - - a38934e303b9 - - 78bbd17d0703 - - e319b5b65879 - e4ee04da1c19 - - d6e72da3ec35 - - 3a72fede57ce - f362150bef41 - 40737febe339 + - 3a72fede57ce + - 3e4f434a69c6 + - d6e72da3ec35 + - e319b5b65879 + - a38934e303b9 - 1069f6db0a0e + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - 618297d23022 + - c88553ec696e + - 0135f1d487a0 + - 72ddd32392cd - fcbeda41d0ac - 7fe36019c073 - - 0135f1d487a0 - - f91cfb73d369 + - 2b95d5c04908 - 8f8df367470d - - 618297d23022 - 9537184d421f - - c88553ec696e - - 2b95d5c04908 - - 72ddd32392cd + - f91cfb73d369 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 - d7e79eb3bcb3 - - ad0dc9f4c9e2 + - 2cf4a1cafc16 - fafb3d685fa9 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 9eaadf03e0df + - 3d18f8c3c0f6 - 8c05afb547fa - ee2beb764a7b - - 7f1cfa4c0e32 - - 8d36959b000d + - 6a1515bb0687 + - 28a6f1908fcc - a1c2aecd7a0d - - 5dc33613c288 + - 8d36959b000d + - bd2a7d1316b9 + - 7f1cfa4c0e32 - 94df24c6bc00 - - 6a1515bb0687 - 43aac8d29685 - ee29337f905c - - 3d18f8c3c0f6 - - 28a6f1908fcc - - bd2a7d1316b9 + - 5dc33613c288 + - 9eaadf03e0df tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - - d37ede8589b2 - - 9f978da6528a - - 86a20ae274fc - - db536ad45f28 - - a250929be21b - 364f4ffec275 + - db536ad45f28 + - d37ede8589b2 - cb903c9dc33d - - 5671e1d3d5ee + - 5d6ed46cc101 - 8858fa037a15 - bcaa0d571ce2 - - c092052ed673 - e3bb03cf207a + - 5671e1d3d5ee + - a250929be21b + - 9f978da6528a + - c092052ed673 + - 86a20ae274fc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 49236b03e4fd + - 3b6a16d82c1b + - 38b91a3190cd - 584beffa972b - - abbc8041e8ec - - 12d66d0d05ac + - 49236b03e4fd - e1a015876aa9 - 230b05597996 - - f95f403841ad - 194e3ceee923 + - 12d66d0d05ac - ed28dd32141c - c5c9f02b6167 - - 38b91a3190cd - - 3b6a16d82c1b + - f95f403841ad + - abbc8041e8ec 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 15b597b60..db0625d3f 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - 17e3b698dd52 + - f198773344e4 - b8a457820315 - 0f1724dd59d2 - - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf - - 22c2a1ac7ae3 + - ac092723240d - a513e3fbb4c5 - 374cb875d38a - - ac092723240d + - 22c2a1ac7ae3 + - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 10c74d0d2..daabc8bd1 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,99 +2,99 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - - 66d7efc06000 - 772e0e89fc68 + - 66d7efc06000 + - 522137aaa9c4 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 4d81e3e2fb63 - 8a794e6d3388 - f22a9297440f + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 2af1346e68c9 - e1317b5502fa - - 818f9b69d8a0 - f1b9a42d6809 - b6ef6d0cb6b7 + - 2af1346e68c9 + - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 + - c80db5d6fd8c - 05143043ca13 + - 947c2eacccb8 - 1588f9076e32 - - c80db5d6fd8c - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 + - 25b46af53232 - 83228baae3c5 - - 29e4122c90de - 9991c4ddde14 - - 25b46af53232 + - 29e4122c90de + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - a07ab242b0b5 - 1a53edc4b438 - 060ca94ac049 - - 841a6cc5fc58 - 53616c8b0865 - - a07ab242b0b5 + - 841a6cc5fc58 - f3dfa4bdf87e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 927586a18553 - - dc4b5fd604a6 - - d4808d5b83da - 2fc89dcd41c8 - 91c4e3331208 + - dc4b5fd604a6 - 40f4447733b2 + - 927586a18553 + - d4808d5b83da tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 25ab6b4e376e - - 36e8d6d5d01b + - 7626ea9c2e1b + - 301e07345c93 - e5a5ad882f1f - c6ae57f774c6 - - 301e07345c93 - - 7626ea9c2e1b + - 36e8d6d5d01b + - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb - - b7c3e9a3b954 + - 02d2be90dedb - f9639b488779 - - 80852884053f + - b7c3e9a3b954 + - 4ed102b922cb - 0630258dcf35 - - 02d2be90dedb + - 80852884053f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: + - caeb57858702 + - 61634a87efc7 - ec69cbe34b73 - 14180f9c831e - - 61634a87efc7 - - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index dc1e35216..fcde78102 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 937aa69e715f - 749c918495f7 - - d5ceb9f3c25b - - 03e9b2fbc005 - - 3ba8d4563129 - - 17062a0decb7 - - 0d4acadabb04 - - f6877ad76b00 - 017aba02828d + - 937aa69e715f - a6d65b0c67af - cd659e8cc5fa + - 03e9b2fbc005 + - 17062a0decb7 + - f6877ad76b00 + - 3ba8d4563129 + - 0d4acadabb04 + - d5ceb9f3c25b 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: - - e188dc7a68e6 - - 64f11cf59c6e - - dfd8b7f78c37 - 2477830927ec - 53646aaaafef + - dfd8b7f78c37 - 3fe632431b68 + - e188dc7a68e6 + - 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: + - 37b497aa133f - 3e1ea2facca6 - 2ff111fac1d7 - - 60afcc2c1d05 - - 37b497aa133f - e7f19d6a9af8 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 6b1e195506a3 - - 8c6cd2650d1f - - 53c0b7a1a0c3 - c0c2d0941de8 - - f54f5baedfdd - - 77b2770508f6 + - 3f4d6399997b + - 037c6e54df11 - 09b53c1d4ab1 + - 8c6cd2650d1f + - f54f5baedfdd - 11a0d50a54e6 - - 037c6e54df11 - 5cc34c3f440d + - 6b1e195506a3 - b3eab4b67562 - - 3f4d6399997b + - 53c0b7a1a0c3 - be1d967337e4 + - 77b2770508f6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 178bdbdb6d24 + - 42ce70172b72 + - 9ee34ba73ebf - 00fbfac99d39 + - e403d27e8f24 + - 178bdbdb6d24 - 1cd2511a396e - - 5ef7ec16b04f - b8f5f6e87f5c - - 9ee34ba73ebf - - ec9cbd6b9a49 - - e403d27e8f24 - - 79b885ce78d7 + - 5ef7ec16b04f - 13022c3d3076 - 45795f582ae9 - - 42ce70172b72 + - ec9cbd6b9a49 + - 79b885ce78d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index 9b0ec42f9..fb48668e5 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -82,8 +82,8 @@ tools: - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 00e66c401366 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -96,8 +96,8 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - 9e3c83d2afc3 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -110,8 +110,8 @@ 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 @@ -217,15 +217,15 @@ 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 owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features @@ -239,17 +239,17 @@ tools: - name: recetox_aplcms_compute_clusters owner: recetox revisions: + - 18ec7635bac6 - f3a18e020cdd - 149b9cc7499b - - 18ec7635bac6 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 @@ -263,25 +263,25 @@ tools: - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - - e7305ba0dd38 - b341cfd4baf8 + - e7305ba0dd38 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - cf061712a184 - - dd7bbc2b99d1 - 17a48d0a80f4 + - dd7bbc2b99d1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - 24278c6b6d1c - - d7f5878a98c3 - 99d118321d5f + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index a363b2ea2..a24a67f84 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -30,101 +30,101 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 - 7c2100246a2f - - 63f86089423e - - 5b5a7af9fbb4 - 65db807336bc + - 5b5a7af9fbb4 + - 63f86089423e + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 1c35dadbe76f - - 18a502a9d287 - 96336c6a2bb7 + - 1c35dadbe76f - 00f5005840fa - 84fd33a60b35 + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - 34e55239e68b - a9f4a217dcd6 - - e8fba04706d3 - addaf9d22850 + - e8fba04706d3 + - 34e55239e68b - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 - - 5fe3edf19b9c + - 8c202e741d68 - 0776d824d896 - 75403243703a - - 8c202e741d68 + - 04c15826a0b8 + - 5fe3edf19b9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - 75c8945b0da2 - - e96bbb9e24ea - 1c9b3bcd4261 - 43c99742158b - 8470de786d47 + - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - 306a40d4bb8f + - 1d75bd0595e2 - 5c865a382933 - - 35176674168c - 84743da21318 + - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - 555ccac8a4c5 - - 78faebd0879c + - 8daf4564ccda - 32c9ea835770 - ac72310b038a + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - - a58e4a43f49c - d60df8727f59 - 7b8cb2b02978 - cae017b76acb + - a58e4a43f49c + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 073608a50ac3 - 7f3b59dee073 - 04144473e59e - - 073608a50ac3 - - 7136e9ab70db - 1bc3657cd694 + - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af + - a7817705348e - 0a1224c4b781 - - d943081510da + - 19299bb1c6af - 9058d8943303 - - a7817705348e + - d943081510da tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -137,12 +137,12 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - c4db8c4de66f - 65d52c693b8e - - b907a3c0434f + - c4db8c4de66f + - a68b985913ab - f8f56dd6449f - dbf1798c0dcc + - b907a3c0434f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -155,9 +155,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6d364c65c946 - 654548ae1357 - 6c84982ee6f7 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -170,24 +170,24 @@ tools: owner: iuc revisions: - 6aad8ca3918b - - bd7a9c6efb10 - e66ab198ec15 + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: + - 7f208f1eb64f - cad93abecac9 - 9704f1a3b32d - - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -223,30 +223,30 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 + - c409a495841f - e88b731dad59 - 79706f10d680 - - c409a495841f + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 094ad9c068af - 172920f67a84 - 714d5a28cc5c - 71ea608ddfa3 - d24841f5c3d2 - - 094ad9c068af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 4137b492233e - - a4d7148ccee4 - a293a742194f + - a4d7148ccee4 - d7e9a3c41657 - 12fb63b5f63f + - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -258,12 +258,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 64bc7acc22a9 - cf87759761eb - 75bedfb2078b - - 97f7bb0851e7 - 6fcb8ac37a3e + - 64bc7acc22a9 - e2c71b852aba + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -281,20 +281,20 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - c82508e76ad1 - 4033827c76b8 - - 2d35528d2141 - 080ea153677c + - 2d35528d2141 + - c82508e76ad1 + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: + - 2cd76b089570 + - 6b7622dda516 - 95bf7479d53c - fc6c328c292f - - 6b7622dda516 - - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -355,10 +355,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe - - cdee7158adf3 - 4a9da2b6c2e3 + - cdee7158adf3 - 328c607150ff + - 20e2f64aa1fe tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -391,8 +391,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -436,8 +436,8 @@ 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 @@ -473,22 +473,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc - - 2cff76cf35c6 - - 3cc4a60615c0 - - 327d9f4cc95f - - 27250f92a01a - 4fd3b5d8706b + - 2cff76cf35c6 - 7f5d7b0e9884 + - 327d9f4cc95f - 0270541aaf46 + - 3cc4a60615c0 + - 27250f92a01a + - e073891b2afc 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 @@ -554,31 +554,31 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - a16313517e55 - - 289b3807e80c - - ff8f55893e7d - - 1a037928504c - 2131d7dca455 + - fd69c607b43f + - 289b3807e80c - 6dee4abadccb - - 1a6cdf55390f - a92a632c4d9b - b89b0765695d - - fd69c607b43f + - 1a6cdf55390f + - ff8f55893e7d - ef65b083bd0c + - a16313517e55 + - 1a037928504c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - 2a8bc1d26d06 - e3a64a1d2a6e + - 2a8bc1d26d06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -609,22 +609,22 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -644,8 +644,8 @@ tools: - 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 @@ -657,8 +657,8 @@ 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 @@ -707,20 +707,20 @@ tools: - name: staramr owner: nml revisions: - - be818ae858e4 - - 141afacabcfa - 4b9a8031ab74 - - 3b22de20bd4b + - 2fd4d4c9c5c2 - aeaa20b96ef2 + - 3b22de20bd4b + - be818ae858e4 - 4d83eccf5f81 - - 2fd4d4c9c5c2 + - 141afacabcfa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - b3c7199d8786 + - 576963db5f1b - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 63fd21d8b..193493f23 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -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: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 584a12f2b..382ca9056 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: - - 9baa871cb1d1 - - 9422c5a87ee2 - 6ae5a7b5a0a2 - - 098506c54016 - - 2263989660f5 - - cd07731e4434 - a74dbfee5a86 - - 48c13389050d + - cd07731e4434 + - 9422c5a87ee2 + - bdfbaf0c10aa - 9eeb13a92d79 - - 8b67dd48fec1 - 80f03df2e2ce + - 8b67dd48fec1 + - 48c13389050d + - 098506c54016 + - 2263989660f5 - 94b8c6013083 - - bdfbaf0c10aa + - 9baa871cb1d1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f0af8936ed41 + - aaa0d6a8b808 - d390fe1567dc - be78f13134e2 - - fc2e49f91e52 - - 2e093badc689 - - aaa0d6a8b808 - - 5abf2c2249aa - - bc3831dd65c1 - - c18157c68134 - '764845535798' + - c18157c68134 - c44f824c051a + - bc3831dd65c1 + - 2e093badc689 + - f0af8936ed41 + - f14193ec1f50 + - 5abf2c2249aa - 3ff17bad4006 - - d7ce0ec78e51 - 4a60927aaca5 - - f14193ec1f50 + - fc2e49f91e52 + - d7ce0ec78e51 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,8 +46,8 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -66,29 +66,29 @@ tools: - name: mafft owner: rnateam revisions: - - f1a5908ea2cb - - bf28a8cff401 + - 8e649f27aa0d - 15974dd17515 - f0d493f8f84f - - c5908940967d + - bf28a8cff401 - a65296ffb4a0 - 6f28e90db932 - - 8e649f27aa0d + - f1a5908ea2cb + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 - e8fdceffea4c + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - 5561a1193611 + - 60698466facd - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -96,16 +96,16 @@ 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: - fb43e8887350 - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer @@ -119,8 +119,8 @@ tools: - name: mummer_show_coords owner: iuc revisions: + - b4124df98b26 - 959c1f8dae95 - cf3c9489c088 - - 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 bdd440f31..5677a4b11 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -24,12 +24,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 72b5e9dda577 - - fc8804320156 - - a7228a7ea146 - 79e9a869f40e - - cb34f00cc10f - 0e9e7fcdd543 + - cb34f00cc10f + - a7228a7ea146 + - fc8804320156 + - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -37,8 +37,8 @@ tools: revisions: - fa11aa8103b2 - 18505fe2bdb1 - - d6cddc06aeae - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -50,15 +50,15 @@ tools: - name: medaka_variant owner: iuc revisions: + - 222669c4afb6 + - 19f3b583a9b3 - 43815fa60f3a + - 2bf63b38ee9b + - 0f5f4a208660 - edf6d4003fad + - cc36773a3681 - ec699520444c - - 0f5f4a208660 - eb746fa6f514 - - 19f3b583a9b3 - - 222669c4afb6 - - 2bf63b38ee9b - - cc36773a3681 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -77,37 +77,37 @@ tools: - name: nanoplot owner: iuc revisions: - - a38bdcec9e4c - - a02b8b3f5a0c + - edbb6c5028f5 + - 0f1c34698076 - 645159bcee2d + - a02b8b3f5a0c - a3c4fe6f49ab - - 0f1c34698076 - - edbb6c5028f5 + - a38bdcec9e4c - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 3b6f94fc7e1d - d219b6d8158a + - 3b6f94fc7e1d - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: + - be95355fef8d - a8d4be409446 - 90a922f32523 - - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - - 449e9aeded2d - d376944466bf + - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -121,8 +121,8 @@ tools: - name: porechop owner: iuc revisions: - - 93d623d9979c - 5f76b20953e5 + - 93d623d9979c - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,8 +142,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -155,8 +155,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 338d15b8d6fb - 336791b5665f + - 338d15b8d6fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -168,8 +168,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -206,8 +206,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - ca22d8497db5 + - 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 fbc75520a..0b4a333f5 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,14 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 - tool_panel_section_label: None - tool_shed_url: toolshed.g2.bx.psu.edu -- name: artic_minion - owner: iuc - revisions: - - 468b90c41cde + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -34,17 +28,17 @@ tools: owner: iuc revisions: - 97b1b5ad1cda - - baceff842902 - adfd6bf710bd - - 3e73c97f025d - d74850cf4e42 + - baceff842902 + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - 1586b111d2a3 + - 83da94c0e4a6 - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -58,18 +52,18 @@ tools: owner: iuc revisions: - 13851aefa67a - - 1e34d2e3d285 + - e4b4837f06f5 - 2f27f3b86827 - - 19b6a2f0dbe2 - ed1518ce2237 - - e4b4837f06f5 + - 1e34d2e3d285 + - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -81,23 +75,23 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - - 48a42ca61006 - - 5711fc06a63e - 38ccd4589990 + - 5711fc06a63e + - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -137,10 +131,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - - 52b6a4d98009 - 172815da3d41 + - 52b6a4d98009 - b4b2b284230a + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -165,9 +159,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - fea85c467896 - 19bbd19b74b3 - 87febc68b45b - - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -199,36 +193,36 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 0cb27ea69dc1 + - d8dc037e3c13 + - 4ba60cb14cb0 - 5fe20c915fa6 - 9c43baa60906 + - 0cb27ea69dc1 - 2c61c30a57e7 - - d8dc037e3c13 - - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - 9d09724f2bf1 - - 0db22932bc39 - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - 29c738066906 - - 6e24e79d3d69 - df30a2f1db55 + - 6e24e79d3d69 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -246,9 +240,9 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - 3e4d45aca422 - - ad90c2da4f38 - 1865e693d8b2 + - ad90c2da4f38 + - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -267,16 +261,16 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - d63c1442407f + - 64deddb6a8ec - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - 9946bc39c834 + - 625fd9476402 - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -331,8 +325,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -801,10 +795,10 @@ tools: - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - 58a870ef434c - f77f7a7f3b83 - 9a22227bb6d0 + - ab5b7f6b7198 - ba7b0f11e470 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 32a970a92..19fdc0fb8 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,65 +33,65 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - b89cac5156ec - - 8834daeb9892 + - d7c7ef3353fe - d033ffc1c161 - - 107d3ba7024a - - 5a7c56a5cc08 + - 3b8b5bde0bd9 + - b89cac5156ec + - '841557158611' - 81e66674859e - 26de3a7b1cb9 - - '841557158611' - - c78f3d7dd1db - f04a1264e2a2 - - cce7b18495e4 - - 3b8b5bde0bd9 - - 6a457678efcb - - a6619171428e + - 8834daeb9892 - f73435dc282b - - d7c7ef3353fe - 3f59ebfbfe3d + - a6619171428e + - 6a457678efcb + - cce7b18495e4 + - c78f3d7dd1db + - 5a7c56a5cc08 + - 107d3ba7024a tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - aa8cc71438cf + - 5fcd1ece3a6e - 7a2092844346 + - df47d4845b62 + - a185b079b095 - 4755f52427c4 - - 5fcd1ece3a6e + - 659517798cc4 - e75442c7f4da - - a185b079b095 - - 6a726db04d4b - - aa8cc71438cf - - b0af57c1a968 - 3b96e92e8ec3 - - 6283babe736e - - 5b777002c2de + - 6a726db04d4b - 88c4aa435ded - 6223845127ea + - 6283babe736e + - 5b777002c2de + - b0af57c1a968 - 02b8758214b0 - - 659517798cc4 - - df47d4845b62 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - - c1d53e95327f - 0878b7fd5260 - - 70acec670c30 - - 111bd54f6bc4 - f97743d52b87 - b8476e82ac20 + - 111bd54f6bc4 + - c1d53e95327f + - d1c340a5664b + - 70acec670c30 - 24d024316465 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd - 9e10ba792be2 - daddf188c13f + - feb40665d7cd - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: - - a2099fb98cdb + - 03ed9524dcd1 + - 2fa9d4f1b48f + - ca337cce3888 + - 5f8727ff21e7 + - 36912871ccdc + - b6abccb1f25b + - 437e28791761 - 42a174224817 + - 14ae456b8cc5 + - a2099fb98cdb + - 81804a978fc0 + - abf6dbe8c9d7 - 9d61d3fa046c - - b7e297c2ede6 + - 8ad84c5753ea - 3a43c3982401 - - 36912871ccdc - - b6abccb1f25b - - ca337cce3888 - - 5f8727ff21e7 - 2f1019071464 - - 03ed9524dcd1 - 83a69484cb87 - - 2fa9d4f1b48f - - 8ad84c5753ea - ca0d8cf80567 - - 81804a978fc0 - - 437e28791761 - - abf6dbe8c9d7 - - 14ae456b8cc5 - 7bb8726be37c + - b7e297c2ede6 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac - ea30d3089354 + - 73a469f7dc96 - ba29b5e2a4be - a4b71be30c3c - - 73a469f7dc96 - b1e68bbe4cef + - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 9b2b122d0415 - f1ccc8a6eb05 - - 15ac71df11a0 - - 809e42326fc2 - - 91887494eb97 - - e88a7de55d6e - dbe2b2204555 + - 9b2b122d0415 + - e88a7de55d6e + - 91887494eb97 + - 809e42326fc2 + - 15ac71df11a0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index a2806c7d0..6fdfca02a 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: + - fc288950c3b7 + - 881d7645d1bf + - 7d34178f2812 + - b502c227b5e6 - f9242e01365a + - 1aac2a13842a - f6ced08779c4 - - 881d7645d1bf - - fc288950c3b7 - 3f254c5ced1d - - 1aac2a13842a - - b502c227b5e6 - a1f0b3f4b781 - - 7d34178f2812 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 861f969a4..1aa6e447c 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - a58f7eb0df2c + - 2f7702fd0a4c - 6ab1a261520a + - d00e15139065 - 3bd420ec162d + - 5b85006245f3 + - c0e71cb2bd1b - eb085b3dbaf8 - - d00e15139065 - ca90d17ff51b - - 2f7702fd0a4c - - a58f7eb0df2c - - e4a053d67e24 - - c0e71cb2bd1b - - 5b85006245f3 - 7fbec959cf2b + - e4a053d67e24 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 c6ed9654e..9ef461bb1 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,92 +2,92 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b18329a8ac14 + - b574b84afc4d + - f28ad96b76dc - 0a18ac48ac53 + - 277dc652246e - ece627528a78 - 4c177985028a - - 277dc652246e - - b574b84afc4d - - f28ad96b76dc + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - 525f201b86c1 + - e215f71d7983 - e988563cc6e5 + - a9a28e46d54a - b41107d8fe89 - - e215f71d7983 - - 525f201b86c1 - bf06d196e23d - - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 - 8da3511c9467 - 56da27be956a - 4fbffddde8cd + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 890845926d4b - - 528fb09022be - a8157342d9a3 - - b8c79e70516d - f23d67e28cc8 + - b8c79e70516d + - 528fb09022be + - 890845926d4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 25b83cbd596a - a95a82eb4d50 + - a69865da6f80 - ae304a72db7b + - 25b83cbd596a - 59e85306eae5 - 80600735685d - - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - ed9ed1e6cca2 - - 611d80c0e29d - - e0669b1854b1 - - 798da6bdff3d - f1897eb07081 + - 611d80c0e29d + - ed9ed1e6cca2 - 83aac7741200 + - 798da6bdff3d + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - 5a35e3a8d013 - - d426a9107a6c + - a7fb9b395ddf - 74b61bf5bc4b + - d426a9107a6c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff + - df2187f9013b - 91f0f5922011 - 82f6c2f4332d - - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 - 1693b2126f30 - - 10566783d718 - ba92b59cd529 + - 043f9c91f686 + - 10566783d718 - d2483487e077 - c5aa9fca18c6 tool_panel_section_label: Proteomics @@ -107,8 +107,8 @@ tools: - name: diann owner: galaxyp revisions: - - bf0728e000cd - ff8c9e0e8a7b + - bf0728e000cd - 9fa3dbf06f17 - ae4dc0c041f9 tool_panel_section_label: Proteomics @@ -122,9 +122,9 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d0ea7589e95f - eac99effe86f - d263296cd73e + - d0ea7589e95f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify @@ -138,16 +138,16 @@ 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: - - d6a4dfdad269 - - 0d2e93e01e68 - ce1a157a41bd + - 0d2e93e01e68 + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,9 +159,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - d286ff4600dd - 160538a890a6 - e66f552a3c47 - - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -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 + - e42225f8a659 + - 9c52362ae7bb - 37d669de2828 - - 7f432d87c82c - - 837224ad1694 - - 2133b0be850a - 4d17fcdeb8ff - - e42225f8a659 - - 97a7f34fcb6a - - 1f39c833f65f + - 2133b0be850a - f522c08e900c - - 9c52362ae7bb + - 97a7f34fcb6a + - 7f432d87c82c + - 837224ad1694 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,35 +202,35 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 85b8866f06d7 - a72ac2c7cc5b - - 0ed07016d668 - e63db1aa82ee + - 85b8866f06d7 + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 1974224d63c2 - - 352b37c66d97 - 990b4560ead7 + - 352b37c66d97 - 767c1d761aaf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - deaf035bbe9f - 35cc7ca0bdc7 - 99450519d727 + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c - c1343e3389ca + - e79958768a2c - 06f6826d380c - c7745841de24 tool_panel_section_label: Proteomics @@ -238,19 +238,19 @@ tools: - name: metaquantome_stat owner: galaxyp revisions: - - d46d64e7964d - - da986f83631b - b9d453dca8d3 + - da986f83631b + - d46d64e7964d - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: + - 944b43462104 - 9bf325045235 - 8bd7734309f6 - 1199751329b0 - - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -270,10 +270,10 @@ tools: - name: msstats owner: galaxyp revisions: + - de7593c29499 + - 593839e1f2c3 - 8212e342e482 - 28434abe6c5c - - 593839e1f2c3 - - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -286,36 +286,36 @@ tools: - name: openms_consensusid owner: galaxyp revisions: + - 4e77b8f12cd3 + - 01dbaf6a57e0 - f4be248c3d47 - 8960fb791701 - - 01dbaf6a57e0 - - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - 25529df60a81 - - 370141bc0da3 - 06cca574e337 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - 518b1730cf2a - - f7fef900f5b2 - - 9cdf15d3cfc8 - c9eff69a7c62 + - 9cdf15d3cfc8 - 6ccbf9a2072c + - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 9876bda3ec53 - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 + - 9876bda3ec53 - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -323,18 +323,18 @@ tools: owner: galaxyp revisions: - 890025d6e426 - - 1595601708ec - 41859bbdc16e + - 1595601708ec - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 2a93a25f0599 - 9b7977080f6d - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -349,9 +349,9 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: - - febd569ad26f - 5ad830edc021 - 4af67edd5aef + - febd569ad26f - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -359,9 +359,9 @@ tools: owner: galaxyp revisions: - 92352a475eed - - 39e8fde08881 - - b2fc8da99bcc - 27cba4c5fc42 + - 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name: openms_multiplexresolver owner: galaxyp revisions: - - 021fdb80f204 - - d0304fb829c0 - 4e66c4e73909 + - d0304fb829c0 + - 021fdb80f204 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - - 2735db4dd8d9 - bf32e0bcf554 - 8098330f6d91 + - 2735db4dd8d9 + - ee860980edc6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - 08488066d588 + - 0ced5bc9f4dd - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - 2a9ff56cb279 + - de7a553552a6 - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - e8f64a7dc470 - c1809c05ae8c - 1bf940c18d93 - - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 496cf619e311 - f861ec9fbe59 + - 496cf619e311 - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - c99d5004b74f - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 8b814eafce2c - 4bb198c0bd3e - 89254095cbf6 - - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: + - f82b320ceb90 - f9ed7e074900 - 05ec9fb05ed1 - - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - - 18826fb8e5db - d31426ef20f6 + - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -530,35 +530,35 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - 6b01678ec2fc - - 3d8d4ada5405 - decc397c3b7e + - 3d8d4ada5405 - 5ae104d0da6e + - 6b01678ec2fc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - d6aca689dd48 - - 5182338d5e7c + - dd173849c3d8 - 539a3a4dcc9e + - 5182338d5e7c + - d6aca689dd48 - e039cc5c7aed - - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - - 16026cdb1330 - d426affe977c + - 16026cdb1330 + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - dd71e020e2aa + - 43b9ed22e8ce - 9c70a651a53e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -566,32 +566,32 @@ tools: owner: galaxyp revisions: - 9020199dba0a - - d063e2fe4ba4 - 1b03536aa3c9 + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - f036e8cf1a55 - - ad2ba3a95a02 - 78c080d36945 + - ad2ba3a95a02 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - - c8b225c69a7f - 5c2a97a234d6 - 7f6a1f27553e + - fb52e95a370c + - c8b225c69a7f 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 @@ -603,21 +603,21 @@ 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: - 3ec27b4cee7c - - da885ca16cb2 - - 07ff622ec007 - - 3634c90301af - - 943a34df6047 + - 7fdd9119cc4f - a72c48001f7c + - 3634c90301af - 1beff3ddce58 - - 7fdd9119cc4f + - da885ca16cb2 + - 943a34df6047 + - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -679,8 +679,8 @@ tools: revisions: - 12692567c7f9 - 265c35540faa - - a371252a2cf6 - 1a5690a5eedc + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index faed49ccd..f318375d8 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,108 +2,108 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 289b7d6b69a4 - - e345aadf914f - - 42201b90e3f4 + - 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revisions: - - a3e86cd9cac7 - c9b77ced9a78 - - 1544278c272e - - 3d70c2996730 - 8a55d29c8fcf + - 3d70c2996730 + - 1544278c272e - d30e36c48c93 + - a3e86cd9cac7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - e2db212d64ad - 887cf585cafc - - a5969aa9347e - - 564c33e5c3e3 + - e2db212d64ad - 7b881f5f5ad5 - b242deb58952 + - a5969aa9347e + - 564c33e5c3e3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 9a171f9a450b - b4bab607eb05 - e897c74a48bb - 8cff84759bf6 - bd5ff77e2036 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: + - 5e10f396979e + - adc7a7610d4f - 6dafad990086 + - 4f65e343ecdf - 887e0991eb24 - 33f0793edf93 - - adc7a7610d4f - - 4f65e343ecdf - - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 43e3eeb2e0ec - c287418eb288 - - c5d7050e4ad7 - 4e280b27a831 + - 43e3eeb2e0ec - 17d39bf0a63a + - c5d7050e4ad7 - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - a819ec3b362d - 0b8c84a7fdb5 - 09b8edb56d80 - d9bf483266a1 - - a819ec3b362d - 9586f08634c0 - cd034465d4a4 tool_panel_section_label: RAD-seq @@ -111,23 +111,23 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - bf0e43ab0416 - - 95351dd0fd3f + - a9c34a289493 - a4b4bd84f69e + - 95351dd0fd3f - 2645575d1bf2 - - a9c34a289493 - 69842dd5aa48 + - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - - d033e1ccb386 - - 912f904a6e1e - - bb0475c884ff - 8a35a3bc6752 - d1fda11e602f + - bb0475c884ff + - 912f904a6e1e + - d033e1ccb386 + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 72e68301d..0a4dea406 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,16 +2,16 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - 2d4e3aff9dc7 + - cf01dd6c6b1f - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 32e542c2a773 - 703a2cb3fb38 + - 32e542c2a773 - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -80,8 +80,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -94,16 +94,16 @@ tools: - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - 6a6717a5f421 + - cf747d1bd79a - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -127,9 +127,9 @@ tools: - name: describe_samples owner: iuc revisions: + - e3b16fd7dd08 - 3b36efd62b3e - 0693ccd171c4 - - e3b16fd7dd08 - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -137,39 +137,39 @@ tools: owner: iuc revisions: - cd9874cb9019 - - 24a09ca67621 - - 8fe98f7094de - - 9a882d108833 - 6a3a025714d3 - - 0696db066a5b + - 24a09ca67621 - d027d1f4984e + - 0696db066a5b + - 9a882d108833 + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - b47c006d90c5 + - df929f257179 - 9a7c5b6d8f1e - 62adf13b86ea - 2872c633f07e - - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 070900306913 - - 334ce9b1bac5 - - a8305cf0c951 + - ae2aad0a6d50 + - 9bdff28ae1b1 - f2843df56434 - - 555659de7321 - - 0cb907a2a810 + - 334ce9b1bac5 + - 6e53e565fc6a - 3d89af8a44f0 - - 9bdff28ae1b1 - df0c8d0a5992 - - ae2aad0a6d50 - - 6e53e565fc6a + - a8305cf0c951 - 5bf899c13979 + - 070900306913 + - 555659de7321 + - 0cb907a2a810 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -188,17 +188,17 @@ tools: - name: featurecounts owner: iuc revisions: - - f3a5f075498f - - a56fbe2d6ba7 - af814359d244 - - e6a2a912677a - - 90d16db017d7 - 6f66ae7c5f7a + - a56fbe2d6ba7 - 7db9d3ea71c9 + - e6a2a912677a + - ea04b737afa0 - a37612abf7f9 + - 90d16db017d7 + - f3a5f075498f - 38b6d12edc68 - f9d49f5cb597 - - ea04b737afa0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -222,8 +222,8 @@ tools: - name: gffcompare owner: iuc revisions: - - f99dd58de04f - 0f710191a66d + - f99dd58de04f - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,21 +236,21 @@ tools: - name: hisat2 owner: iuc revisions: + - 3fb01a8c902d - a86e80d3c09c + - 6c19daec423d + - 26371a1df031 - d4b55e2beb12 - f4af63aaf57a - - 6c19daec423d - - 3fb01a8c902d - 6ab42baa56e9 - - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - 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: isoformswitchanalyzer @@ -262,11 +262,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 + - 01247aaf0a10 + - 1c75aa5de15e - ce5d418183c5 - 5ae5c312d718 - - 1c75aa5de15e - - 01247aaf0a10 + - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -281,14 +281,14 @@ tools: - name: limma_voom owner: iuc revisions: - - 0921444c832d + - d6f5fa4ee473 - 32511f586472 - - 708348a17fa1 - e827f9aae031 + - 0921444c832d - 97e06a4c7c75 - - 119b069fc845 - - d6f5fa4ee473 + - 708348a17fa1 - 58c35179ebf0 + - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -300,8 +300,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -345,20 +345,20 @@ tools: owner: iuc revisions: - 4df95e2d7f61 - - e132e7d02a3e - - 4014de1b6daf - - b0f2be869d6d - - 4074fc1940e2 - - b9e04854e2bb - - 79de45b5069b - - 99b17b74a8cd - - 3ea5a2a63fa2 - - c772497b2c32 - - 980d2a2e1180 - 7ed2edc1337f - 0a563fd2f22e + - 980d2a2e1180 - 5ec75f5dae3c + - 99b17b74a8cd - c7c55b694974 + - 79de45b5069b + - e132e7d02a3e + - b9e04854e2bb + - 4074fc1940e2 + - 3ea5a2a63fa2 + - 4014de1b6daf + - c772497b2c32 + - b0f2be869d6d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -370,36 +370,36 @@ tools: - name: salmon owner: bgruening revisions: - - 53e9709776a0 - - cc05793bb896 + - 2c0ca397d302 - ebab418107f5 + - 53e9709776a0 - f4d5237a84f6 + - 49121db48873 + - cc05793bb896 - e3d32471da11 - 15cd64d7c58b - - 49121db48873 - - 2c0ca397d302 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - fab6ff46e019 - c0fd285eb553 - - 8c28affc7c48 - 56242ff81c84 + - 8c28affc7c48 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - 914cfcba0ec8 + - 258d696dbd7e - 1ebd14235b92 - - 76d290331481 - ae618321f34a + - cbf488da3b2c - dd4df992d93d - cef79931dda5 - - cbf488da3b2c - - 914cfcba0ec8 - - 258d696dbd7e + - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -429,19 +429,19 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - - ffd1300599a1 - c6334cb383ff - d0d4cef4f967 + - 0db979fead3a + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - - d6a479fd4281 - 74217fbfba4d - ba3720d7e68b + - bcc5f03f1900 + - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -456,64 +456,64 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - - 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: - - 870ac06dff8e - - 34a018cbee9c - be3f26533209 + - 34a018cbee9c + - 870ac06dff8e - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 5192f657f305 - 33406f5a445c + - 65e7dea767ea - c5fbddcac63a - - 5192f657f305 - 05ab8d5e04a2 - - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 6f0fb35b799c + - 1fdb25a8384d - a35cba31d904 + - 6f0fb35b799c - e406ac71165d - - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - 7c7fbf13aadd + - c2c039e421af - 964b7efe2639 - 37a1129c89d2 - - c2c039e421af tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: + - 24e94d84adc9 - 047c22569787 - 1d689e4e1caf - - 24e94d84adc9 - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 3a4ac03d1266 - - 9871104ea630 - - 04bb8bb7c198 - 1812dbc5bb7b + - 04bb8bb7c198 + - 9871104ea630 + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -533,13 +533,13 @@ tools: revisions: - 32b86cd8eb50 - 8f1c3df4dd49 - - 48636f857c4b - - cee61b3fcf78 - - d2bc35f3d1c5 - 9fa24d5aac68 + - cee61b3fcf78 - c9cfec002f71 - d84caa5a98ad + - 48636f857c4b - db1f362cca3e + - d2bc35f3d1c5 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 b2c45c52e..9eed3b471 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -4,6 +4,7 @@ tools: revisions: - 1a052c827e88 - 080fd5739bb4 + - 27e16a30667a - 473382134e56 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 f9314e32a..53f560055 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,18 +2,18 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 3c661e57a88f - 88eedb4abea0 - 10184eaa85fc + - 3c661e57a88f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 993b19f20c76 - - 1dfd95ee241e - 108db6635177 - cb20f99fd45b + - 993b19f20c76 + - 1dfd95ee241e 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: - - 19ece8afbaab - 30a201c9c310 - e7fd6754d093 + - 19ece8afbaab - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - 17b35d23731f - e38af83df163 + - 17b35d23731f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -130,9 +130,9 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a - 12749212f61b - 46c6639921f1 + - 9149ad20699a - 6856f8a01905 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -140,9 +140,9 @@ tools: owner: devteam revisions: - 33208952b99d - - 92ec40abcdcf - - 26b4f9f98aca - 06dc50b7b711 + - 26b4f9f98aca + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,10 +160,10 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - - b3d99709fe1a - b906586a6596 + - 66e23b11feae - 720217c23995 + - b3d99709fe1a - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -177,21 +177,21 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c + - fe34990e5ce7 - db17d5321bad - cc61ade70eb8 - - fe34990e5ce7 - 22970df7a40e + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: + - 7a6034296ae9 - 811fc2d75ad4 - 7def34e6cf4d - - 7a6034296ae9 - - 88b8c2916784 - fa5d3e61e429 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -204,21 +204,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 - - 740ce0a18f0d - cae2794d2deb + - b40e2d865d52 - 65a38e8c8e2a + - 740ce0a18f0d - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 + - 8da515fbc1bf - b61f5d6a7f25 - - 583abf29fc8e - 9da0311ab1dd - - 8da515fbc1bf + - 583abf29fc8e + - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -231,8 +231,8 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - 85e38b31e8b3 + - db000c6007a0 - 30388d878f81 - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM @@ -246,54 +246,54 @@ 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: - - cab3f8d35989 - - d54a4df48867 - 6c2c1836728b - e613c1ad4c4c + - d54a4df48867 + - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - - bcedabb53ddf - 135c85f4cfaf - - bd850490c7f1 - 818030fa6bbf - 5d9ae78f34d3 + - b7f7826ef1cd + - bcedabb53ddf + - bd850490c7f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 541082d03bef - 3a0efe14891f + - 145f6d74ff5e + - 541082d03bef - 24c5d43cb545 - 5a08c09b9311 - - 145f6d74ff5e - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - b72793637686 - - c370440f901e - 2dce91e11ca7 - - bf328cec6a42 - - 350bbc5c2ffd - b01db2684fa5 - - 6be888be75f9 + - c370440f901e + - 350bbc5c2ffd - 5826298f6a73 + - b72793637686 - 32dc5f781059 - 0dbf49c414ae + - bf328cec6a42 + - 6be888be75f9 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 f4060b6c2..8b49db552 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 - - 6f6537780379 - - 59bb6d34fca6 - - d147d6455873 - - 480d9e9d156b - 4aab5ae907b6 + - 59bb6d34fca6 + - ea5e944f447d - 5cb6146337d8 + - 480d9e9d156b + - 6f6537780379 + - d147d6455873 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 2a0f7fec4..14a762631 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,10 +8,10 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - ecb9ea6269ee - - e32b215b7c04 - f2000bc73102 + - e32b215b7c04 + - e4c01dcece8b - c9944a2600f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -20,60 +20,60 @@ tools: revisions: - e1c3c2f2a834 - c0b037b12765 - - 707023fa62fe - cfaf5a405371 + - 707023fa62fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - cfc3f5a57dc6 + - fb9e030ffae4 - d330b3082107 + - 93dd15e13e6a - 32e547223c9e + - cfc3f5a57dc6 - 55e35e9203cf - 00712416fdaa - - fb9e030ffae4 - - 93dd15e13e6a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - 0bf7fddf90c7 + - 6f0d0c784f09 + - 688357ad5e61 + - 39e945f0b2c1 - b9fac48532eb - 038e32885fec - ee98d611afc6 - - 6f0d0c784f09 - - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - ed4996a16f7f - - 43cb7b5a6fe7 - - 7e8c677a7b71 + - 3d748954434b - 9bd945a03d7b - b85871dd69f9 + - 43cb7b5a6fe7 + - ed4996a16f7f + - 7e8c677a7b71 - d4af736e7b83 - - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - fe75d2414dc0 - - a4774b7b2e85 - 2e8022f1923c + - a4774b7b2e85 + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: + - 0e70b2dfe4be - 769d815e4b0d - 02b1fe7aed76 - - 0e70b2dfe4be - 4fff5a293013 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -82,26 +82,26 @@ tools: revisions: - a90f8efe08b4 - aa4a6f0916b4 - - c29e7bb492bf - 344c2af50552 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - 050cf43887d3 - 5b7c81b35b89 - - b13d3e4c48e1 - c32347702e12 - - 050cf43887d3 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 1d77986f9ddc - - ae969fdb8442 - 239193b96d72 + - 1d77986f9ddc - 02fc39c8610d + - 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 - - 8855361fcfc5 - - 2c1200fba922 - a9caad671439 + - 2c1200fba922 + - 8855361fcfc5 + - cfe1e6c28d95 - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,8 +178,8 @@ tools: - 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 @@ -192,8 +192,8 @@ tools: - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - f47ac4a0b337 - 013e53ccc7ac + - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol @@ -220,8 +220,8 @@ tools: - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - 40fee49bc6c3 - f881c94fb3b3 + - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix @@ -234,8 +234,8 @@ tools: - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - b05f662f9f35 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions @@ -248,29 +248,29 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - 2ba6cee8e4db + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - ea19190ce5e0 - 62b720dceb56 + - ea19190ce5e0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate @@ -325,22 +325,22 @@ tools: - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - b376ef118807 + - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -400,26 +400,26 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - f36828ebdc54 + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations 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 - - e98619de2776 - - eeab712b0b99 - - 4b0adaa31c95 - 59be31ac9dc3 + - e98619de2776 + - 7784821452ac - 0f1aaff9b22d + - 4b0adaa31c95 + - eeab712b0b99 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -431,16 +431,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 - 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 @@ -466,27 +466,27 @@ tools: owner: iuc revisions: - 7e014059a88d - - c4f39bf4a068 - 0bff0ee0683a - - a4b734cd253b + - c4f39bf4a068 - f911a64454fb + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - d45f092caf24 - b83fbc90161e - - 43c146e25a43 + - d45f092caf24 - 7608d5faee41 + - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - f3eb2291da05 - 2b0d3e2f402a + - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -500,11 +500,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 72979cac22b2 - 44b935f2271b - - e93b008c637a - 2af7c5086a96 + - e93b008c637a - c92d0f9338c5 + - 72979cac22b2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -522,27 +522,27 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - aaa5da8e73a9 - - f9353ee6a0d4 - - 178242b82297 - - 6acb08931836 + - 77b91b9bdf52 - 6f83f8fd381f + - f9353ee6a0d4 - b2df381a6004 - - 77b91b9bdf52 + - aaa5da8e73a9 - 4d8f983cd751 + - 6acb08931836 + - 178242b82297 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - d636ce5cde16 - - 713a0c65b1fe - - 72a6bebab2a5 - b409c2486353 + - a03ff8633507 + - 713a0c65b1fe + - d636ce5cde16 + - 3c86f71498bc - a97abb8cd15b + - 72a6bebab2a5 - 277313130da5 - - 3c86f71498bc - - a03ff8633507 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -552,70 +552,70 @@ tools: - c5d3684f7c4c - c0a80a16560f - 5e9171dc8244 - - f54f0f0598ad - - 6bd82ed14acd - 18262103fa61 - - 6c145a6868cc - 5c3ebe2adc77 + - 6bd82ed14acd + - 6c145a6868cc + - f54f0f0598ad tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 94c19fb1281c - - ab55fe8030b6 - d844935c906c - - 5dada6f76047 - - 9f354c7c8c92 - - c9cb76cf8d6c - 3bcd5445cd7a + - ab55fe8030b6 - 7b9fafe32c86 + - 94c19fb1281c + - c9cb76cf8d6c + - 9f354c7c8c92 - a407e7f8bdc1 + - 5dada6f76047 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 7647e5cd1b8b + - 6adf98e782f3 - 95777145cb92 - - dbbe1ea8ecb1 - 9b0cdb8cf6be - - 6adf98e782f3 - f7446fd8d5e7 - - 6f5349dd5c49 - - 1072ce66b426 + - dbbe1ea8ecb1 - 2dfb2227a16c + - 1072ce66b426 + - 6f5349dd5c49 + - 7647e5cd1b8b - aa0c474463c2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - f2f6c703da06 - - 215733a383f2 - d18e7a6e5cd4 - - 458e8f43a775 - - c65fce500915 - - b70219da4a96 - 73ab2ac53d06 + - f2f6c703da06 + - b70219da4a96 - a39040ae0a38 - bf2017df9837 + - 215733a383f2 + - 458e8f43a775 + - c65fce500915 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - fd808de478b1 - b834074a9aff + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: + - 7a365ec81b52 - 652923ce664f - b7ea9f09c02f - - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -627,8 +627,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - ef4c80837bc5 + - 81e5bdff4853 - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -641,9 +641,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: + - c99ba278dfa9 - 46fc6751d746 - 9e5c0bb18d08 - - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -883,29 +883,29 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - afb90d3485df + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 88192fe25375 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - fecf9664c885 - 370d45e0d1a8 + - fecf9664c885 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -917,8 +917,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 90e95e9ee190 - 883c33ef3372 + - 90e95e9ee190 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 34f38078c..14bfbb70e 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - 4c07ddedc198 - - 562f3c677828 - 419027d822d6 + - 562f3c677828 - 746e8e4bf929 + - 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 @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - cb1c59d69557 - 7a15159140d1 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,42 +114,42 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 4c4ec859c31a - 9c3e1d3235c8 - - 7442b94d6a1e - - aef56d0e7a61 - 840f29aad145 + - 7442b94d6a1e + - 4c4ec859c31a - b1eda492f063 + - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - 375bbd555f4a - d0352e8b4c10 + - 07843f917990 - 9fda0b82f419 - 30d21a6041f6 - - 375bbd555f4a - - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 2c58b83c9bad + - 4cc980df6265 - cd02bf168d23 - 8b1b2b91f8d0 - - 2c58b83c9bad - 7ae443e6217d - - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - ad7e0b4291ee - - 1dd433d2c92c - e10e776f2109 - bb9fc9d46ea4 + - ad7e0b4291ee - 4bbaf77573ef + - 1dd433d2c92c - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 54ef183db..47d4c731c 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: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 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: - - 6595517c2dd8 - - 02026300aa45 - - 9cd341095afd - - aff5135563c6 + - 13b6f0007d9e - 464b9305180e - be25c075ed54 - 6e8d94597139 - - 13b6f0007d9e + - aff5135563c6 + - 9cd341095afd + - 02026300aa45 + - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 557ec8d7087d - 90f657745fea - - 37cde8134c6a - - 9cc411a62277 - 34d29339abab + - 9cc411a62277 + - 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 - - 83069b38aa85 - - 33d61c89fb8d - 623f3eb7aa48 - - 3a6b78c39dca + - 33d61c89fb8d + - 83069b38aa85 - 2e8f945f7285 - - cf34c344508d - 1ea4e668bf73 + - cf34c344508d + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - ae8c4b2488e7 - - 503bcd6ebe4b - 399da6b5ec21 + - 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: - - f768f6183386 - - bce29ec10b78 - b722161a845a + - f768f6183386 - c4d18aa4ec4a + - 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: - - 9ff72e942410 - - a6f147a050a2 + - 86755160afbf + - ddf54b12c295 - f46f0e4f75c4 + - a6f147a050a2 - 12615d397df7 - - ddf54b12c295 - - 86755160afbf - 74a8bef53a00 - - d698c222f354 - fbf99087e067 + - 9ff72e942410 + - d698c222f354 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 086118cc2..2b3eae029 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -5,12 +5,18 @@ tools: - 00e20a06ff1e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: artic_minion + owner: iuc + revisions: + - 468b90c41cde + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - - 85c57cc9b558 - 0d18a3ba2d1c + - 85c57cc9b558 + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -30,8 +36,8 @@ tools: revisions: - 57def2d7c093 - ef2c525bd8cd - - a5937157062f - 156b60c1530f + - a5937157062f - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -40,45 +46,45 @@ tools: revisions: - 791f73caa0c8 - 09d6e4693887 - - e61c9ac190ad - 435b157bed6d + - e61c9ac190ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 074d44697036 - - 3b4b2121842f - 65432c3abf6c - - e1461b5c52a0 - - dfadc322b065 - 03627f24605f - 4805fe3d8fda + - 074d44697036 + - dfadc322b065 + - e1461b5c52a0 + - 3b4b2121842f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - 9cb929f21cfa - - 701d134358ad - 7dfca164d2e3 + - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu 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- name: vcf2tsv @@ -400,22 +400,22 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 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 @@ -428,8 +428,8 @@ 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 @@ -463,37 +463,37 @@ tools: - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: 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