From 7ca7f0722a186de2e48790986df20ff22ab86a6c Mon Sep 17 00:00:00 2001 From: admin Date: Wed, 26 Jul 2023 22:27:48 +0000 Subject: [PATCH] Jenkins install build 1306. --- automated_tool_installation_log.tsv | 1 + requests/blobtoolkit.yml | 8 - staging.usegalaxy.org.au/annotation.yml | 56 ++-- staging.usegalaxy.org.au/assembly.yml | 196 +++++++------- staging.usegalaxy.org.au/bacterial_typing.yml | 6 +- staging.usegalaxy.org.au/bb_tools.yml | 4 +- staging.usegalaxy.org.au/bed.yml | 16 +- staging.usegalaxy.org.au/blast.yml | 10 +- staging.usegalaxy.org.au/chemicaltoolbox.yml | 52 ++-- staging.usegalaxy.org.au/chip_seq.yml | 6 +- .../collection_operations.yml | 10 +- staging.usegalaxy.org.au/convert_formats.yml | 36 +-- staging.usegalaxy.org.au/deeptools.yml | 98 +++---- .../dna_metabarcoding.yml | 14 +- staging.usegalaxy.org.au/emboss.yml | 2 +- staging.usegalaxy.org.au/epigenetics.yml | 4 +- staging.usegalaxy.org.au/fastafastq.yml | 70 ++--- .../fastq_quality_control.yml | 26 +- staging.usegalaxy.org.au/filter_and_sort.yml | 2 +- staging.usegalaxy.org.au/gemini_tools.yml | 32 +-- staging.usegalaxy.org.au/genome_editing.yml | 8 +- staging.usegalaxy.org.au/get_data.yml | 26 +- .../graphdisplay_data.yml | 58 ++-- staging.usegalaxy.org.au/hca_single_cell.yml | 4 +- staging.usegalaxy.org.au/hicexplorer.yml | 14 +- staging.usegalaxy.org.au/imaging.yml | 20 +- staging.usegalaxy.org.au/ivar.yml | 62 ++--- .../join_subtract_and_group.yml | 6 +- staging.usegalaxy.org.au/machine_learning.yml | 20 +- staging.usegalaxy.org.au/mapping.yml | 42 +-- .../metagenomic_analysis.yml | 76 +++--- staging.usegalaxy.org.au/mothur.yml | 4 +- .../multiple_alignments.yml | 42 +-- staging.usegalaxy.org.au/nanopore.yml | 26 +- staging.usegalaxy.org.au/none.yml | 40 +-- staging.usegalaxy.org.au/phylogenetics.yml | 86 +++--- staging.usegalaxy.org.au/picard.yml | 4 +- staging.usegalaxy.org.au/proteomic_ai.yml | 10 +- staging.usegalaxy.org.au/proteomics.yml | 154 +++++------ staging.usegalaxy.org.au/rad_seq.yml | 74 +++--- staging.usegalaxy.org.au/rna_seq.yml | 142 +++++----- staging.usegalaxy.org.au/sambam.yml | 46 ++-- staging.usegalaxy.org.au/send_data.yml | 4 +- staging.usegalaxy.org.au/single_cell.yml | 46 ++-- staging.usegalaxy.org.au/statistics.yml | 28 +- .../text_manipulation.yml | 32 +-- staging.usegalaxy.org.au/variant_calling.yml | 32 +-- staging.usegalaxy.org.au/vcfbcf.yml | 236 ++++++++--------- staging.usegalaxy.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 68 ++--- usegalaxy.org.au/assembly.yml | 182 ++++++------- usegalaxy.org.au/bacterial_typing.yml | 6 +- usegalaxy.org.au/bb_tools.yml | 2 +- usegalaxy.org.au/bed.yml | 12 +- usegalaxy.org.au/blast.yml | 10 +- usegalaxy.org.au/chemicaltoolbox.yml | 50 ++-- usegalaxy.org.au/chip_seq.yml | 10 +- usegalaxy.org.au/collection_operations.yml | 8 +- usegalaxy.org.au/convert_formats.yml | 22 +- usegalaxy.org.au/deeptools.yml | 96 +++---- usegalaxy.org.au/dna_metabarcoding.yml | 10 +- usegalaxy.org.au/emboss.yml | 6 +- usegalaxy.org.au/epigenetics.yml | 2 +- usegalaxy.org.au/fastafastq.yml | 76 +++--- usegalaxy.org.au/fastq_quality_control.yml | 34 +-- usegalaxy.org.au/filter_and_sort.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 26 +- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 26 +- usegalaxy.org.au/graphdisplay_data.yml | 54 ++-- usegalaxy.org.au/hca_single_cell.yml | 2 +- usegalaxy.org.au/hicexplorer.yml | 10 +- usegalaxy.org.au/imaging.yml | 14 +- usegalaxy.org.au/ivar.yml | 64 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 6 +- usegalaxy.org.au/machine_learning.yml | 18 +- usegalaxy.org.au/mapping.yml | 36 +-- usegalaxy.org.au/metagenomic_analysis.yml | 68 ++--- usegalaxy.org.au/mothur.yml | 4 +- usegalaxy.org.au/multiple_alignments.yml | 38 +-- usegalaxy.org.au/nanopore.yml | 38 +-- usegalaxy.org.au/none.yml | 36 +-- usegalaxy.org.au/phylogenetics.yml | 82 +++--- usegalaxy.org.au/picard.yml | 6 +- usegalaxy.org.au/proteomic_ai.yml | 6 +- usegalaxy.org.au/proteomics.yml | 158 +++++------ usegalaxy.org.au/rad_seq.yml | 68 ++--- usegalaxy.org.au/rna_seq.yml | 140 +++++----- usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 44 +-- usegalaxy.org.au/send_data.yml | 4 +- usegalaxy.org.au/single_cell.yml | 38 +-- usegalaxy.org.au/statistics.yml | 20 +- usegalaxy.org.au/text_manipulation.yml | 34 +-- usegalaxy.org.au/variant_calling.yml | 30 +-- usegalaxy.org.au/vcfbcf.yml | 250 +++++++++--------- 96 files changed, 1957 insertions(+), 1958 deletions(-) delete mode 100644 requests/blobtoolkit.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 997960c6e..d7ed07648 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -5292,3 +5292,4 @@ Install 1302 19/07/23 21:08:31 rmassbank True Installed recetox 0b28816c1c2c lat Install 1304 20/07/23 11:52:47 ramclustr True Installed recetox 9b716db0a786 latest 5/5 5/5 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1304/install_log.txt Install 1304 20/07/23 12:01:32 recetox_xmsannotator_advanced True Tests failed recetox cfd2e19f00a9 latest Staging Testing 0/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1304/install_log.txt Install 1304 20/07/23 12:07:56 riassigner True Errored recetox 4e47a0fa9287 latest Staging Installation Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1304/install_log.txt +Install 1306 27/07/23 08:27:32 blobtoolkit True Tests failed bgruening 53dd00a4ab68 53dd00a4ab68 Staging Testing 0/4 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1306/install_log.txt diff --git a/requests/blobtoolkit.yml b/requests/blobtoolkit.yml deleted file mode 100644 index e8c3fa210..000000000 --- a/requests/blobtoolkit.yml +++ /dev/null @@ -1,8 +0,0 @@ -tools: -- name: blobtoolkit - owner: bgruening - revisions: - - 53dd00a4ab68 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - diff --git a/staging.usegalaxy.org.au/annotation.yml b/staging.usegalaxy.org.au/annotation.yml index 20c9592a1..3a233c4d6 100644 --- a/staging.usegalaxy.org.au/annotation.yml +++ b/staging.usegalaxy.org.au/annotation.yml @@ -4,9 +4,9 @@ tools: revisions: - 78c75f134c16 - 6e9aea89e388 - - 4efdca267d51 - 3f3e247c053d - c2ef298da409 + - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,20 +36,20 @@ tools: - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 - - 1aae04680c4b - f29602ae449e + - 1aae04680c4b + - fe3ca740a485 - 4f2967b27e67 - - 44018dd6b447 - 133f36c29579 + - 44018dd6b447 - b5d8e5475247 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -64,8 +64,8 @@ tools: owner: bgruening revisions: - 09855551d713 - - 28433faa6e42 - ca6d970d931c + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -97,8 +97,8 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -124,32 +124,32 @@ tools: - name: funannotate_clean owner: iuc revisions: + - 30fb23d4c31c - 73428a792541 - a230ea445788 - - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 563a19373357 - - 494f0bb4a993 - 30f08d74024f + - 494f0bb4a993 + - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 - 7abc5f6dd595 + - 2bba2ff070d9 - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 - d3af38b9c7e1 + - b3cf4684e9c7 - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -163,8 +163,8 @@ tools: owner: iuc revisions: - 2aea122fbd25 - - 07d7991bf205 - 79261884facd + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -176,9 +176,9 @@ tools: - name: goseq owner: iuc revisions: + - ef2ad746b589 - 8b3e3657034e - 43798b4caee0 - - ef2ad746b589 - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -204,9 +204,9 @@ tools: - name: interproscan owner: bgruening revisions: + - 74810db257cc - 98cafcbd2578 - c55643c3d813 - - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -232,8 +232,8 @@ tools: owner: iuc revisions: - 370c210d9541 - - d46d803ca6cc - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 @@ -264,11 +264,11 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 + - eaee459f3d69 + - bf68eb663bc3 - d643e3b03500 - a17498c603ec - - bf68eb663bc3 - - eaee459f3d69 + - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -287,8 +287,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: rgi @@ -306,21 +306,21 @@ tools: - name: snpeff owner: iuc revisions: - - 268d162b9c49 + - 5a29ab10dba6 - cfcf33df7fc0 + - 5b80f544c67f - 68693743661e - - 5a29ab10dba6 + - 268d162b9c49 - 5c7b70713fb5 - - 5b80f544c67f - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: + - 09d6806c609e - 2b3e65a4252f - 5fab4f81391d - - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -344,14 +344,14 @@ tools: - name: tbprofiler owner: iuc revisions: - - ba6f87115e13 - 2c68b0c38785 + - ba6f87115e13 + - e1a9d6fd258d - 37213cf56392 - - 45083d070fb8 - ac8250086ac3 - - 037a11682176 - - e1a9d6fd258d - 200c378d85f3 + - 45083d070fb8 + - 037a11682176 - 809dfc93d593 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/assembly.yml b/staging.usegalaxy.org.au/assembly.yml index ac49de98a..c1e9c61c1 100644 --- a/staging.usegalaxy.org.au/assembly.yml +++ b/staging.usegalaxy.org.au/assembly.yml @@ -2,10 +2,10 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - 553bfe8bd0b5 - - 0e93176640ac - 841084c5fc46 + - 0e93176640ac + - 7547fcab5d19 - 890b794c997d - fa5259cc561b - 8f1b150a2487 @@ -14,11 +14,11 @@ tools: - name: bandage owner: iuc revisions: - - b2860df42e16 - ddddce450736 + - b2860df42e16 + - 067592b6b312 - b9e31c5c01c7 - 21e491ad532a - - 067592b6b312 - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -31,39 +31,45 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - a7f16f24e9a1 - - 3371c5bdc17a - 5258e18bbe23 - - 22286dab5aa1 - faee8629b460 + - 3371c5bdc17a + - 22286dab5aa1 + - a7f16f24e9a1 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: blobtoolkit + owner: bgruening + revisions: + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - e4bd1e99bacf - - 602fb8e63aa7 - - 41030a6c03b7 - - 4048d82f0c88 - 5ecdeca79a0d - - cf13a1e03e5b - - 2dd755c1c6ff - 1e62c28ba91d - - 0d243f458b53 - 46ae58b1d792 + - 41030a6c03b7 - f18f0b887c31 + - e824f5d958d0 - bb935709506a - 94170eee0ad8 + - e4bd1e99bacf - 1440ae06552f - - e824f5d958d0 + - 602fb8e63aa7 + - cf13a1e03e5b + - 0d243f458b53 + - 4048d82f0c88 + - 2dd755c1c6ff tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - 86f150c8019d - - 5732f959936a - c5b7390290b1 + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -76,11 +82,11 @@ tools: owner: bgruening revisions: - e27815e82dd4 - - 276f5d8712d5 - - 1ce9b1d72ec3 + - 3ee0ef312022 - 8d4f03b5fe9d + - 1ce9b1d72ec3 - cb8dfd28c16f - - 3ee0ef312022 + - 276f5d8712d5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope @@ -94,9 +100,9 @@ tools: - name: getorganelle owner: iuc revisions: + - 06bcf65179fb - 8b330a577046 - 611219887a48 - - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats @@ -117,18 +123,18 @@ tools: - name: hifiasm owner: bgruening revisions: - - da9d8bf98802 - - f3c89da3af16 - - 71740308d412 - - 045c7c3d8e59 + - 5bec28269d95 + - 5f625c63b8bc + - 2061fb3b81b4 - 366a11d316a7 + - da9d8bf98802 - 3f7be05a1597 - - 5f625c63b8bc - - 9ef6920c3089 - - 5bec28269d95 - - ec9e21e9c71b - 6505bd37670d - - 2061fb3b81b4 + - ec9e21e9c71b + - 045c7c3d8e59 + - f3c89da3af16 + - 9ef6920c3089 + - 71740308d412 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -146,9 +152,9 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - - 7518ee87b53d - de387b2b2803 + - 7518ee87b53d + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury @@ -162,21 +168,21 @@ tools: - name: meryl owner: iuc revisions: + - eadfd71dde37 - 29dabd8db6f2 - 51c2360aa807 - - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - eb7a370f6588 + - e731ea24e48d - fd128c111ab0 + - 3ca2d2a9068c - 2ecf5a570907 - - e731ea24e48d - f338e9942b27 - 606b09cc9860 - - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -188,11 +194,11 @@ tools: - name: miniasm owner: iuc revisions: - - 80d1250bd5fd - - a7b889b90140 - - 8dee0218ac7d - - 73a3846701e1 - 8b6d0d85252b + - 73a3846701e1 + - 8dee0218ac7d + - a7b889b90140 + - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -204,9 +210,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - - 15200570e926 - 64a1c751d99b + - 15200570e926 + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -218,73 +224,73 @@ tools: - name: pretext_map owner: iuc revisions: - - 02831bf9e95f - dfb8a4497339 - - 8fef980d48b5 + - 02831bf9e95f - d256a51a656b - 2b16ba799da9 - bbe19ef04a74 + - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - e9bd16ba5ebd - 76d4cbefff85 + - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 342a1d1fed7b - - 72472698a2df + - 875d0f36d66f - 3061c8b029e5 - - 675488238c96 + - 72472698a2df + - 59db8ea8c845 - ebb0dcdb621a - - 875d0f36d66f - 7594365c546b - - 59db8ea8c845 + - 675488238c96 - 6fcbee531de6 + - 342a1d1fed7b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e - 39bed8de8017 - - e100a765370e - d865b62f501c - - cd06929b224b - a199cd7ac344 + - e100a765370e + - cd06929b224b + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: + - f11b994b7eb2 - 2b2a352488fa - 33b7d8481a76 - 3edba9afc9bc - - f11b994b7eb2 - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - - e122f9101584 - - 1d06c8b38e77 - ef69617ecb42 - 378e55aeeb25 + - e122f9101584 + - 1d06c8b38e77 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - ba7b0f11e470 - - ab5b7f6b7198 - f77f7a7f3b83 + - ab5b7f6b7198 - 9a22227bb6d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -297,140 +303,140 @@ tools: - name: shovill owner: iuc revisions: + - f698c7604b3b - d9f6a00b6db7 - - 865119fcb694 - ad80238462c1 - - 196a599ec43d - - f698c7604b3b + - 865119fcb694 - 83ead2be47b2 + - 196a599ec43d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 5a0ddb4dc3a4 - 5e0825476fb7 - 24e471d13fe9 - - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 - 904bf932cf78 + - 7490b213baa9 - 1fc82fe7ebef + - 051fd2db8a27 - 1bb12736175c - - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 34305b013402 - - d6e617c4e338 - 808b3a0a6716 - ad8b536d1caa + - d6e617c4e338 + - 34305b013402 - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - b8002c3f7141 + - 6b5a5842531e - e5a3b75a271f + - 8d4b90bf9caf - 21da31ed41a1 - - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 - - 328aa71f0f3c - 86f66ab58e14 - - 2a10645aeadd + - 328aa71f0f3c + - 9de69775f512 - f1532cb33c75 + - 2a10645aeadd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 340bc17f49cf - - 6aad515a5270 + - e41dcb0e913b - 1708851f8804 - 85fb02c43042 - - e41dcb0e913b + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 249f6a28c751 - - d159735a6a9f - b65a43f70b99 - - b3490b036c5a + - d159735a6a9f + - 249f6a28c751 - d5fb354f745d + - b3490b036c5a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - b7829778729f - - 9006e5836729 - - d2d1df21dfb9 - dd7ad84f3943 - 33368fec3b70 + - 9006e5836729 - 7897763d14ec + - d2d1df21dfb9 + - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - 505a9833ab5d - 189e837009c9 - - 6f4c8ad6ea01 - ced385aa976d - - 505a9833ab5d + - 6f4c8ad6ea01 - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 9ded6109434a - d40ed4eb0c0e - - 19bdfd1e6fe3 - - 356afed970b4 + - 9ded6109434a - e59bee4565b3 + - 356afed970b4 + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - b23249f81bc4 - - 6dd935e4984b + - 4688ae3b49b5 - 80a17897564d - ebd801e712bc - - 4688ae3b49b5 + - b23249f81bc4 + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b5e35a2ca4f3 - - 59bd28f6265d - - 937ea677d437 - b64696992ee9 + - 937ea677d437 + - 59bd28f6265d - cb1e3db43020 + - b5e35a2ca4f3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - 05bd7504fdb2 - 383bb5ad32e2 - 6015aa0303f2 - cb4768eeca3b - - 05bd7504fdb2 - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -438,29 +444,29 @@ tools: owner: iuc revisions: - 9e3e80cc4ad4 - - 0a3a602cd1e3 - - e92675014ac9 - 6e26c9afd301 + - e92675014ac9 - d10bdad2fd17 + - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 08256557922f - - 5da9a0e2fb2d - 8d09f8be269e + - 5da9a0e2fb2d - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - - d81360ea69d8 + - 4a53b89fa703 - 37d88f41c810 - 0e2b4e3f9ca1 - - 4a53b89fa703 + - 82398ba86ba7 + - d81360ea69d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/staging.usegalaxy.org.au/bacterial_typing.yml b/staging.usegalaxy.org.au/bacterial_typing.yml index b08d02e83..3ed5e7b4a 100644 --- a/staging.usegalaxy.org.au/bacterial_typing.yml +++ b/staging.usegalaxy.org.au/bacterial_typing.yml @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: - - 31812e7a1315 - ded48b36f3b7 - - 8e8dc9a1e3e5 - 1f5641a52664 + - 8e8dc9a1e3e5 + - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 17fcac7ddf54 - - 5c8ff92e38a9 - 24a7a95867b0 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bb_tools.yml b/staging.usegalaxy.org.au/bb_tools.yml index 26700f340..434a88153 100644 --- a/staging.usegalaxy.org.au/bb_tools.yml +++ b/staging.usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 204a131e47db - - a9c9d768b751 - 159b04e36791 + - a9c9d768b751 + - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bed.yml b/staging.usegalaxy.org.au/bed.yml index 894713796..181769236 100644 --- a/staging.usegalaxy.org.au/bed.yml +++ b/staging.usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - 87ee588b3d45 - - 589e7e57fd6d - - 07e8b80f278c - - e19bebe96cd2 + - b28e0cfa7ba1 + - dde39ba9c031 - a8eabd2838f6 - - a1a923cd89e8 - - ce3c7f062223 - 0a5c785ac6db - - b28e0cfa7ba1 + - a1a923cd89e8 + - e19bebe96cd2 + - 07e8b80f278c + - 87ee588b3d45 + - 589e7e57fd6d - a68aa6c1204a - - dde39ba9c031 + - ce3c7f062223 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/blast.yml b/staging.usegalaxy.org.au/blast.yml index 35cec9280..eef0d632c 100644 --- a/staging.usegalaxy.org.au/blast.yml +++ b/staging.usegalaxy.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: + - 54f751e413f4 - 62c9df8382c2 - f921014aba5a - 1e3323a44643 - - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,12 +23,12 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - acf4e47b734c - - 2889433c7ae1 - - 0e3cf9594bb7 - - 5edc472ec434 - e25d3acf6e68 + - 5edc472ec434 + - 0e3cf9594bb7 + - 2889433c7ae1 + - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.usegalaxy.org.au/chemicaltoolbox.yml b/staging.usegalaxy.org.au/chemicaltoolbox.yml index 73b18440b..989383c8e 100644 --- a/staging.usegalaxy.org.au/chemicaltoolbox.yml +++ b/staging.usegalaxy.org.au/chemicaltoolbox.yml @@ -3,12 +3,12 @@ tools: owner: chemteam revisions: - f4230f116196 + - c8cdde00b105 - 27ee142314a9 - - 095ad4d096d1 - - 710301bc46fa - 6ca543ec1bf8 - da6bd1975a71 - - c8cdde00b105 + - 710301bc46fa + - 095ad4d096d1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -74,8 +74,8 @@ 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: enumerate_charges @@ -100,63 +100,63 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 3b8a9d5ced85 - 79cfd9ead848 - - 0fac8e2afc13 - 88076940fa94 - bfb65cb551d8 - - 3b8a9d5ced85 + - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - d532b7e5f64b - 55918daa5651 - - f5d979cb4b54 + - b46d4b4d995c + - d532b7e5f64b - 715cd0e87781 + - f5d979cb4b54 - eb6564a60136 - - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 - 5579659312e6 - - d2f955aea23a + - f26afd1b7104 - fdf2cc80adb5 - 97872d87ba80 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - bc31d02be922 - 319a28774da9 - d1d0efda35c0 - - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: + - 2c349b027a01 - 070e3ecc3fda - 4da9ee404eab - - 2c349b027a01 - - ed736e6eee39 - cac1886249a2 + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - d1f803b5943c + - 525ca7c8065f + - 807aa4c9293d + - 2e219a2d9327 - da8753545526 + - c0c9a5024177 + - d1f803b5943c - f197e34c33a9 - 73008ef1f487 - - 2e219a2d9327 - - 807aa4c9293d - - c0c9a5024177 - - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate @@ -164,20 +164,20 @@ tools: revisions: - 27ea4e1a3f95 - c4fbab8e03c5 - - 7568ae18908a + - 2c8ed1b52bf7 - 61094e01eff9 - 1809414a9454 - - 2c8ed1b52bf7 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: + - ccfbd956a2d3 + - ba83f0923369 - 730ef07b90ae - d7ec25187599 - - ccfbd956a2d3 - 79e8ab8f1e81 - - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -196,9 +196,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - e6011617c748 - 1400d1977e7b + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -229,9 +229,9 @@ tools: owner: bgruening revisions: - 85fad59f8168 - - d4c67ced6abc - - bf99565cec1f - 9b48456a96fe + - bf99565cec1f + - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.usegalaxy.org.au/chip_seq.yml b/staging.usegalaxy.org.au/chip_seq.yml index cc3d12efe..4cbd40f66 100644 --- a/staging.usegalaxy.org.au/chip_seq.yml +++ b/staging.usegalaxy.org.au/chip_seq.yml @@ -29,10 +29,10 @@ tools: - name: macs2 owner: iuc revisions: + - 495a4173006f - 640d3af5d833 - - 424aefbd7777 - f5d67c722d67 - - 495a4173006f + - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -52,8 +52,8 @@ tools: owner: devteam revisions: - 4a14714649b4 - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.usegalaxy.org.au/collection_operations.yml b/staging.usegalaxy.org.au/collection_operations.yml index 5bb9beae0..6fdbbbd6b 100644 --- a/staging.usegalaxy.org.au/collection_operations.yml +++ b/staging.usegalaxy.org.au/collection_operations.yml @@ -2,37 +2,37 @@ 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 - - 830961c48e42 - 90981f86000f + - 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_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - 0046692724f9 + - 6cbe2f30c2d7 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.usegalaxy.org.au/convert_formats.yml b/staging.usegalaxy.org.au/convert_formats.yml index b87306434..7114614e2 100644 --- a/staging.usegalaxy.org.au/convert_formats.yml +++ b/staging.usegalaxy.org.au/convert_formats.yml @@ -8,33 +8,33 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 5e1240a87bcb - 0b3c3ad92827 - - a3b86937ead6 - 4a6ee918c13a + - 5e1240a87bcb + - f3a19509108a - e3cbd2287f63 + - a3b86937ead6 - 367b1ed91207 - - f3a19509108a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: + - 54ccb7e1f49a - bd46669113b9 - - 501c21cce614 - - 1b5fc03380d4 - - 72ed72122deb - - 33c99804a32f - 584008e574b2 - e525f9ffb9ac - - 54ccb7e1f49a + - 33c99804a32f + - 1b5fc03380d4 + - 501c21cce614 + - 72ed72122deb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - 11c3eb512633 - a0d092f27fdf + - 11c3eb512633 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -46,8 +46,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -60,8 +60,8 @@ tools: - 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: fml_gff3togtf @@ -73,8 +73,8 @@ 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 @@ -105,32 +105,32 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 8190f6083c0d + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 63769c4217a7 - - 26c6706bfb07 - 92ac8e086317 - - 19e45916daf9 - b9b385097f13 + - 63769c4217a7 + - 19e45916daf9 + - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.usegalaxy.org.au/deeptools.yml b/staging.usegalaxy.org.au/deeptools.yml index 137724a4d..370f6fdd1 100644 --- a/staging.usegalaxy.org.au/deeptools.yml +++ b/staging.usegalaxy.org.au/deeptools.yml @@ -4,119 +4,119 @@ tools: revisions: - 29451af70c52 - e821645ef8fc - - 5f6d123679f4 - - 268e91e540ee - de72ba3ed6f2 - a1ca9bccc7f2 + - 5f6d123679f4 + - 268e91e540ee tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 2d2cf5c1ea8a - - 5d11599b8a7d + - 0e143b4c3987 - 12af64f93288 - - 7a7fd0f5f15d - bb1e4f63e0e6 - - 0e143b4c3987 + - 7a7fd0f5f15d + - 2d2cf5c1ea8a + - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c + - 7c1beb6d6eca - dc059492a995 - - 1d848bc4585f - 195e98217334 - - 7c1beb6d6eca + - 81b1e3e1fc6c + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - a67ac707496a - 26e7304d6737 - - 93eb012d9eed - - bfff7454b59a + - a67ac707496a - 3d211717a775 + - 93eb012d9eed - 71aa86af6762 + - bfff7454b59a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - b8858746dc1f - - 2bc10a9ca58b - - 29fcfd36e90a - - dd0b7398bb96 - 56d5b797ce84 + - dd0b7398bb96 + - 29fcfd36e90a + - 2bc10a9ca58b - 5be24eba848d + - b8858746dc1f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 - ee3a1b0f45f1 - - 7ef978dc1b8a + - 7e6bcd2e5128 - 9384cd033f30 - c3e012dfe21f - 72bfafe3330b + - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fd1275e01605 - - b73e213add0c - - d9a637e83828 - 9470f29702f8 + - d9a637e83828 + - fd1275e01605 + - 167788df3b46 - 514fa53b5efb + - b73e213add0c - fb9cf9c97ec4 - - 167788df3b46 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - 5bffaa8354a1 - - 2c37ce318bc3 - - 86febdcc4283 - - a02cfa31e9cb - ca0616bb2cdf + - a02cfa31e9cb + - 86febdcc4283 - c34d11ea4ba6 + - 2c37ce318bc3 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 192ef85c0b0b + - 004aea905d4d - 2d466b530754 - - 78f405266706 - 69a8621ca2f0 - - 192ef85c0b0b - 1fcb7adc39b8 - - 004aea905d4d + - 78f405266706 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 + - 459cfa861f0b + - 2f9e4843f480 + - d9ce4897dbb2 - d580d6acd1df + - 9ecba5e225a6 - 3c9f0c486cca - db940c262830 - - d9ce4897dbb2 - - 459cfa861f0b - - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 2c66e43f1c86 + - fbe773640707 - 32e451def88c - f264afa9fa6f - - fbe773640707 + - 2c66e43f1c86 - fd408d755394 - bd7db9e2f2cb tool_panel_section_label: DeepTools @@ -124,10 +124,10 @@ tools: - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 + - 7fda5607e777 - 56bce3c82278 + - 4e12ea27f788 - 7e361d147872 - - 7fda5607e777 - 9368fbc49c8b - 3b9d990a0a0e tool_panel_section_label: DeepTools @@ -135,44 +135,44 @@ tools: - name: deeptools_plot_enrichment owner: bgruening revisions: - - b1779366c8e9 + - d9114ef1c8a5 + - e65d16fb2724 - 94ca68515826 - - ce4ce3316f74 - c03c3384cd81 - - e65d16fb2724 - - d9114ef1c8a5 + - ce4ce3316f74 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - d57251071381 - - 23f7c5f1fdaf - f8fc4e5aff9d - 793665fff0f8 - - 2da482e408b8 - b88ebb3672a1 + - 2da482e408b8 + - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 - ba6efa77fb79 - - a4dfb122e52b - c60570fa602f + - a4dfb122e52b - 512155688d98 - 010e58e9d822 + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 00d869ea03a1 - - 38e3f226248b + - c899e0ccff8c - aa200e4f3939 + - 38e3f226248b + - 00d869ea03a1 - 4d678170d29b - - c899e0ccff8c - 69264da0ce77 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,8 +181,8 @@ tools: revisions: - d806504e96d9 - c361b12d207a - - aac8444d6681 - - a2d70c4fd406 - 10301d137111 + - a2d70c4fd406 + - aac8444d6681 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/dna_metabarcoding.yml b/staging.usegalaxy.org.au/dna_metabarcoding.yml index 82683792b..e4e99fa23 100644 --- a/staging.usegalaxy.org.au/dna_metabarcoding.yml +++ b/staging.usegalaxy.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - f82cefbbcea5 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -16,8 +16,8 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - 374fd9feb032 + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -30,36 +30,36 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 83fbdf93d51e - 94f412098ac8 + - 83fbdf93d51e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 3bf57dadf7cd - 76e69de726b2 + - 3bf57dadf7cd tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - e614dcabd870 + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat owner: iuc revisions: - - 723a93febe89 - 39320fee9d70 + - 723a93febe89 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/staging.usegalaxy.org.au/emboss.yml b/staging.usegalaxy.org.au/emboss.yml index 68ea85a08..df5ff4121 100644 --- a/staging.usegalaxy.org.au/emboss.yml +++ b/staging.usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - 63dd26468588 - 832c20329690 - ce385837c160 - - 63dd26468588 - dba489bfcd62 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/epigenetics.yml b/staging.usegalaxy.org.au/epigenetics.yml index 6ace8e3e5..5d22aeed0 100644 --- a/staging.usegalaxy.org.au/epigenetics.yml +++ b/staging.usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - 29bdbc353f20 - 62f5fab76dfb - - d82648ad25a3 + - 29bdbc353f20 - 6da3972210ee + - d82648ad25a3 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.usegalaxy.org.au/fastafastq.yml b/staging.usegalaxy.org.au/fastafastq.yml index 7b975d622..cb51b5cd4 100644 --- a/staging.usegalaxy.org.au/fastafastq.yml +++ b/staging.usegalaxy.org.au/fastafastq.yml @@ -8,21 +8,21 @@ tools: - name: cutadapt owner: lparsons revisions: + - 49370cb85f0f - c053d4cad713 - - 135b80fb1ac2 - 288f97432497 - - 5915ea1ec9b1 - 4e5056fefd88 - - 660cffd8d92a - - 093678460093 - - 8c0175e03cee - - e4691e1589d3 - - 44e2cc14f75b - de6cebe3c043 - - 49370cb85f0f - - 8665bcc8b847 + - 44e2cc14f75b - 48f587c13075 + - 660cffd8d92a - c4b82dce8335 + - 8665bcc8b847 + - e4691e1589d3 + - 8c0175e03cee + - 135b80fb1ac2 + - 5915ea1ec9b1 + - 093678460093 - c5e2e5902201 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,8 +49,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 25b8736c627a - 717aee069681 + - 25b8736c627a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -62,15 +62,15 @@ 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 + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -90,9 +90,9 @@ tools: - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - - 0dbb995c7d35 - 9c620a950d3a + - 0dbb995c7d35 + - 56022eb50bbd - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,8 +105,8 @@ tools: - name: fastp owner: iuc revisions: - - 1d8fe9bc4cb0 - 65b93b623c77 + - 1d8fe9bc4cb0 - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,8 +154,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -175,9 +175,9 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - 35e38452bb3f - 249c8393f2d4 + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -196,15 +196,15 @@ 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 owner: devteam revisions: - - 33794bdb7fe0 - b63b2bfb3ea3 + - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -216,16 +216,16 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 - - 567d5b3c52b1 - 09070cacefd8 + - 567d5b3c52b1 + - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - 8abdedf55101 + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -246,25 +246,25 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - - 02f8a17a4ebd - b29d37ca9e41 + - 02f8a17a4ebd + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: + - e246088b6e34 - 6027ef51ef91 - 0c2907307ba4 - - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 61b4cedc8934 - 547e8d00f11c - 377ac2829eac - - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -282,8 +282,8 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -295,8 +295,8 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -314,15 +314,15 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - bf04bd405d5b + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -334,10 +334,10 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 - - b557acca0b56 - 8250ea3a1501 + - b557acca0b56 - 24013bf85a6f + - e654095ab143 - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -356,12 +356,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 27ac32a22ad2 - - 7accf7407811 - 9fa7803d1c51 + - f3759eec3018 - 828dba98cdb4 - 6a675c3aa610 - - f3759eec3018 + - 27ac32a22ad2 + - 7accf7407811 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.usegalaxy.org.au/fastq_quality_control.yml b/staging.usegalaxy.org.au/fastq_quality_control.yml index 401827309..fb840b420 100644 --- a/staging.usegalaxy.org.au/fastq_quality_control.yml +++ b/staging.usegalaxy.org.au/fastq_quality_control.yml @@ -2,9 +2,9 @@ tools: - name: fastq_quality_filter owner: devteam revisions: + - e41385662e5e - 7b4468117008 - ce9cd02d5b88 - - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -17,13 +17,13 @@ tools: - name: fastqc owner: devteam revisions: - - 9da02be9c6cc - - 5ec9f6bceaee - - e7b2202befea - - 3d0c7bdf12f5 - ff9530579d1f - - 2b0c9d9fc6ca - f2e8552cf1d0 + - 3d0c7bdf12f5 + - e7b2202befea + - 2b0c9d9fc6ca + - 9da02be9c6cc + - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -36,8 +36,8 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 - 18a51655db17 + - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics @@ -50,23 +50,23 @@ tools: - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - 41b2ad601cf0 + - a72af9de6bf5 - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 75c93c70d094 + - 3d93dd18d9f8 - 5e33b465d8d5 - f7985e0479b9 - - abfd8a6544d7 - - 9a913cdee30e - - 3d93dd18d9f8 - b2f1f75d49c4 - - bf675f34b056 + - 75c93c70d094 - 1c2db0054039 + - 9a913cdee30e + - abfd8a6544d7 + - bf675f34b056 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/staging.usegalaxy.org.au/filter_and_sort.yml b/staging.usegalaxy.org.au/filter_and_sort.yml index 5b44a1c25..7946b577d 100644 --- a/staging.usegalaxy.org.au/filter_and_sort.yml +++ b/staging.usegalaxy.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 diff --git a/staging.usegalaxy.org.au/gemini_tools.yml b/staging.usegalaxy.org.au/gemini_tools.yml index 892adbe86..4fad859ac 100644 --- a/staging.usegalaxy.org.au/gemini_tools.yml +++ b/staging.usegalaxy.org.au/gemini_tools.yml @@ -2,23 +2,23 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - f2f3bc622a16 - 8f53b238a360 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,29 +31,29 @@ 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 owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump 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 @@ -79,16 +79,16 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 2550239feed5 - 184aa4e686e2 + - 2550239feed5 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -122,23 +122,23 @@ tools: - name: gemini_query owner: iuc revisions: - - 840fb4850be3 - da74170c55c7 + - 840fb4850be3 - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -151,21 +151,21 @@ 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 owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/genome_editing.yml b/staging.usegalaxy.org.au/genome_editing.yml index 301093442..f729cfa4c 100644 --- a/staging.usegalaxy.org.au/genome_editing.yml +++ b/staging.usegalaxy.org.au/genome_editing.yml @@ -2,29 +2,29 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/staging.usegalaxy.org.au/get_data.yml b/staging.usegalaxy.org.au/get_data.yml index dac3357c2..55f7411fa 100644 --- a/staging.usegalaxy.org.au/get_data.yml +++ b/staging.usegalaxy.org.au/get_data.yml @@ -2,45 +2,45 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - e9df53a75f3c - - 983bf725dfc2 - c1b437242fee + - 983bf725dfc2 + - e9df53a75f3c - b39347891609 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 1c58de56d587 - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 83c7d564b128 - - c441583adae5 - - e08a7ad4378b - - 1790dcf3c32d - - 6ea73833cf67 - 7068f48d0ef9 - 5e6237d58b0c + - aad3885b3216 + - 83c7d564b128 + - 653e89d73fc4 - 9a776b080193 - 4df8de2d0e48 - - 653e89d73fc4 - - f5ea3ce9b9b0 - 69ebb7f46e45 - - aad3885b3216 + - f5ea3ce9b9b0 + - 1790dcf3c32d + - c441583adae5 + - 6ea73833cf67 + - e08a7ad4378b tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 7863f1abcdda - 34758ab8aaa4 - - 75b3b3d0adbf - 9aaa46d45472 - - 7863f1abcdda + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface diff --git a/staging.usegalaxy.org.au/graphdisplay_data.yml b/staging.usegalaxy.org.au/graphdisplay_data.yml index aeedb318e..a83a9a960 100644 --- a/staging.usegalaxy.org.au/graphdisplay_data.yml +++ b/staging.usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - ae9994cf526f + - 290a11559985 + - fd59d783248a - 4b519282a05b - - 7f13dc906cb9 - df7356989ac1 - - fd59d783248a + - ae9994cf526f + - a64dc31ab7f2 + - 7f13dc906cb9 - c4bde687c846 - 740057a5126d - - 290a11559985 - - a64dc31ab7f2 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -41,31 +41,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - 3b37b1b1c3a7 - ca7cb0eaad62 + - 3b37b1b1c3a7 - '566197475670' + - 53460afd5115 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 10515715c940 + - d3a9e32672ec + - 391a4cc45fea - 3d059e9c2fba + - 10515715c940 - da4c086cff5b - - 391a4cc45fea - - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - 1acf88921176 - e3a675da7fd0 - 3b12bf9b4b87 + - 299307abd804 - 5fe1dc76176e - d0fc8b746d57 + - 1acf88921176 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -77,15 +77,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - cf1df6b2220a - 5d6f8f0bef7c + - cf1df6b2220a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - a490b70e46fc - 8f62f666dcb6 + - a490b70e46fc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -98,17 +98,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 836d1aa3e89a - - 17359b808b01 - a6e57ff585c0 - - 2bb2e07a7a21 - - 4542035c1075 - - ca2def38369c - - 1cfc579079a6 - - 6cd09d7b5f37 + - 17359b808b01 - 112eb40ba6cf - fd5dbf0f732e + - 2bb2e07a7a21 + - ca2def38369c - 667e17248bfe + - 836d1aa3e89a + - 4542035c1075 + - 6cd09d7b5f37 + - 1cfc579079a6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -140,15 +140,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb 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 @@ -173,14 +173,14 @@ tools: - name: pygenometracks owner: iuc revisions: - - 4ac4e7083b7e - - 14e7c35f3d00 - - 360df4999907 - - 7dd841a32245 - 326a3db8d9d1 + - 360df4999907 + - 2824d77cd8f8 + - 14e7c35f3d00 + - 4ac4e7083b7e - 59fd173ac850 - a1abfa420d9d - - 2824d77cd8f8 + - 7dd841a32245 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot @@ -200,7 +200,7 @@ 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.usegalaxy.org.au/hca_single_cell.yml b/staging.usegalaxy.org.au/hca_single_cell.yml index 650427647..82e8916e7 100644 --- a/staging.usegalaxy.org.au/hca_single_cell.yml +++ b/staging.usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph diff --git a/staging.usegalaxy.org.au/hicexplorer.yml b/staging.usegalaxy.org.au/hicexplorer.yml index f5ae5ee6b..ff8924d1f 100644 --- a/staging.usegalaxy.org.au/hicexplorer.yml +++ b/staging.usegalaxy.org.au/hicexplorer.yml @@ -2,40 +2,40 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 921a2da49a0c - - 29f66c353bcb - 9edf8894a22d + - 29f66c353bcb + - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 78fb5e286609 - - 5746d61f0a91 - d404277cc87a + - 5746d61f0a91 + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - 4d511437b1e5 + - 9e357a8b2ec3 - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - 41dbf4d162a2 - 0ba4f56a3613 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 9939786dd9c9 - - 7babd8a46fe0 - 5308ca68ef3d + - 7babd8a46fe0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/imaging.yml b/staging.usegalaxy.org.au/imaging.yml index 195d49e97..521dbacb2 100644 --- a/staging.usegalaxy.org.au/imaging.yml +++ b/staging.usegalaxy.org.au/imaging.yml @@ -53,8 +53,8 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - 0e4dccaafef5 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -80,8 +80,8 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -94,8 +94,8 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f8fa0f6718a3 - d0178bdcd00e + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color @@ -108,8 +108,8 @@ tools: - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - 993faa34333b + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -129,36 +129,36 @@ tools: - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b 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 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - e972e07c7845 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 980aed9e8fd5 - 407925835dd9 + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape @@ -191,8 +191,8 @@ tools: - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile diff --git a/staging.usegalaxy.org.au/ivar.yml b/staging.usegalaxy.org.au/ivar.yml index bc333d924..dfcb07477 100644 --- a/staging.usegalaxy.org.au/ivar.yml +++ b/staging.usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: + - f362150bef41 - e319b5b65879 - - 17f911830a8c - - 1069f6db0a0e - d6e72da3ec35 + - 17f911830a8c - a38934e303b9 - - e4ee04da1c19 - 78bbd17d0703 - - f362150bef41 + - e4ee04da1c19 + - 1069f6db0a0e - 3e4f434a69c6 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 2b95d5c04908 - 0135f1d487a0 - - 9537184d421f - 72ddd32392cd - - 7fe36019c073 - - c88553ec696e - 1ef5b6e3e09d + - 9537184d421f + - c88553ec696e - 8f8df367470d + - 7fe36019c073 - f91cfb73d369 + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 + - fafb3d685fa9 - ad0dc9f4c9e2 - d7e79eb3bcb3 - - fafb3d685fa9 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: + - 7f1cfa4c0e32 - 43aac8d29685 - - ee29337f905c - - 8c05afb547fa - - 3d18f8c3c0f6 - bd2a7d1316b9 - - 9eaadf03e0df - 69797fa273c3 + - 6a1515bb0687 + - 8c05afb547fa - 28a6f1908fcc - ee2beb764a7b + - 9eaadf03e0df - 8d36959b000d + - 3d18f8c3c0f6 + - ee29337f905c - 94df24c6bc00 - - 7f1cfa4c0e32 - - 6a1515bb0687 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - d37ede8589b2 - - 8858fa037a15 + - e3bb03cf207a + - bcaa0d571ce2 + - 9f978da6528a + - c092052ed673 - 364f4ffec275 - - db536ad45f28 + - 5d6ed46cc101 - cb903c9dc33d + - d37ede8589b2 - 0893a1dbb807 - - 5d6ed46cc101 - - bcaa0d571ce2 - - c092052ed673 - - e3bb03cf207a - - 9f978da6528a + - db536ad45f28 + - 8858fa037a15 - 5671e1d3d5ee tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 12d66d0d05ac + - 3b6a16d82c1b - 045d6d00f606 - - c5c9f02b6167 - - 38b91a3190cd - - 49236b03e4fd - - e1a015876aa9 - ed28dd32141c + - 584beffa972b + - 38b91a3190cd - f95f403841ad - - 3b6a16d82c1b + - 12d66d0d05ac + - e1a015876aa9 + - 49236b03e4fd - 230b05597996 - - 584beffa972b + - c5c9f02b6167 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/join_subtract_and_group.yml b/staging.usegalaxy.org.au/join_subtract_and_group.yml index 6bb634fbd..efa8155cb 100644 --- a/staging.usegalaxy.org.au/join_subtract_and_group.yml +++ b/staging.usegalaxy.org.au/join_subtract_and_group.yml @@ -2,10 +2,10 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 + - 0f1724dd59d2 - f198773344e4 - 17e3b698dd52 - - 0f1724dd59d2 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose @@ -13,7 +13,7 @@ tools: revisions: - 374cb875d38a - ac092723240d - - 22c2a1ac7ae3 - ba0c40780ecf + - 22c2a1ac7ae3 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/machine_learning.yml b/staging.usegalaxy.org.au/machine_learning.yml index 84720a0bf..3c6fa6220 100644 --- a/staging.usegalaxy.org.au/machine_learning.yml +++ b/staging.usegalaxy.org.au/machine_learning.yml @@ -14,60 +14,60 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: - - f1b9a42d6809 - e1317b5502fa - b6ef6d0cb6b7 + - f1b9a42d6809 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 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 29e4122c90de - 83228baae3c5 + - 29e4122c90de + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - 1a53edc4b438 + - 841a6cc5fc58 - 53616c8b0865 - a07ab242b0b5 - - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 40f4447733b2 + - 2fc89dcd41c8 - 91c4e3331208 - dc4b5fd604a6 - - 2fc89dcd41c8 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - - e5a5ad882f1f - 301e07345c93 + - c6ae57f774c6 - 25ab6b4e376e + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - 4ed102b922cb - - b7c3e9a3b954 - 02d2be90dedb + - b7c3e9a3b954 - f9639b488779 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/mapping.yml b/staging.usegalaxy.org.au/mapping.yml index 0598c8e65..5afd9549f 100644 --- a/staging.usegalaxy.org.au/mapping.yml +++ b/staging.usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - a6d65b0c67af - - 017aba02828d - - 03e9b2fbc005 + - 3ba8d4563129 - 749c918495f7 + - 017aba02828d + - cd659e8cc5fa - 17062a0decb7 - 937aa69e715f - - 3ba8d4563129 - - cd659e8cc5fa + - 03e9b2fbc005 - f6877ad76b00 + - a6d65b0c67af tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -28,11 +28,11 @@ tools: - name: bwa owner: devteam revisions: - - dfd8b7f78c37 - - e188dc7a68e6 - - 53646aaaafef - 3fe632431b68 - 64f11cf59c6e + - e188dc7a68e6 + - 53646aaaafef + - dfd8b7f78c37 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -44,41 +44,41 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - 2ff111fac1d7 - - 3e1ea2facca6 + - e7f19d6a9af8 - 60afcc2c1d05 + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 - - 037c6e54df11 - - c0c2d0941de8 - - 09b53c1d4ab1 + - 77b2770508f6 - 8c6cd2650d1f - 53c0b7a1a0c3 - - f54f5baedfdd - - 3f4d6399997b - 6b1e195506a3 + - c0c2d0941de8 + - 037c6e54df11 + - 11a0d50a54e6 + - 09b53c1d4ab1 + - f54f5baedfdd - b3eab4b67562 + - 3f4d6399997b - be1d967337e4 - - 77b2770508f6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 9ee34ba73ebf - 79b885ce78d7 - - 1cd2511a396e + - 13022c3d3076 - e403d27e8f24 + - 00fbfac99d39 - ec9cbd6b9a49 - - 13022c3d3076 - b8f5f6e87f5c - 178bdbdb6d24 - - 00fbfac99d39 + - 1cd2511a396e + - 9ee34ba73ebf tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.usegalaxy.org.au/metagenomic_analysis.yml b/staging.usegalaxy.org.au/metagenomic_analysis.yml index 3f5ea973d..8b5380671 100644 --- a/staging.usegalaxy.org.au/metagenomic_analysis.yml +++ b/staging.usegalaxy.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -34,55 +34,55 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - 63f86089423e + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - 1c35dadbe76f - 84fd33a60b35 + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - f732237754fc - 34e55239e68b - a9f4a217dcd6 - - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - 0776d824d896 - - 04c15826a0b8 - 8c202e741d68 + - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - e96bbb9e24ea - 1c9b3bcd4261 + - e96bbb9e24ea - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 1d75bd0595e2 - 306a40d4bb8f - 84743da21318 - - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - 8daf4564ccda + - ac72310b038a - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -98,8 +98,8 @@ tools: owner: iuc revisions: - 1bc3657cd694 - - 04144473e59e - 7f3b59dee073 + - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts @@ -120,23 +120,23 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - dbf1798c0dcc - c4db8c4de66f + - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - fa35f1106d3e - 15dbb444df71 + - fa35f1106d3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - - 654548ae1357 - 6d364c65c946 + - 654548ae1357 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -148,25 +148,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - 6aad8ca3918b - bd7a9c6efb10 - e66ab198ec15 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - d77397f09da1 - - c6676a890f50 - b084117133af + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - cad93abecac9 - - 9704f1a3b32d - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -178,25 +178,25 @@ tools: - name: humann_regroup_table owner: iuc revisions: + - c409a495841f - 79706f10d680 - 31c6d107e7a5 - - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - d24841f5c3d2 - 714d5a28cc5c - 172920f67a84 + - d24841f5c3d2 - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - 12fb63b5f63f + - d7e9a3c41657 - 4137b492233e - a4d7148ccee4 tool_panel_section_label: Metagenomic Analysis @@ -207,25 +207,25 @@ tools: - cf87759761eb - 6fcb8ac37a3e - 75bedfb2078b - - e2c71b852aba - 64bc7acc22a9 + - e2c71b852aba tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - 080ea153677c - 4033827c76b8 - c82508e76ad1 + - 5e5a999ffaa9 + - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - 95bf7479d53c - 6b7622dda516 + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -291,8 +291,8 @@ tools: - name: kraken2 owner: iuc revisions: - - 328c607150ff - e674066930b2 + - 328c607150ff - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -305,8 +305,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -325,15 +325,15 @@ tools: - name: kraken owner: devteam revisions: - - aec58624706f - 8ba2174315aa + - aec58624706f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: mash_sketch @@ -357,18 +357,18 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc - - 4fd3b5d8706b - 0270541aaf46 - - 27250f92a01a + - 4fd3b5d8706b + - e073891b2afc - 2cff76cf35c6 + - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -441,13 +441,13 @@ tools: - name: metaphlan owner: iuc revisions: + - ff8f55893e7d - 1a6cdf55390f - - b89b0765695d - a92a632c4d9b - a16313517e55 - - 2131d7dca455 - 6dee4abadccb - - ff8f55893e7d + - 2131d7dca455 + - b89b0765695d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -496,8 +496,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 3bd5f5afb9b1 + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -527,11 +527,11 @@ tools: - name: staramr owner: nml revisions: - - be818ae858e4 - - 4d83eccf5f81 - 2fd4d4c9c5c2 - - aeaa20b96ef2 + - 4d83eccf5f81 - 4b9a8031ab74 + - be818ae858e4 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus diff --git a/staging.usegalaxy.org.au/mothur.yml b/staging.usegalaxy.org.au/mothur.yml index 22f68431e..0ee576bb4 100644 --- a/staging.usegalaxy.org.au/mothur.yml +++ b/staging.usegalaxy.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 @@ -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.usegalaxy.org.au/multiple_alignments.yml b/staging.usegalaxy.org.au/multiple_alignments.yml index 8e8f5efe8..b9bdc0282 100644 --- a/staging.usegalaxy.org.au/multiple_alignments.yml +++ b/staging.usegalaxy.org.au/multiple_alignments.yml @@ -2,34 +2,34 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 6ae5a7b5a0a2 - - bdfbaf0c10aa - - 48c13389050d - - a74dbfee5a86 + - 9422c5a87ee2 - 8b67dd48fec1 - - cd07731e4434 - 9baa871cb1d1 - - 80f03df2e2ce - - 9422c5a87ee2 + - cd07731e4434 + - a74dbfee5a86 - 2263989660f5 + - 48c13389050d + - 6ae5a7b5a0a2 + - 80f03df2e2ce + - bdfbaf0c10aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - d7ce0ec78e51 - - c18157c68134 - - 5abf2c2249aa - - '764845535798' - - f14193ec1f50 - - bc3831dd65c1 - - fc2e49f91e52 - - 4a60927aaca5 - be78f13134e2 + - bc3831dd65c1 - d390fe1567dc + - f14193ec1f50 + - 2e093badc689 + - '764845535798' + - fc2e49f91e52 - aaa0d6a8b808 + - c18157c68134 - f0af8936ed41 - - 2e093badc689 + - d7ce0ec78e51 + - 4a60927aaca5 + - 5abf2c2249aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -61,18 +61,18 @@ tools: - name: mafft owner: rnateam revisions: - - f1a5908ea2cb - a65296ffb4a0 - - c5908940967d - 15974dd17515 + - f1a5908ea2cb - f0d493f8f84f + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -92,15 +92,15 @@ tools: - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 636b049e6141 + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords diff --git a/staging.usegalaxy.org.au/nanopore.yml b/staging.usegalaxy.org.au/nanopore.yml index 41f606e2f..ebec05ae9 100644 --- a/staging.usegalaxy.org.au/nanopore.yml +++ b/staging.usegalaxy.org.au/nanopore.yml @@ -8,18 +8,18 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 79e9a869f40e + - 72b5e9dda577 - a7228a7ea146 + - 79e9a869f40e - 0e9e7fcdd543 - cb34f00cc10f - - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - fa11aa8103b2 - db25ec99c3ea + - fa11aa8103b2 - 682d1e2c8be4 - d6cddc06aeae tool_panel_section_label: Nanopore @@ -27,14 +27,14 @@ tools: - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - - ec699520444c - - 2bf63b38ee9b - - 19f3b583a9b3 - 0f5f4a208660 - 43815fa60f3a - cc36773a3681 - 222669c4afb6 + - 19f3b583a9b3 + - edf6d4003fad + - 2bf63b38ee9b + - ec699520444c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -53,10 +53,10 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - 0f1c34698076 - - edbb6c5028f5 - 645159bcee2d + - edbb6c5028f5 + - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -76,8 +76,8 @@ tools: - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - 449e9aeded2d + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -90,9 +90,9 @@ tools: - name: porechop owner: iuc revisions: + - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 - - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -124,8 +124,8 @@ 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 @@ -144,8 +144,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.usegalaxy.org.au/none.yml b/staging.usegalaxy.org.au/none.yml index 28741da66..18d4aacc0 100644 --- a/staging.usegalaxy.org.au/none.yml +++ b/staging.usegalaxy.org.au/none.yml @@ -14,15 +14,15 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 96d2000977ab - 58341ad4fb42 + - 96d2000977ab tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -73,16 +73,16 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - edacc4bcd3cb - 2f27f3b86827 - ed1518ce2237 + - edacc4bcd3cb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -100,9 +100,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 5711fc06a63e - 48a42ca61006 - 38ccd4589990 - - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -115,8 +115,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -129,8 +129,8 @@ 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 @@ -150,9 +150,9 @@ tools: owner: iuc revisions: - 5bcf0e24f42c - - b4b2b284230a - 27a6a256cd23 - 172815da3d41 + - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -177,16 +177,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - 87febc68b45b - fea85c467896 - 19bbd19b74b3 - - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan 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 @@ -210,9 +210,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 - 4ba60cb14cb0 - 5fe20c915fa6 + - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -232,18 +232,18 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - 6e24e79d3d69 - - df30a2f1db55 - 29c738066906 + - df30a2f1db55 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - ad90c2da4f38 - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -262,16 +262,16 @@ 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 - 94a50db37d1a + - 625fd9476402 - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1016,23 +1016,23 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbcavity owner: bgruening revisions: - - 7e5c2e4bc227 - 744a777e9f90 + - 7e5c2e4bc227 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock owner: bgruening revisions: - - c362398df83b - - e4b7d1507a75 - a22969b08177 + - e4b7d1507a75 + - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.usegalaxy.org.au/phylogenetics.yml b/staging.usegalaxy.org.au/phylogenetics.yml index f7b2a81cb..ac1281335 100644 --- a/staging.usegalaxy.org.au/phylogenetics.yml +++ b/staging.usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_absrel @@ -29,84 +29,84 @@ tools: revisions: - 3b8b5bde0bd9 - 6a457678efcb - - 8834daeb9892 - - d7c7ef3353fe - - '841557158611' - - a6619171428e - 81e66674859e - - cce7b18495e4 - - 3f59ebfbfe3d - 5a7c56a5cc08 - - b89cac5156ec - - f04a1264e2a2 - - 107d3ba7024a - - c78f3d7dd1db - f73435dc282b - 26de3a7b1cb9 + - d7c7ef3353fe + - b89cac5156ec - d033ffc1c161 + - a6619171428e + - f04a1264e2a2 + - 3f59ebfbfe3d + - 8834daeb9892 + - c78f3d7dd1db + - cce7b18495e4 + - 107d3ba7024a + - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 02b8758214b0 - - e75442c7f4da - - 3b96e92e8ec3 - - 7a2092844346 - - aa8cc71438cf - - b0af57c1a968 - 6223845127ea - - 4755f52427c4 + - a185b079b095 + - aa8cc71438cf + - 3b96e92e8ec3 - 5fcd1ece3a6e - - 6a726db04d4b - 659517798cc4 - - 88c4aa435ded + - e75442c7f4da - 6283babe736e - - a185b079b095 - - df47d4845b62 + - 4755f52427c4 - 5b777002c2de + - 02b8758214b0 + - 6a726db04d4b + - 7a2092844346 + - b0af57c1a968 + - 88c4aa435ded + - df47d4845b62 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 524d31add34a - - b8476e82ac20 - 9b892d7f82cc - - d1c340a5664b + - 524d31add34a - f97743d52b87 + - d1c340a5664b + - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 128ba8da994f - daddf188c13f - - feb40665d7cd + - 128ba8da994f - 9e10ba792be2 + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - 437e28791761 - - a2099fb98cdb - - ca0d8cf80567 - - 36912871ccdc - - b6abccb1f25b - 2fa9d4f1b48f - - 3a43c3982401 - - 83a69484cb87 + - 5f8727ff21e7 + - 81804a978fc0 + - 03ed9524dcd1 - b7e297c2ede6 - - 14ae456b8cc5 - - ca337cce3888 + - 3a43c3982401 + - b6abccb1f25b - abf6dbe8c9d7 - 7bb8726be37c + - ca0d8cf80567 + - 14ae456b8cc5 + - ca337cce3888 + - 83a69484cb87 + - 36912871ccdc - 9d61d3fa046c - - 03ed9524dcd1 - 42a174224817 - - 81804a978fc0 - - 5f8727ff21e7 + - a2099fb98cdb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -119,20 +119,20 @@ tools: owner: iuc revisions: - ba29b5e2a4be - - a4b71be30c3c - ea30d3089354 - - 73a469f7dc96 + - a4b71be30c3c - 29ff6a849eac + - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - f1ccc8a6eb05 - - e88a7de55d6e - 15ac71df11a0 - - 809e42326fc2 - - 91887494eb97 - dbe2b2204555 + - e88a7de55d6e + - 91887494eb97 + - 809e42326fc2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/picard.yml b/staging.usegalaxy.org.au/picard.yml index 7ca6d5564..229eb79b8 100644 --- a/staging.usegalaxy.org.au/picard.yml +++ b/staging.usegalaxy.org.au/picard.yml @@ -4,9 +4,9 @@ tools: revisions: - 881d7645d1bf - b502c227b5e6 - - f6ced08779c4 - - 7d34178f2812 - a1f0b3f4b781 + - 7d34178f2812 + - f6ced08779c4 - fc288950c3b7 - 1aac2a13842a - 585027e65f3b diff --git a/staging.usegalaxy.org.au/proteomic_ai.yml b/staging.usegalaxy.org.au/proteomic_ai.yml index d654d457d..c1cdaa662 100644 --- a/staging.usegalaxy.org.au/proteomic_ai.yml +++ b/staging.usegalaxy.org.au/proteomic_ai.yml @@ -2,13 +2,13 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - 5b85006245f3 - c0e71cb2bd1b - - 3bd420ec162d - - d00e15139065 + - eb085b3dbaf8 + - ca90d17ff51b - 7fbec959cf2b - - 5b85006245f3 + - 3bd420ec162d - a58f7eb0df2c - - ca90d17ff51b - - eb085b3dbaf8 + - d00e15139065 tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/proteomics.yml b/staging.usegalaxy.org.au/proteomics.yml index eab868c5d..f8df04985 100644 --- a/staging.usegalaxy.org.au/proteomics.yml +++ b/staging.usegalaxy.org.au/proteomics.yml @@ -2,85 +2,85 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 - - 0a18ac48ac53 - - 277dc652246e - - b574b84afc4d - f28ad96b76dc - b18329a8ac14 + - b574b84afc4d + - ece627528a78 + - 277dc652246e + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - 525f201b86c1 + - e988563cc6e5 - bf06d196e23d - e215f71d7983 - - 525f201b86c1 - b41107d8fe89 - - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - bb6397b94018 - 8da3511c9467 + - bb6397b94018 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - 528fb09022be - - f23d67e28cc8 - - a8157342d9a3 - b8c79e70516d + - a8157342d9a3 + - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 80600735685d - a69865da6f80 - - 25b83cbd596a - - 59e85306eae5 - a95a82eb4d50 + - 80600735685d + - 59e85306eae5 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - ed9ed1e6cca2 - - f1897eb07081 - - 798da6bdff3d - 611d80c0e29d + - 798da6bdff3d - e0669b1854b1 + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - 74b61bf5bc4b - - a7fb9b395ddf - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - df2187f9013b - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 + - d2483487e077 + - 10566783d718 - c5aa9fca18c6 + - 043f9c91f686 - 1693b2126f30 - - 10566783d718 - - d2483487e077 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -104,16 +104,16 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d0ea7589e95f - d263296cd73e + - d0ea7589e95f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 0fa397f4f40b - 4081e4faa4ab + - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -138,92 +138,92 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - 160538a890a6 - d286ff4600dd + - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: + - 8934bc76bb52 + - 97a7f34fcb6a + - f522c08e900c - 2133b0be850a - 837224ad1694 - - f522c08e900c - - 97a7f34fcb6a - - e42225f8a659 - - 8934bc76bb52 - - 1f39c833f65f - - 4d17fcdeb8ff - 7f432d87c82c + - 1f39c833f65f + - e42225f8a659 - 37d669de2828 + - 4d17fcdeb8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - 0ed07016d668 + - '860429737408' - 85b8866f06d7 - a72ac2c7cc5b - - '860429737408' tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 4187b6df1a40 - - 352b37c66d97 - - 990b4560ead7 - 1974224d63c2 + - 990b4560ead7 + - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - 99450519d727 - - 4f359549383c - a1daafbf5233 - deaf035bbe9f + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 40ca115438d2 - c1343e3389ca - - e79958768a2c - c7745841de24 + - e79958768a2c + - 40ca115438d2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 + - da986f83631b - b648e45fd3cf + - d2eac53666f0 - d46d64e7964d - - da986f83631b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - eb811f3018ea + - 9bf325045235 - 944b43462104 - 1199751329b0 - - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -271,41 +271,41 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - f7fef900f5b2 - - 9cdf15d3cfc8 - c9eff69a7c62 - 518b1730cf2a + - f7fef900f5b2 + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 + - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 890025d6e426 - - 41859bbdc16e - 658494a2cb00 + - 41859bbdc16e + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 9b7977080f6d + - 6634cad7d797 - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 05d5e1ddc985 - 0bb5056cb775 + - 05d5e1ddc985 - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -320,17 +320,17 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 - 39e8fde08881 + - 27cba4c5fc42 - 92352a475eed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 9e26f5c770f8 - - 0efbc235f314 - d413dc49d650 + - 0efbc235f314 + - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver @@ -344,8 +344,8 @@ tools: - name: openms_idfilter owner: galaxyp revisions: - - 382cde407f81 - ca799a7246e7 + - 382cde407f81 - c427a8628cbe - c55dddc5844a tool_panel_section_label: Proteomics @@ -353,17 +353,17 @@ tools: - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - 39caaa778d2e + - 8ddb7bab1138 - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - f817513840a9 - 8d4db262964c - 18f93351f8b6 - - f817513840a9 - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -371,15 +371,15 @@ tools: owner: galaxyp revisions: - c69f69d7867a - - 111c3a00136d - 5d9f175dff81 + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - 476b5e296979 + - 0e52c85f3b15 - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -393,16 +393,16 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - a407b6790342 - 2b2a7551a857 + - a407b6790342 - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - d0304fb829c0 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter @@ -416,15 +416,15 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - a2a6e9551046 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 8c01da82292c - 2a9ff56cb279 + - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -458,46 +458,46 @@ tools: - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - bc63b4d12779 - 2aebe58de46e + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 3d8d4ada5405 - 5ae104d0da6e + - 3d8d4ada5405 + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - 539a3a4dcc9e - - dd173849c3d8 + - e039cc5c7aed - 5182338d5e7c + - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -509,8 +509,8 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - 9020199dba0a + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -522,16 +522,16 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - - 7f6a1f27553e - c8b225c69a7f + - 7f6a1f27553e + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -544,14 +544,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 3ec27b4cee7c - - 7fdd9119cc4f + - 943a34df6047 + - 1beff3ddce58 - a72c48001f7c - 3634c90301af - - 943a34df6047 + - 7fdd9119cc4f + - 3ec27b4cee7c - 07ff622ec007 - da885ca16cb2 - - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -605,9 +605,9 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: + - 12692567c7f9 - 265c35540faa - 1a5690a5eedc - - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.usegalaxy.org.au/rad_seq.yml b/staging.usegalaxy.org.au/rad_seq.yml index b3a5932f7..976a5a937 100644 --- a/staging.usegalaxy.org.au/rad_seq.yml +++ b/staging.usegalaxy.org.au/rad_seq.yml @@ -3,11 +3,11 @@ tools: owner: iuc revisions: - 2f1d464ebfd2 - - 110a346daf36 + - cd5f98911089 - e345aadf914f - - 289b7d6b69a4 - 42201b90e3f4 - - cd5f98911089 + - 110a346daf36 + - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -20,11 +20,11 @@ tools: owner: iuc revisions: - c207119ba5f6 - - 0cd2df8af811 - - 0345dbaaa79b - 8501601a118d - - fcce77c09289 - 42d9087b4789 + - 0345dbaaa79b + - 0cd2df8af811 + - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - 33486216eec0 + - 89eb29319bf4 - ad5ab22ffe24 + - 33486216eec0 - 405a212b32ab - - 04db7fd6b238 - - 89eb29319bf4 - 421c33b8bf17 + - 04db7fd6b238 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: - - 7b72fde3d27e + - f6e91108b7b1 - eb784fa07f80 - 1d839ead7ad3 - fa51dc5e8386 - - f6e91108b7b1 - 7370bb65bad4 + - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - 3d70c2996730 - - c9b77ced9a78 - - 8a55d29c8fcf - - 1544278c272e - d30e36c48c93 + - 8a55d29c8fcf - a3e86cd9cac7 + - 1544278c272e + - c9b77ced9a78 + - 3d70c2996730 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: - - 564c33e5c3e3 - - a5969aa9347e - b242deb58952 - - e2db212d64ad - 887cf585cafc - 7b881f5f5ad5 + - 564c33e5c3e3 + - a5969aa9347e + - e2db212d64ad tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - - 8cff84759bf6 + - b4bab607eb05 - 9a171f9a450b - bd5ff77e2036 - - b4bab607eb05 + - e897c74a48bb + - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 5e10f396979e - adc7a7610d4f - - 33f0793edf93 + - 887e0991eb24 + - 5e10f396979e - 4f65e343ecdf + - 33f0793edf93 - 6dafad990086 - - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - 43e3eeb2e0ec + - 17d39bf0a63a - 4e280b27a831 - c5d7050e4ad7 - - 17d39bf0a63a - - c287418eb288 + - 43e3eeb2e0ec - 97575d01f06b + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -155,11 +155,11 @@ tools: owner: iuc revisions: - 0b8c84a7fdb5 - - 09b8edb56d80 - 9586f08634c0 - - a819ec3b362d - - d9bf483266a1 - cd034465d4a4 + - d9bf483266a1 + - 09b8edb56d80 + - a819ec3b362d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,11 +171,11 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - 69842dd5aa48 - - a9c34a289493 + - a4b4bd84f69e - bf0e43ab0416 - 2645575d1bf2 - - a4b4bd84f69e + - a9c34a289493 + - 69842dd5aa48 - 95351dd0fd3f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -189,11 +189,11 @@ tools: owner: iuc revisions: - 912f904a6e1e - - bb0475c884ff + - d1fda11e602f - 8a35a3bc6752 + - bb0475c884ff - d033e1ccb386 - cfb504394ae1 - - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - - d504d945a655 - 95286af4139b + - d504d945a655 + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.usegalaxy.org.au/rna_seq.yml b/staging.usegalaxy.org.au/rna_seq.yml index cb8ac56af..170bbc288 100644 --- a/staging.usegalaxy.org.au/rna_seq.yml +++ b/staging.usegalaxy.org.au/rna_seq.yml @@ -9,8 +9,8 @@ tools: - name: arriba_get_filters owner: iuc revisions: - - 32e542c2a773 - 125d20cb23d7 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -46,22 +46,22 @@ 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 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: - - cf747d1bd79a - 6a6717a5f421 + - cf747d1bd79a - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -74,8 +74,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 9a854107dbb2 - 6cbfede05833 + - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -99,10 +99,10 @@ tools: - name: describe_samples owner: iuc revisions: - - e3b16fd7dd08 - 8f0181aacb7a - - 0693ccd171c4 - 57f477b57c35 + - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -114,12 +114,12 @@ tools: - name: deseq2 owner: iuc revisions: + - d027d1f4984e - 8fe98f7094de - 0696db066a5b - - 24a09ca67621 - - cd9874cb9019 - 6a3a025714d3 - - d027d1f4984e + - cd9874cb9019 + - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -131,8 +131,8 @@ tools: - name: dexseq owner: iuc revisions: - - b47c006d90c5 - 2872c633f07e + - b47c006d90c5 - df929f257179 - 62adf13b86ea tool_panel_section_label: RNA-seq @@ -147,12 +147,12 @@ tools: owner: iuc revisions: - 334ce9b1bac5 - - 555659de7321 + - 6e53e565fc6a - 9bdff28ae1b1 - - df0c8d0a5992 - - 3d89af8a44f0 - f2843df56434 - - 6e53e565fc6a + - 3d89af8a44f0 + - 555659de7321 + - df0c8d0a5992 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -164,8 +164,8 @@ 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 @@ -183,16 +183,16 @@ tools: - name: featurecounts owner: iuc revisions: - - 90d16db017d7 - - 38b6d12edc68 + - 6f66ae7c5f7a + - af814359d244 - ea04b737afa0 - - a56fbe2d6ba7 - 7db9d3ea71c9 - - a37612abf7f9 - - af814359d244 - - 6f66ae7c5f7a - f3a5f075498f + - a56fbe2d6ba7 + - 38b6d12edc68 + - a37612abf7f9 - e6a2a912677a + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -216,9 +216,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 - f99dd58de04f + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -236,13 +236,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - f4af63aaf57a + - 3fb01a8c902d - 6c19daec423d - - a86e80d3c09c + - 26371a1df031 - d4b55e2beb12 + - a86e80d3c09c - 6ab42baa56e9 - - 3fb01a8c902d + - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -260,8 +260,8 @@ tools: - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -279,11 +279,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - ce5d418183c5 - - 1c75aa5de15e - - 01247aaf0a10 - 5ae5c312d718 + - 1c75aa5de15e - 87c11c05d238 + - ce5d418183c5 + - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -310,13 +310,13 @@ tools: - name: limma_voom owner: iuc revisions: - - 0921444c832d + - e827f9aae031 + - 32511f586472 - 97e06a4c7c75 - 708348a17fa1 - - e827f9aae031 - - 58c35179ebf0 - d6f5fa4ee473 - - 32511f586472 + - 0921444c832d + - 58c35179ebf0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -334,8 +334,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -377,18 +377,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 99b17b74a8cd - - b9e04854e2bb + - 4074fc1940e2 - 3ea5a2a63fa2 + - c7c55b694974 + - 5ec75f5dae3c - 4df95e2d7f61 - - 4074fc1940e2 - e132e7d02a3e + - b9e04854e2bb - 0a563fd2f22e - - 5ec75f5dae3c - 7ed2edc1337f + - 99b17b74a8cd - c772497b2c32 - 980d2a2e1180 - - c7c55b694974 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -413,11 +413,11 @@ tools: owner: bgruening revisions: - 49121db48873 - - cc05793bb896 - e3d32471da11 - - 53e9709776a0 - - 2c0ca397d302 - ebab418107f5 + - 2c0ca397d302 + - 53e9709776a0 + - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -429,22 +429,22 @@ tools: - name: seurat owner: iuc revisions: + - 8c28affc7c48 - 56242ff81c84 - - fab6ff46e019 - c0fd285eb553 - - 8c28affc7c48 + - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 914cfcba0ec8 + - 1ebd14235b92 + - ae618321f34a - cef79931dda5 - - 76d290331481 + - 914cfcba0ec8 - 258d696dbd7e - - ae618321f34a - - 1ebd14235b92 - dd4df992d93d + - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -474,10 +474,10 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - d0d4cef4f967 - ffd1300599a1 - 0db979fead3a + - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -489,10 +489,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - - a009c96c5c18 - bcc5f03f1900 + - d6a479fd4281 - 74217fbfba4d + - a009c96c5c18 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -504,9 +504,9 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - c2b82a94493e - 56162e446004 + - 478f36effca1 - 75f4e1859ed7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -520,8 +520,8 @@ tools: owner: iuc revisions: - c0096052b35b - - fab23c3b5258 - 3f4094b6a565 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -533,10 +533,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 - 41db7569b4ba - - 4687ecf0eb2d + - be3f26533209 - 34a018cbee9c + - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -548,11 +548,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 05ab8d5e04a2 - 33406f5a445c + - ae501908a17f - c5fbddcac63a - 5192f657f305 - - 05ab8d5e04a2 - - ae501908a17f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -565,9 +565,9 @@ tools: owner: iuc revisions: - 1fdb25a8384d + - 6f0fb35b799c - e406ac71165d - aa38fa8c5815 - - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -579,9 +579,9 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - ba460ccf0006 - - 964b7efe2639 - c2c039e421af + - 964b7efe2639 + - ba460ccf0006 - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -594,10 +594,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - c63338cf419f - eafea3083352 - - 1d689e4e1caf - 047c22569787 + - c63338cf419f + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -609,10 +609,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 1b1a25f93f80 - 9871104ea630 + - 1812dbc5bb7b - 3a4ac03d1266 + - 1b1a25f93f80 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -624,14 +624,14 @@ tools: - name: trinity owner: iuc revisions: + - c9cfec002f71 + - d84caa5a98ad + - db1f362cca3e + - 32b86cd8eb50 - cee61b3fcf78 - d2bc35f3d1c5 - - db1f362cca3e - 77cf519a812e - - 32b86cd8eb50 - - c9cfec002f71 - 48636f857c4b - - d84caa5a98ad tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -644,9 +644,9 @@ tools: owner: iuc revisions: - 9e61bc67866f + - 6fd16fad465d - 4383070d29ed - 2b093007fab9 - - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.usegalaxy.org.au/sambam.yml b/staging.usegalaxy.org.au/sambam.yml index 9e5eb0090..e595b5539 100644 --- a/staging.usegalaxy.org.au/sambam.yml +++ b/staging.usegalaxy.org.au/sambam.yml @@ -68,8 +68,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -81,8 +81,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -107,17 +107,17 @@ tools: - name: samtool_filter2 owner: devteam revisions: + - dc6ff68ea5e8 - 649a225999a5 - 56c31114ad4a - - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - 12749212f61b - - 9149ad20699a - 46c6639921f1 + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -129,9 +129,9 @@ tools: - name: samtools_calmd owner: devteam revisions: + - 06dc50b7b711 - 33208952b99d - 92ec40abcdcf - - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -143,9 +143,9 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 720217c23995 - - b3d99709fe1a - a8d69aee190e + - b3d99709fe1a + - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -157,10 +157,10 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - cc61ade70eb8 + - 22970df7a40e - fe34990e5ce7 - db17d5321bad - - 22970df7a40e + - cc61ade70eb8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -172,10 +172,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: + - 7def34e6cf4d - 811fc2d75ad4 - 7a6034296ae9 - 88b8c2916784 - - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -187,18 +187,18 @@ tools: - name: samtools_merge owner: iuc revisions: - - 740ce0a18f0d - b40e2d865d52 - 36677f429310 + - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - fa7ad9b89f4a - - 583abf29fc8e - 9da0311ab1dd + - fa7ad9b89f4a - 329deb17a9f7 + - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -224,8 +224,8 @@ tools: owner: devteam revisions: - db000c6007a0 - - 30388d878f81 - bb8cfc6f6e0c + - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -256,9 +256,9 @@ tools: - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - - cab3f8d35989 - 6c2c1836728b + - cab3f8d35989 + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -270,10 +270,10 @@ tools: - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - 5d9ae78f34d3 - - bcedabb53ddf + - b7f7826ef1cd - 135c85f4cfaf + - bcedabb53ddf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -285,10 +285,10 @@ tools: - name: samtools_stats owner: devteam revisions: + - 1cc79f49b8d5 + - 5a08c09b9311 - 24c5d43cb545 - 3a0efe14891f - - 5a08c09b9311 - - 1cc79f49b8d5 - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -301,13 +301,13 @@ tools: - name: samtools_view owner: iuc revisions: + - b01db2684fa5 + - 5826298f6a73 - 350bbc5c2ffd + - c370440f901e - b72793637686 - bf328cec6a42 - - c370440f901e - 0dbf49c414ae - - 5826298f6a73 - - b01db2684fa5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.usegalaxy.org.au/send_data.yml b/staging.usegalaxy.org.au/send_data.yml index 95cd40293..1584e58c8 100644 --- a/staging.usegalaxy.org.au/send_data.yml +++ b/staging.usegalaxy.org.au/send_data.yml @@ -3,9 +3,9 @@ tools: owner: iuc revisions: - 4aab5ae907b6 - - d147d6455873 + - a62c4a11a67d - 59bb6d34fca6 + - d147d6455873 - 6f6537780379 - - a62c4a11a67d tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/single_cell.yml b/staging.usegalaxy.org.au/single_cell.yml index 4ff26978c..1c3dea258 100644 --- a/staging.usegalaxy.org.au/single_cell.yml +++ b/staging.usegalaxy.org.au/single_cell.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - 00712416fdaa - - fb9e030ffae4 - cfc3f5a57dc6 + - fb9e030ffae4 - 32e547223c9e - 55e35e9203cf tool_panel_section_label: Single-cell @@ -18,11 +18,11 @@ tools: - name: anndata_inspect owner: iuc revisions: - - ee98d611afc6 - b9fac48532eb - - 39e945f0b2c1 - 038e32885fec + - ee98d611afc6 - 688357ad5e61 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -34,11 +34,11 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b - 43cb7b5a6fe7 - - b85871dd69f9 - - 3d748954434b - d4af736e7b83 + - 3d748954434b + - 9bd945a03d7b + - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -52,8 +52,8 @@ tools: revisions: - 8855361fcfc5 - 2c1200fba922 - - cdf4443d5625 - a9caad671439 + - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -71,15 +71,15 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 282819d09a4f - 7ffaa0968da3 + - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 2ba99a52bd44 - 56371b5a2da9 + - 2ba99a52bd44 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -98,9 +98,9 @@ tools: - name: raceid_clustering owner: iuc revisions: + - 0bff0ee0683a - f911a64454fb - 7e014059a88d - - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -119,8 +119,8 @@ tools: owner: iuc revisions: - 37a47c4fd84d - - 2b0d3e2f402a - f3eb2291da05 + - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -146,8 +146,8 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 2af7c5086a96 - 44b935f2271b + - 2af7c5086a96 - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,9 +174,9 @@ tools: - name: scanpy_filter owner: iuc revisions: + - b409c2486353 - a97abb8cd15b - 3c86f71498bc - - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -188,10 +188,10 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 5e9171dc8244 - cc0deb593fc8 - - c5d3684f7c4c - 6c145a6868cc + - 5e9171dc8244 + - c5d3684f7c4c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -204,8 +204,8 @@ tools: owner: iuc revisions: - a407e7f8bdc1 - - ab55fe8030b6 - 3bcd5445cd7a + - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -218,8 +218,8 @@ tools: owner: iuc revisions: - aa0c474463c2 - - 6adf98e782f3 - dbbe1ea8ecb1 + - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -231,9 +231,9 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: + - 215733a383f2 - bf2017df9837 - f2f6c703da06 - - 215733a383f2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -245,9 +245,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - b834074a9aff - fd808de478b1 - 8f333f90d8d6 + - b834074a9aff tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -260,8 +260,8 @@ tools: owner: iuc revisions: - b7ea9f09c02f - - 652923ce664f - 7a365ec81b52 + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -273,9 +273,9 @@ 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 @@ -287,9 +287,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - - c99ba278dfa9 - 9e5c0bb18d08 + - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca diff --git a/staging.usegalaxy.org.au/statistics.yml b/staging.usegalaxy.org.au/statistics.yml index 6e27d206f..7c68a906d 100644 --- a/staging.usegalaxy.org.au/statistics.yml +++ b/staging.usegalaxy.org.au/statistics.yml @@ -32,25 +32,25 @@ tools: - name: datamash_ops owner: iuc revisions: - - 4c07ddedc198 + - 562f3c677828 - 2f3c6f2dcf39 + - 4c07ddedc198 - 746e8e4bf929 - - 562f3c677828 - 419027d822d6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - - 7a15159140d1 - cb1c59d69557 + - 7a15159140d1 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,35 +120,35 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - aef56d0e7a61 - - b1eda492f063 - 9c3e1d3235c8 - 840f29aad145 + - b1eda492f063 + - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 07843f917990 - d0352e8b4c10 + - 07843f917990 - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - - 4cc980df6265 - 2c58b83c9bad + - 4cc980df6265 + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 1dd433d2c92c - 4bbaf77573ef - - 7dd3fb35904f + - 1dd433d2c92c - ad7e0b4291ee + - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.usegalaxy.org.au/text_manipulation.yml b/staging.usegalaxy.org.au/text_manipulation.yml index c60d2fcc6..18bebe958 100644 --- a/staging.usegalaxy.org.au/text_manipulation.yml +++ b/staging.usegalaxy.org.au/text_manipulation.yml @@ -20,21 +20,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - be25c075ed54 + - 02026300aa45 - 464b9305180e - - 6e8d94597139 - 9cd341095afd - - 02026300aa45 - - 13b6f0007d9e - 626658afe4cb + - 13b6f0007d9e + - 6e8d94597139 - 6595517c2dd8 + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -71,8 +71,8 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - 37cde8134c6a + - 9cc411a62277 - 34d29339abab - 4d5aae46f850 tool_panel_section_label: Text Manipulation @@ -98,28 +98,28 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 623f3eb7aa48 + - 2e8f945f7285 - 33d61c89fb8d - cf34c344508d - 83069b38aa85 + - 623f3eb7aa48 - 1ea4e668bf73 - - 2e8f945f7285 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 503bcd6ebe4b - 399da6b5ec21 - ae8c4b2488e7 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -131,8 +131,8 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a - bce29ec10b78 + - b722161a845a - c29d2f80a066 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -146,12 +146,12 @@ tools: - name: text_processing owner: bgruening revisions: - - 0a8c6b61f0f4 - - f46f0e4f75c4 + - a6f147a050a2 + - d698c222f354 - 74a8bef53a00 - - 9ff72e942410 - ddf54b12c295 - - d698c222f354 - - a6f147a050a2 + - f46f0e4f75c4 + - 0a8c6b61f0f4 + - 9ff72e942410 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/variant_calling.yml b/staging.usegalaxy.org.au/variant_calling.yml index 620e5aa8d..d7567e4f1 100644 --- a/staging.usegalaxy.org.au/variant_calling.yml +++ b/staging.usegalaxy.org.au/variant_calling.yml @@ -2,9 +2,9 @@ tools: - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - - 0d18a3ba2d1c - 85c57cc9b558 + - 0d18a3ba2d1c + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,49 +16,49 @@ tools: - name: freebayes owner: devteam revisions: + - 57def2d7c093 - ef2c525bd8cd + - 04fa42777df9 - a5937157062f - 156b60c1530f - - 57def2d7c093 - - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - 09d6e4693887 + - 435b157bed6d - 791f73caa0c8 - e61c9ac190ad - - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 03627f24605f - 65432c3abf6c + - 03627f24605f - 3b4b2121842f - - e1461b5c52a0 - - dfadc322b065 - 4805fe3d8fda + - dfadc322b065 - 074d44697036 + - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - 701d134358ad + - 7dfca164d2e3 - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - c27549b9aa1f - - f4473557ffc7 - 971e07ca4456 + - f4473557ffc7 - 426d707dfc47 + - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi @@ -84,11 +84,11 @@ tools: - name: snippy owner: iuc revisions: - - 5bbf9eada9c2 - d220115f882b + - c9a8ef2aa380 + - 5bbf9eada9c2 - 9bccc8404a3c - fa016f1eea1a - - c9a8ef2aa380 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -130,18 +130,18 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 40f0591deda0 - e7aff4a85df5 - - ee4a90760848 - 3b1e7c170b10 - - 40f0591deda0 + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - adc0645b945c - 02d81b994ef5 - 4934c0ac6197 - - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic diff --git a/staging.usegalaxy.org.au/vcfbcf.yml b/staging.usegalaxy.org.au/vcfbcf.yml index de36d59df..532033020 100644 --- a/staging.usegalaxy.org.au/vcfbcf.yml +++ b/staging.usegalaxy.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: + - b7ea370b8f5d - 6a88248893c4 + - 8a2e296c07ef - e075b1be5abb - - 3f62d4939d54 - ebe5fc018e72 - - 8a2e296c07ef + - 3f62d4939d54 - 265fe0f9ea64 - - b7ea370b8f5d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -20,13 +20,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 0fba2c15b40d - - 544cb432072b - - 22637b1a55bf - c37b684e7f4e + - 544cb432072b - b03984136ce4 - - f0d44631365f + - 0fba2c15b40d - 21687e35f066 + - 22637b1a55bf + - f0d44631365f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,13 +39,13 @@ tools: owner: iuc revisions: - 3a7084316a6e + - bf1f4994f104 - 8ca3647c90fd - - 0238f68ad641 - 01d6b7d6365e - - 8627b2b383b4 - 8408bffd5616 + - 0238f68ad641 - 6d35a3780bfd - - bf1f4994f104 + - 8627b2b383b4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -57,14 +57,14 @@ tools: - name: bcftools_concat owner: iuc revisions: + - 9b5abbf50d23 - 6b6c992d3a14 - 03e0645395d2 - - 81426b3cf18b - - 62ca6da715bf - 08296952d12f - - d144af39073a + - 62ca6da715bf - f430a1ec7ee4 - - 9b5abbf50d23 + - 81426b3cf18b + - d144af39073a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -76,13 +76,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: + - 147de996e34f + - 95c6f3f4c77f - 1829900b5dcd + - 2363ef414c9b - e522022137f6 - d37e313a41be - d3081540d175 - - 147de996e34f - - 2363ef414c9b - - 95c6f3f4c77f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,13 +94,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - cacc9970727a - b14ff40958cb + - 348cd212dbad + - 9b29129fb491 - 09f37afb3621 - 92c0aff8b53e + - cacc9970727a - 1137ce8efc1e - - 9b29129fb491 - - 348cd212dbad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -112,12 +112,12 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 55c0e906c14c - de68c11034f6 - - ecc9192912b8 - - 4935320a59a8 - 1f2183a23823 - 367ba501b6eb + - 4935320a59a8 + - ecc9192912b8 + - 55c0e906c14c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 039ea3f1dea9 - - ae68ceb4cca3 - 64a8f7dae3ad - 6c790a091c7c - f01b2c9506b9 + - 039ea3f1dea9 - 7cbf3c66d4ad + - ae68ceb4cca3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -146,13 +146,13 @@ tools: - name: bcftools_filter owner: iuc revisions: - - cdb7b4927742 + - e7452697afd9 + - 33bd9301568c - 963a3635b2e1 + - 277719af4dd7 - 656a916779fe + - cdb7b4927742 - 6ea7170a016d - - 277719af4dd7 - - e7452697afd9 - - 33bd9301568c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -164,13 +164,13 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 5a321fab1fe4 - - 26d97cdd5410 - 3eac729e66c9 - - a1213a0b7b66 + - 501bfb078342 - b7f0f59baa7e + - a1213a0b7b66 + - 5a321fab1fe4 + - 26d97cdd5410 - a29a2f40b665 - - 501bfb078342 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -182,14 +182,14 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 5f27e814a119 - - d7d1663559e9 - - 63aabc920911 - c803c34361e0 - 768d04526638 + - d7d1663559e9 + - 63aabc920911 + - 5f27e814a119 - 97d19c008d15 - - 709dd8291b83 - 81e4014fa809 + - 709dd8291b83 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -201,13 +201,13 @@ tools: - name: bcftools_merge owner: iuc revisions: - - b1eba148b35b - - 7ba36babba2d - - 85ee7e6c4204 - b931e65638b8 - - af163c712539 + - b1eba148b35b - 86296490704e - 2215287d5cc9 + - af163c712539 + - 7ba36babba2d + - 85ee7e6c4204 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - f506df85c652 - - cf06b44624c7 - - 03191140c66a - ce9396ddcb2b + - 5660b21a0dbd + - 4e1d23e5c691 - 37757ffb4c5f - 9c711df3258d - - 5660b21a0dbd + - cf06b44624c7 + - 03191140c66a + - f506df85c652 - 31ea13dfe5e6 - - 4e1d23e5c691 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,12 +239,12 @@ tools: - name: bcftools_norm owner: iuc revisions: + - 021693fdadaa - 48291658fdf6 - - 19905c025d2a - a404f786a94c - 6deb4d549bc9 + - 19905c025d2a - ebb2e12a6de1 - - 021693fdadaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 5ad5d4243987 - - c450406f722b - be6b217710af + - 5ad5d4243987 - 97e8145d7e30 - 69d8b7567281 - - f7879f1e77f9 - 71c78e0eea52 + - c450406f722b + - f7879f1e77f9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: + - 0fe007201caf - 79f7a1acc2cd - 52f9e4a660e3 - - 89720ec3d58e - 2514e684f8a3 - - d31a2e310a52 - cc7f9a4e186b - - 0fe007201caf + - d31a2e310a52 + - 89720ec3d58e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -292,13 +292,13 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 99f4a81a47be - 0a62420cb9cd - 80e6e399ccd0 + - 75ddd081f608 - 026a989b7cee + - 99f4a81a47be - 1411bef27a75 - 230e424bde67 - - 75ddd081f608 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - c01be0ab9806 - - 5808f77b2bb6 + - ba20340426fe - 5acfca5a76af - - e493702b19eb - 444e6a756c35 - - ba20340426fe - bca7ce81688f + - 5808f77b2bb6 + - e493702b19eb + - c01be0ab9806 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -328,13 +328,13 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 12152af85697 - - d52b8947b269 - 7fe09ad6a939 - - 68fec03a63b7 - f2482aa4862e - - 157ffcdd3fa7 - 4d236c696844 + - d52b8947b269 + - 12152af85697 + - 157ffcdd3fa7 + - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -346,13 +346,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 8f2fc0ab30fb - - 27e2611639a9 - - 29ba253e2e05 - - 0e5d11004815 - - cbe39e530cbf - 6f8e223f78f3 + - cbe39e530cbf + - 0e5d11004815 - 8dbce095986c + - 27e2611639a9 + - 29ba253e2e05 + - 8f2fc0ab30fb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,12 +364,12 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 3ff5654b4e7d - - e0a856def0b0 + - 9708e3086f32 - af36eb5418fe - a367a15c6de5 - a8630d4fbaf8 - - 9708e3086f32 + - e0a856def0b0 + - 3ff5654b4e7d - 88bb477f45f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -382,13 +382,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: + - 6ce175385dd9 - 31c096c6b156 - - 03e30f06f15f - 4ed46189d6c6 - - 6ce175385dd9 - - 5c9729d54721 - - 2f4eef1f0d22 - 96d0145c041a + - 2f4eef1f0d22 + - 5c9729d54721 + - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 2c4941386820 + - 11af7fce71cf - 09f5e45a8212 - - 40daf124be88 - 262bba5b90ef + - 2c4941386820 - 46eb13bc2c73 - - 11af7fce71cf - a1aad8b559c6 + - 40daf124be88 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -418,14 +418,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 743cd1472aeb - - 0594ea1417c8 - - 6cbb9c47795c - - 4b796b58938b - 12038f59c0f4 + - 4b796b58938b + - 882b2e649602 - 8cb121b6a1d2 + - 743cd1472aeb - f272b8ba0983 - - 882b2e649602 + - 6cbb9c47795c + - 0594ea1417c8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -437,12 +437,12 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: + - adee7e8b746f - dba06328556a - 8c3ff4ef1190 + - eccb508bb678 - 18cf9de1cf73 - - adee7e8b746f - 238f78e38a8b - - eccb508bb678 - cced6715f926 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -455,13 +455,13 @@ tools: - name: bcftools_query owner: iuc revisions: - - 3ce32adc55b2 - - a850902cac64 - - e0ad88dec40d - - c9935c9e8a24 - e53501abf992 + - a850902cac64 - f64e7ca2efd2 + - 3ce32adc55b2 + - c9935c9e8a24 - 9f36041495a3 + - e0ad88dec40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -473,13 +473,13 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - 8057cf55fa41 - d68c43202172 - fd3539749127 - - 79489d5685dd - - 8057cf55fa41 + - d43eb39b989e - 4db0695a6fc7 + - 79489d5685dd - b7be725976b6 - - d43eb39b989e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -491,12 +491,12 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 58091e1be01b + - 1ccf0e7fb4f6 - 5296d26b0373 + - 58091e1be01b + - 6a636d58dfc2 - b0d39ef600a7 - bdc67eeb0bc9 - - 6a636d58dfc2 - - 1ccf0e7fb4f6 - 78cd8b69da4c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -509,13 +509,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - e8af591435d1 - b641062a2587 + - 4d3ce9dc1525 + - b17394940c7a + - e8af591435d1 - baa8823f8073 - - '388983871932' - a2f8dc22d7c0 - - b17394940c7a - - 4d3ce9dc1525 + - '388983871932' tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,13 +527,13 @@ tools: - name: bcftools_view owner: iuc revisions: + - e6b5cbbf449b + - 59fa8742285e - 3a233c8eb814 - 38d75661c235 - - abc3ced31cd1 - 3ca3de4e5291 - d1f8f55f564d - - 59fa8742285e - - e6b5cbbf449b + - abc3ced31cd1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -552,50 +552,50 @@ 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: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 9fd5d91eb91b - 690b1d846263 + - 9fd5d91eb91b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -608,8 +608,8 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -622,8 +622,8 @@ tools: - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - fa24bf0598f4 + - eae7c08ebb6f - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -644,22 +644,22 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - 8254e0fe7358 - b07ef36cf7e6 + - 8254e0fe7358 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -672,15 +672,15 @@ 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 @@ -693,8 +693,8 @@ tools: - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - dd44c3f416c3 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/staging.usegalaxy.org.au/viral_tools.yml b/staging.usegalaxy.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/staging.usegalaxy.org.au/viral_tools.yml +++ b/staging.usegalaxy.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 073187688..66b15a436 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - 78c75f134c16 - - 6e9aea89e388 - - 4efdca267d51 - c2ef298da409 + - 4efdca267d51 - 3f3e247c053d + - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,36 +36,36 @@ tools: - name: annotatemyids owner: iuc revisions: + - fe3ca740a485 - 133f36c29579 - - 4f2967b27e67 - - f29602ae449e - - 44018dd6b447 - 1aae04680c4b + - 44018dd6b447 + - f29602ae449e + - 4f2967b27e67 - b5d8e5475247 - - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 - 6519ebe25019 - 7be22100e5e1 + - dc027fa56d55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 28433faa6e42 - 09855551d713 - ca6d970d931c + - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -116,9 +116,9 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 582fd74dc2a1 - 9f2455341fac - 14f588312c56 + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean @@ -132,25 +132,25 @@ tools: - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - - 563a19373357 - 30f08d74024f + - 563a19373357 + - 494f0bb4a993 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - 7abc5f6dd595 - 2bba2ff070d9 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - d3af38b9c7e1 - - b3cf4684e9c7 - 52af33194019 + - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -162,9 +162,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 07d7991bf205 - 79261884facd + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -176,10 +176,10 @@ tools: - name: goseq owner: iuc revisions: - - 8b3e3657034e - - 602de62d995b - - 43798b4caee0 - ef2ad746b589 + - 43798b4caee0 + - 602de62d995b + - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -205,8 +205,8 @@ tools: owner: bgruening revisions: - 74810db257cc - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -232,15 +232,15 @@ tools: owner: iuc revisions: - d46d803ca6cc - - 370c210d9541 - 3c1a01127868 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -264,10 +264,10 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - a17498c603ec - d643e3b03500 - bf68eb663bc3 - - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -279,15 +279,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training @@ -299,10 +299,10 @@ tools: - name: snpeff owner: iuc revisions: - - 5c7b70713fb5 - - 8f92c2b26e6d - 5b80f544c67f + - 5c7b70713fb5 - 5a29ab10dba6 + - 8f92c2b26e6d - 268d162b9c49 - 68693743661e - cfcf33df7fc0 @@ -311,9 +311,9 @@ tools: - name: snpsift owner: iuc revisions: - - 09d6806c609e - 5fab4f81391d - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -337,22 +337,22 @@ tools: - name: tbprofiler owner: iuc revisions: - - 037a11682176 - - ba6f87115e13 - - e1a9d6fd258d - - 809dfc93d593 - 37213cf56392 - - ac8250086ac3 - - 2c68b0c38785 + - 809dfc93d593 + - e1a9d6fd258d - 45083d070fb8 + - ba6f87115e13 - 200c378d85f3 + - 037a11682176 + - ac8250086ac3 + - 2c68b0c38785 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 87bb8718d..7d6073159 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,24 +2,24 @@ tools: - name: abyss owner: iuc revisions: - - 0e93176640ac - fa5259cc561b - 553bfe8bd0b5 + - 0e93176640ac - 841084c5fc46 - - 890b794c997d - - 7547fcab5d19 - 8f1b150a2487 + - 7547fcab5d19 + - 890b794c997d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - ddddce450736 - 067592b6b312 - - b2860df42e16 - - 21e491ad532a - 94fe43e75ddc - b9e31c5c01c7 - - ddddce450736 + - 21e491ad532a + - b2860df42e16 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -31,38 +31,38 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - a7f16f24e9a1 - 3371c5bdc17a - 22286dab5aa1 - faee8629b460 + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 1440ae06552f - - 46ae58b1d792 - - 2dd755c1c6ff - - 1e62c28ba91d - - 94170eee0ad8 - - e4bd1e99bacf - 0d243f458b53 - - 4048d82f0c88 - - e824f5d958d0 - - 41030a6c03b7 - - cf13a1e03e5b - 602fb8e63aa7 + - e4bd1e99bacf + - 94170eee0ad8 + - cf13a1e03e5b - 5ecdeca79a0d + - 2dd755c1c6ff + - 46ae58b1d792 + - e824f5d958d0 + - 41030a6c03b7 + - 4048d82f0c88 + - 1440ae06552f - bb935709506a + - 1e62c28ba91d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - c5b7390290b1 - - 5732f959936a - 86f150c8019d + - 5732f959936a + - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -74,12 +74,12 @@ tools: - name: flye owner: bgruening revisions: - - 1ce9b1d72ec3 - - cb8dfd28c16f - e27815e82dd4 + - 1ce9b1d72ec3 - 3ee0ef312022 - - 276f5d8712d5 - 8d4f03b5fe9d + - 276f5d8712d5 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope @@ -101,8 +101,8 @@ tools: - name: gfastats owner: bgruening revisions: - - 3fba9c77550a - 690c2caa367e + - 3fba9c77550a - 3ef480892a9f - 5127a713de83 tool_panel_section_label: Assembly @@ -116,18 +116,18 @@ tools: - name: hifiasm owner: bgruening revisions: - - 71740308d412 - - 9ef6920c3089 - - da9d8bf98802 - - ec9e21e9c71b - - 5f625c63b8bc - - 2061fb3b81b4 + - 045c7c3d8e59 + - 366a11d316a7 + - 5bec28269d95 - 3f7be05a1597 + - ec9e21e9c71b - 6505bd37670d - - 045c7c3d8e59 + - 71740308d412 - f3c89da3af16 - - 5bec28269d95 - - 366a11d316a7 + - 2061fb3b81b4 + - da9d8bf98802 + - 9ef6920c3089 + - 5f625c63b8bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -145,37 +145,37 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - de387b2b2803 - 7518ee87b53d + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b - 9d79beb19ac3 - 39edec572bae + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - - eadfd71dde37 - 51c2360aa807 + - eadfd71dde37 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f338e9942b27 - - eb7a370f6588 + - fd128c111ab0 + - e731ea24e48d - 2ecf5a570907 - 606b09cc9860 - - e731ea24e48d + - f338e9942b27 - 3ca2d2a9068c - - fd128c111ab0 + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -187,11 +187,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8b6d0d85252b - - 8dee0218ac7d + - a7b889b90140 - 73a3846701e1 - 80d1250bd5fd - - a7b889b90140 + - 8b6d0d85252b + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -203,9 +203,9 @@ tools: - name: novoplasty owner: iuc revisions: + - 7c2f5268d01c - 15200570e926 - 64a1c751d99b - - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -217,12 +217,12 @@ tools: - name: pretext_map owner: iuc revisions: - - 8fef980d48b5 - - 2b16ba799da9 + - bbe19ef04a74 - dfb8a4497339 - 02831bf9e95f - d256a51a656b - - bbe19ef04a74 + - 2b16ba799da9 + - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -236,33 +236,33 @@ tools: - name: quast owner: iuc revisions: - - 875d0f36d66f - 59db8ea8c845 + - 875d0f36d66f + - 3061c8b029e5 - ebb0dcdb621a + - 6fcbee531de6 + - 72472698a2df - 675488238c96 - 342a1d1fed7b - - 6fcbee531de6 - 7594365c546b - - 72472698a2df - - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 - cd06929b224b - - aa39b19ca11e - 39bed8de8017 + - a199cd7ac344 - e100a765370e + - aa39b19ca11e - d865b62f501c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 3edba9afc9bc - 2b2a352488fa + - 3edba9afc9bc - f8564b2d7f63 - f11b994b7eb2 - 33b7d8481a76 @@ -273,17 +273,17 @@ tools: revisions: - e122f9101584 - 53c2bc8c2ae3 + - 378e55aeeb25 - ef69617ecb42 - 1d06c8b38e77 - - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - f77f7a7f3b83 - - 9a22227bb6d0 - ba7b0f11e470 + - 9a22227bb6d0 + - f77f7a7f3b83 - ab5b7f6b7198 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -296,59 +296,59 @@ tools: - name: shovill owner: iuc revisions: + - 83ead2be47b2 - ad80238462c1 - - 865119fcb694 - d9f6a00b6db7 - f698c7604b3b - 196a599ec43d - - 83ead2be47b2 + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 24e471d13fe9 - 5a0ddb4dc3a4 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1bb12736175c - - 1fc82fe7ebef - 051fd2db8a27 + - 1fc82fe7ebef - 7490b213baa9 + - 1bb12736175c - 904bf932cf78 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 34305b013402 + - ad8b536d1caa - d6e617c4e338 + - 34305b013402 - fee85957cebe - - ad8b536d1caa - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - - 6b5a5842531e - e5a3b75a271f + - 8d4b90bf9caf - 21da31ed41a1 - b8002c3f7141 + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 - - 86f66ab58e14 - 2a10645aeadd - 328aa71f0f3c + - 86f66ab58e14 + - 9de69775f512 - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -356,108 +356,108 @@ tools: owner: iuc revisions: - e41dcb0e913b - - 85fb02c43042 - 340bc17f49cf - - 6aad515a5270 - 1708851f8804 + - 85fb02c43042 + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 - b3490b036c5a - - 249f6a28c751 - - d159735a6a9f + - b65a43f70b99 - d5fb354f745d + - d159735a6a9f + - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - 9006e5836729 - - d2d1df21dfb9 + - 33368fec3b70 - 7897763d14ec - - b7829778729f + - d2d1df21dfb9 - dd7ad84f3943 + - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - 6f4c8ad6ea01 - - ced385aa976d - 8f631679571f - - 505a9833ab5d - 189e837009c9 + - ced385aa976d + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: + - d40ed4eb0c0e + - e59bee4565b3 - 356afed970b4 - 19bdfd1e6fe3 - - e59bee4565b3 - - d40ed4eb0c0e - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 80a17897564d - 4688ae3b49b5 - ebd801e712bc - - 6dd935e4984b - b23249f81bc4 - - 80a17897564d + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - b64696992ee9 + - 937ea677d437 - cb1e3db43020 - 59bd28f6265d - b5e35a2ca4f3 - - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 383bb5ad32e2 - - 6015aa0303f2 - - 05bd7504fdb2 - cb4768eeca3b + - 6015aa0303f2 - 2628f6790eda + - 383bb5ad32e2 + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - d10bdad2fd17 + - 6e26c9afd301 + - e92675014ac9 - 9e3e80cc4ad4 - 0a3a602cd1e3 - - e92675014ac9 - - 6e26c9afd301 - - d10bdad2fd17 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 920677cd220f - 08256557922f - 8d09f8be269e - 5da9a0e2fb2d - - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 4a53b89fa703 - - 82398ba86ba7 - 37d88f41c810 + - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 73e6b4aa3..e2d3e7279 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -9,17 +9,17 @@ tools: - name: mlst owner: iuc revisions: + - 1f5641a52664 + - 31812e7a1315 - 8e8dc9a1e3e5 - ded48b36f3b7 - - 31812e7a1315 - - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 24a7a95867b0 - 17fcac7ddf54 - 5c8ff92e38a9 - - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 434a88153..35dcfef42 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - a9c9d768b751 - 204a131e47db + - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 6d0356195..243c58e65 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: + - 0a5c785ac6db + - e19bebe96cd2 - b28e0cfa7ba1 - 07e8b80f278c - - e19bebe96cd2 - - 589e7e57fd6d - 87ee588b3d45 - - a68aa6c1204a + - a8eabd2838f6 - ce3c7f062223 - - dde39ba9c031 - - 0a5c785ac6db + - 589e7e57fd6d + - a68aa6c1204a - a1a923cd89e8 - - a8eabd2838f6 + - dde39ba9c031 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 a9fad4ffa..4079d8570 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,20 +8,20 @@ tools: - name: diamond owner: bgruening revisions: - - 54f751e413f4 - - f921014aba5a - 62c9df8382c2 + - 54f751e413f4 - 1e3323a44643 + - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - - acf4e47b734c - - 2889433c7ae1 - 0e3cf9594bb7 + - 2889433c7ae1 - e25d3acf6e68 + - 6f386c5dc4fb + - acf4e47b734c - 5edc472ec434 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 63d3c8eea..3621ea7e1 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - c8cdde00b105 - f4230f116196 - - 27ee142314a9 - - 095ad4d096d1 + - c8cdde00b105 + - da6bd1975a71 - 6ca543ec1bf8 + - 27ee142314a9 - 710301bc46fa - - da6bd1975a71 + - 095ad4d096d1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -81,8 +81,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -101,9 +101,9 @@ tools: owner: chemteam revisions: - 79cfd9ead848 - - 3b8a9d5ced85 - - bfb65cb551d8 - 88076940fa94 + - bfb65cb551d8 + - 3b8a9d5ced85 - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,37 +111,37 @@ tools: owner: chemteam revisions: - 715cd0e87781 + - b46d4b4d995c + - f5d979cb4b54 - 55918daa5651 - d532b7e5f64b - - f5d979cb4b54 - eb6564a60136 - - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 - - d2f955aea23a - fdf2cc80adb5 - - dae135dfd519 + - d2f955aea23a + - f26afd1b7104 - 5579659312e6 + - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - bc31d02be922 - - 319a28774da9 - d1d0efda35c0 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - cac1886249a2 - - ed736e6eee39 - 4da9ee404eab + - ed736e6eee39 + - cac1886249a2 - 070e3ecc3fda - 2c349b027a01 tool_panel_section_label: ChemicalToolBox @@ -149,14 +149,14 @@ tools: - name: gmx_sim owner: chemteam revisions: + - 2e219a2d9327 + - c0c9a5024177 - 525ca7c8065f - - f197e34c33a9 - 73008ef1f487 - d1f803b5943c - - 2e219a2d9327 - - c0c9a5024177 - 807aa4c9293d - da8753545526 + - f197e34c33a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate @@ -164,27 +164,27 @@ tools: revisions: - 61094e01eff9 - c4fbab8e03c5 - - 1809414a9454 - 7568ae18908a - 27ea4e1a3f95 - 2c8ed1b52bf7 + - 1809414a9454 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - ba83f0923369 - - 730ef07b90ae - 79e8ab8f1e81 - ccfbd956a2d3 + - 730ef07b90ae + - d7ec25187599 + - ba83f0923369 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: natural_product_likeness @@ -196,9 +196,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e2c36f62e22f - b59c91adeac1 - e6011617c748 + - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -228,8 +228,8 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - d4c67ced6abc + - 85fad59f8168 - 9b48456a96fe - bf99565cec1f tool_panel_section_label: ChemicalToolBox diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 13ab0a108..75adcb6f9 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - - fa56d93f7980 - c97a786e8fb5 + - fa56d93f7980 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,17 +16,17 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 424aefbd7777 - f5d67c722d67 - - 495a4173006f + - 424aefbd7777 - 640d3af5d833 + - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 6ea678946..51ad0d4a9 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -10,9 +10,9 @@ tools: owner: nml revisions: - 90981f86000f - - 25136a2b0cfe - - 830961c48e42 - 33151a38533a + - 830961c48e42 + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -25,14 +25,14 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - 6cbe2f30c2d7 + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index dbcb9a07a..9c3ffcc4f 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,26 +8,26 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 0b3c3ad92827 - - e3cbd2287f63 + - 367b1ed91207 - 4a6ee918c13a + - e3cbd2287f63 - 5e1240a87bcb - f3a19509108a - - 367b1ed91207 + - 0b3c3ad92827 - a3b86937ead6 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e525f9ffb9ac - - bd46669113b9 - - 54ccb7e1f49a + - 1b5fc03380d4 - 584008e574b2 - 501c21cce614 - - 1b5fc03380d4 - - 72ed72122deb + - e525f9ffb9ac - 33c99804a32f + - 54ccb7e1f49a + - 72ed72122deb + - bd46669113b9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -52,8 +52,8 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 186b8d913e6c - 8979c288aefb + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -118,11 +118,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 63769c4217a7 + - 92ac8e086317 - 19e45916daf9 + - 63769c4217a7 - 26c6706bfb07 - b9b385097f13 - - 92ac8e086317 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index b1bcf72c3..2896f3165 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -4,185 +4,185 @@ tools: revisions: - 268e91e540ee - 5f6d123679f4 - - e821645ef8fc - de72ba3ed6f2 - - 29451af70c52 + - e821645ef8fc - a1ca9bccc7f2 + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e143b4c3987 + - 5d11599b8a7d - 7a7fd0f5f15d - bb1e4f63e0e6 - - 0e143b4c3987 - 12af64f93288 - - 5d11599b8a7d - 2d2cf5c1ea8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 7c1beb6d6eca - - 81b1e3e1fc6c - dc059492a995 - - 1d848bc4585f + - 7c1beb6d6eca - 195e98217334 + - 1d848bc4585f + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 71aa86af6762 - - 93eb012d9eed - 3d211717a775 - - a67ac707496a - - 26e7304d6737 + - 93eb012d9eed - bfff7454b59a + - 26e7304d6737 + - a67ac707496a + - 71aa86af6762 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 2bc10a9ca58b - - 29fcfd36e90a - 56d5b797ce84 + - 2bc10a9ca58b - dd0b7398bb96 - b8858746dc1f - 5be24eba848d + - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 9384cd033f30 - - 72bfafe3330b - ee3a1b0f45f1 - - c3e012dfe21f + - 72bfafe3330b - 7e6bcd2e5128 + - 9384cd033f30 + - c3e012dfe21f - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - b73e213add0c - 514fa53b5efb - fb9cf9c97ec4 - - fd1275e01605 - - d9a637e83828 - 9470f29702f8 - - b73e213add0c - 167788df3b46 + - fd1275e01605 + - d9a637e83828 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: + - ca0616bb2cdf + - a02cfa31e9cb + - c34d11ea4ba6 - 86febdcc4283 - 2c37ce318bc3 - 5bffaa8354a1 - - ca0616bb2cdf - - c34d11ea4ba6 - - a02cfa31e9cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - 004aea905d4d - - 78f405266706 - - 69a8621ca2f0 - 1fcb7adc39b8 - 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: - - 2f9e4843f480 - d580d6acd1df - 459cfa861f0b - - d9ce4897dbb2 - - 9ecba5e225a6 - db940c262830 - 3c9f0c486cca + - 2f9e4843f480 + - d9ce4897dbb2 + - 9ecba5e225a6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fd408d755394 - - fbe773640707 - 2c66e43f1c86 + - bd7db9e2f2cb - 32e451def88c + - fbe773640707 - f264afa9fa6f - - bd7db9e2f2cb + - fd408d755394 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 56bce3c82278 - 7e361d147872 - - 9368fbc49c8b - - 3b9d990a0a0e - 4e12ea27f788 + - 3b9d990a0a0e - 7fda5607e777 + - 9368fbc49c8b + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - e65d16fb2724 - - ce4ce3316f74 - - 94ca68515826 - - d9114ef1c8a5 - c03c3384cd81 + - e65d16fb2724 - b1779366c8e9 + - d9114ef1c8a5 + - 94ca68515826 + - ce4ce3316f74 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - b88ebb3672a1 - - f8fc4e5aff9d - 2da482e408b8 - d57251071381 + - f8fc4e5aff9d - 793665fff0f8 + - b88ebb3672a1 - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - c60570fa602f - - a4dfb122e52b - - a7849312d328 - 010e58e9d822 - ba6efa77fb79 + - c60570fa602f - 512155688d98 + - a7849312d328 + - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 38e3f226248b - 69264da0ce77 - - 00d869ea03a1 - 4d678170d29b - - aa200e4f3939 - c899e0ccff8c + - 38e3f226248b + - 00d869ea03a1 + - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - d806504e96d9 - c361b12d207a - - a2d70c4fd406 - - aac8444d6681 + - d806504e96d9 - 10301d137111 + - aac8444d6681 + - a2d70c4fd406 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index e07a4cfcf..71acc956f 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -16,29 +16,29 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - 374fd9feb032 + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - fe7ec8a3d35e - e9e49cf06b42 + - fe7ec8a3d35e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 83fbdf93d51e + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 3bf57dadf7cd - 76e69de726b2 + - 3bf57dadf7cd tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 723a93febe89 - 39320fee9d70 + - 723a93febe89 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index e9a6db869..f664232e7 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 - - dba489bfcd62 - - 63dd26468588 - 832c20329690 + - 63dd26468588 + - dba489bfcd62 + - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 32fd93f8d..85a3f9836 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -17,7 +17,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index ba2a1f9bf..db36bfdec 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,36 +8,36 @@ tools: - name: cutadapt owner: lparsons revisions: - - 288f97432497 - - 44e2cc14f75b + - 660cffd8d92a - c5e2e5902201 - - e4691e1589d3 - - de6cebe3c043 - - 49370cb85f0f - 4e5056fefd88 - - c4b82dce8335 - - 135b80fb1ac2 - - 8665bcc8b847 - - 093678460093 - - 5915ea1ec9b1 + - e4691e1589d3 - 8c0175e03cee - - 660cffd8d92a + - 135b80fb1ac2 - c053d4cad713 + - 8665bcc8b847 + - 288f97432497 + - 44e2cc14f75b - 48f587c13075 + - 5915ea1ec9b1 + - 093678460093 + - 49370cb85f0f + - c4b82dce8335 + - de6cebe3c043 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - f666895cbebd - 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 @@ -62,8 +62,8 @@ tools: - 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 @@ -77,17 +77,17 @@ tools: owner: iuc revisions: - 9c620a950d3a - - cd0874854f51 - - 56022eb50bbd - 0dbb995c7d35 + - 56022eb50bbd + - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbf9c561ef29 - - 65b93b623c77 - 1d8fe9bc4cb0 + - 65b93b623c77 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -100,8 +100,8 @@ tools: - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -128,8 +128,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -142,37 +142,37 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - - 249c8393f2d4 - 35e38452bb3f + - 249c8393f2d4 + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -184,8 +184,8 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 - 09070cacefd8 + - 567d5b3c52b1 - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -200,8 +200,8 @@ tools: owner: devteam revisions: - bdf1ce174e39 - - 736b8f6ee456 - cb1e251cac37 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -214,25 +214,25 @@ tools: - name: fastx_renamer owner: devteam revisions: + - 3599f5451ee2 - 02f8a17a4ebd - b29d37ca9e41 - - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - e246088b6e34 + - 6027ef51ef91 - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 61b4cedc8934 - 377ac2829eac - 547e8d00f11c - - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -244,8 +244,8 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -264,8 +264,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -278,11 +278,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 8250ea3a1501 - 24013bf85a6f + - a535cf1e5da4 + - 8250ea3a1501 - e654095ab143 - b557acca0b56 - - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -294,11 +294,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 - - 7accf7407811 - 9fa7803d1c51 - - 828dba98cdb4 + - 7accf7407811 - 6a675c3aa610 + - f3759eec3018 + - 828dba98cdb4 - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index e8bc9dc43..fba279090 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,9 +2,9 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - e41385662e5e - - 7b4468117008 - ce9cd02d5b88 + - 7b4468117008 + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -17,63 +17,63 @@ tools: - name: fastqc owner: devteam revisions: - - e7b2202befea + - ff9530579d1f - 2b0c9d9fc6ca - - 3d0c7bdf12f5 + - e7b2202befea + - 5ec9f6bceaee - f2e8552cf1d0 - - ff9530579d1f - 9da02be9c6cc - - 5ec9f6bceaee + - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - 8880fb74ef56 - - a72af9de6bf5 - 41b2ad601cf0 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - b2f1f75d49c4 - - bf675f34b056 - - abfd8a6544d7 + - 75c93c70d094 - 3d93dd18d9f8 - - 5e33b465d8d5 - - 1c2db0054039 - c1a4b5f3b432 - - 75c93c70d094 + - 1c2db0054039 + - 5e33b465d8d5 + - b2f1f75d49c4 - 9a913cdee30e + - bf675f34b056 + - abfd8a6544d7 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - cd7e644cae1d - 949f01671246 - 084bbd8ba7b8 - - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 5b44a1c25..7946b577d 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: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 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 26a257991..98a2b5c92 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,23 +2,23 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - 8f53b238a360 - - 0c8f7322f8fc - f2f3bc622a16 + - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -79,30 +79,30 @@ 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: - - 45296e47d565 - cf61daf064fe + - 45296e47d565 - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -115,23 +115,23 @@ tools: - name: gemini_qc owner: iuc revisions: - - 9e83673fa6d2 - 86e46972e183 + - 9e83673fa6d2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query owner: iuc revisions: - - 840fb4850be3 - da74170c55c7 - 666f60a9331a + - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -144,15 +144,15 @@ tools: - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 0fe27413f..18d33de94 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f 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 6d7643433..e56cb3f7b 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,51 +3,51 @@ tools: owner: galaxyp revisions: - e9df53a75f3c - - b39347891609 - c1b437242fee - 983bf725dfc2 + - b39347891609 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - - e063168e0a81 - 28587613264f + - e063168e0a81 + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 83c7d564b128 - - aad3885b3216 + - e08a7ad4378b - 5e6237d58b0c - - 69ebb7f46e45 - - 6ea73833cf67 - - 9a776b080193 - f5ea3ce9b9b0 + - 653e89d73fc4 + - 4df8de2d0e48 + - 9a776b080193 + - 69ebb7f46e45 + - aad3885b3216 - 7068f48d0ef9 + - 83c7d564b128 - c441583adae5 - - e08a7ad4378b + - 6ea73833cf67 - 1790dcf3c32d - - 653e89d73fc4 - - 4df8de2d0e48 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - 7863f1abcdda - 34758ab8aaa4 + - 9aaa46d45472 - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - af5eccf83605 - 054483e27a35 + - 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 8ef69eae5..941ace098 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: - - 7f13dc906cb9 + - df7356989ac1 + - fd59d783248a + - 740057a5126d - 4b519282a05b + - 290a11559985 - c4bde687c846 - ae9994cf526f - - fd59d783248a - a64dc31ab7f2 - - 740057a5126d - - df7356989ac1 - - 290a11559985 + - 7f13dc906cb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,37 +28,37 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - f95284aa2946 + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - - ca7cb0eaad62 - 3b37b1b1c3a7 - - '566197475670' + - ca7cb0eaad62 - 53460afd5115 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - da4c086cff5b - - 3d059e9c2fba - d3a9e32672ec - - 10515715c940 + - 3d059e9c2fba - 391a4cc45fea + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - e3a675da7fd0 - - d0fc8b746d57 - - 1acf88921176 - 3b12bf9b4b87 + - e3a675da7fd0 - 5fe1dc76176e + - 1acf88921176 + - d0fc8b746d57 - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,8 +78,8 @@ tools: - name: graphlan owner: iuc revisions: - - a490b70e46fc - 8f62f666dcb6 + - a490b70e46fc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -91,17 +91,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 836d1aa3e89a - - fd5dbf0f732e - - 4542035c1075 - - 667e17248bfe - - 6cd09d7b5f37 - 2bb2e07a7a21 - a6e57ff585c0 - - 17359b808b01 - - ca2def38369c + - 836d1aa3e89a + - 4542035c1075 - 1cfc579079a6 + - ca2def38369c + - fd5dbf0f732e + - 6cd09d7b5f37 - 112eb40ba6cf + - 667e17248bfe + - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -120,8 +120,8 @@ tools: owner: iuc revisions: - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -166,14 +166,14 @@ tools: - name: pygenometracks owner: iuc revisions: - - 14e7c35f3d00 - - a1abfa420d9d - - 4ac4e7083b7e - - 2824d77cd8f8 - 7dd841a32245 - - 360df4999907 - 326a3db8d9d1 + - 2824d77cd8f8 + - 360df4999907 + - 14e7c35f3d00 + - 4ac4e7083b7e - 59fd173ac850 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 240e4b143..c2bb385d2 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 3448bc1ab..66f3f53bb 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,17 +2,17 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - 9edf8894a22d - 921a2da49a0c - 29f66c353bcb - - 9edf8894a22d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - d404277cc87a - - 78fb5e286609 - 5746d61f0a91 + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins @@ -26,16 +26,16 @@ tools: - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - - 0ba4f56a3613 - 41dbf4d162a2 + - 0ba4f56a3613 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: + - 7babd8a46fe0 - 5308ca68ef3d - 9939786dd9c9 - - 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 16c8a9d8c..6fab85659 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -33,8 +33,8 @@ tools: - name: bfconvert owner: imgteam revisions: - - b07f4839ca77 - f3360fbeda64 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -53,8 +53,8 @@ tools: - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - e917a2424690 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -73,15 +73,15 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - df3ad3ba5c6f + - cdf8e3c57dae tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -101,8 +101,8 @@ tools: - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects @@ -115,8 +115,8 @@ tools: - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - c09dcda1143f + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -184,8 +184,8 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 19c0224c7..c4fb89eba 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 3e4f434a69c6 - 1069f6db0a0e + - e4ee04da1c19 + - d6e72da3ec35 + - e319b5b65879 + - 3e4f434a69c6 - f362150bef41 - 78bbd17d0703 - 17f911830a8c - - d6e72da3ec35 - a38934e303b9 - - e4ee04da1c19 - - e319b5b65879 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e + - 9537184d421f + - 2b95d5c04908 - 8f8df367470d - - 7fe36019c073 - - f91cfb73d369 - 0135f1d487a0 - - 1ef5b6e3e09d - - 2b95d5c04908 - - 9537184d421f - 72ddd32392cd + - f91cfb73d369 + - 7fe36019c073 + - 1ef5b6e3e09d + - c88553ec696e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - - 2cf4a1cafc16 - fafb3d685fa9 + - ad0dc9f4c9e2 - d7e79eb3bcb3 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 7f1cfa4c0e32 - 43aac8d29685 - - 8c05afb547fa - - 69797fa273c3 - - 9eaadf03e0df + - 3d18f8c3c0f6 - 94df24c6bc00 - - ee2beb764a7b - 28a6f1908fcc + - 9eaadf03e0df - 8d36959b000d - - 6a1515bb0687 - ee29337f905c - - 3d18f8c3c0f6 - bd2a7d1316b9 + - 7f1cfa4c0e32 + - ee2beb764a7b + - 8c05afb547fa + - 6a1515bb0687 + - 69797fa273c3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5671e1d3d5ee - bcaa0d571ce2 - - c092052ed673 - - db536ad45f28 - d37ede8589b2 + - 0893a1dbb807 + - 5671e1d3d5ee - 364f4ffec275 - - cb903c9dc33d + - 9f978da6528a - 8858fa037a15 - 5d6ed46cc101 + - c092052ed673 + - cb903c9dc33d - e3bb03cf207a - - 0893a1dbb807 - - 9f978da6528a + - db536ad45f28 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 045d6d00f606 - - e1a015876aa9 - - 584beffa972b - - 230b05597996 - - 3b6a16d82c1b - 49236b03e4fd - f95f403841ad - - 38b91a3190cd - - 12d66d0d05ac - ed28dd32141c + - 3b6a16d82c1b + - 38b91a3190cd - c5c9f02b6167 + - 12d66d0d05ac + - 230b05597996 + - e1a015876aa9 + - 584beffa972b + - 045d6d00f606 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 4d7919ab7..4773a22e5 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,8 +2,8 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - f198773344e4 + - b8a457820315 - 17e3b698dd52 - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group @@ -11,9 +11,9 @@ tools: - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf - - 22c2a1ac7ae3 - ac092723240d + - ba0c40780ecf - 374cb875d38a + - 22c2a1ac7ae3 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 38d7355b6..024d05d9d 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -14,17 +14,17 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: + - b6ef6d0cb6b7 - e1317b5502fa - f1b9a42d6809 - - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - 05143043ca13 - 947c2eacccb8 + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction @@ -38,37 +38,37 @@ tools: - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 - 1a53edc4b438 - - 53616c8b0865 - 841a6cc5fc58 + - 53616c8b0865 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 40f4447733b2 - - 2fc89dcd41c8 - 91c4e3331208 + - 2fc89dcd41c8 - dc4b5fd604a6 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - c6ae57f774c6 + - e5a5ad882f1f - 301e07345c93 - 25ab6b4e376e - - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 02d2be90dedb - b7c3e9a3b954 - - f9639b488779 - 4ed102b922cb + - f9639b488779 + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 17260a526..a5d9101b5 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - a6d65b0c67af - - f6877ad76b00 - 749c918495f7 + - 03e9b2fbc005 - 17062a0decb7 - - 3ba8d4563129 - - 937aa69e715f - 017aba02828d - cd659e8cc5fa - - 03e9b2fbc005 + - a6d65b0c67af + - 3ba8d4563129 + - f6877ad76b00 + - 937aa69e715f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -29,9 +29,9 @@ tools: owner: devteam revisions: - 3fe632431b68 - - dfd8b7f78c37 - e188dc7a68e6 - 53646aaaafef + - dfd8b7f78c37 - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -44,26 +44,26 @@ tools: - name: lastz owner: devteam revisions: - - 60afcc2c1d05 - - 3e1ea2facca6 - 2ff111fac1d7 - e7f19d6a9af8 + - 3e1ea2facca6 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - b3eab4b67562 + - c0c2d0941de8 - 037c6e54df11 - - 3f4d6399997b - 77b2770508f6 - - 53c0b7a1a0c3 - - 8c6cd2650d1f - 09b53c1d4ab1 - - c0c2d0941de8 - - f54f5baedfdd - 11a0d50a54e6 + - f54f5baedfdd - be1d967337e4 + - 53c0b7a1a0c3 + - b3eab4b67562 + - 8c6cd2650d1f + - 3f4d6399997b - 6b1e195506a3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -71,14 +71,14 @@ tools: owner: iuc revisions: - b8f5f6e87f5c + - 00fbfac99d39 - 1cd2511a396e - 79b885ce78d7 - - 00fbfac99d39 - - ec9cbd6b9a49 + - 9ee34ba73ebf - 13022c3d3076 - - 178bdbdb6d24 - e403d27e8f24 - - 9ee34ba73ebf + - ec9cbd6b9a49 + - 178bdbdb6d24 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 7497bfe5a..c44a29f6a 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - 388e6678fa98 - 7f1aaa1932d8 + - 388e6678fa98 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: combine_metaphlan2_humann2 @@ -22,8 +22,8 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - 63f86089423e + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada @@ -37,41 +37,41 @@ tools: - name: dada2_filterandtrim owner: iuc revisions: - - 34e55239e68b - a9f4a217dcd6 + - 34e55239e68b - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 8c202e741d68 - 0776d824d896 + - 8c202e741d68 - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: + - 8470de786d47 - e96bbb9e24ea - 1c9b3bcd4261 - - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - 306a40d4bb8f - 84743da21318 + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - ac72310b038a - 8daf4564ccda - 555ccac8a4c5 - - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile @@ -85,8 +85,8 @@ tools: - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - 7f3b59dee073 + - 04144473e59e - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -94,22 +94,22 @@ tools: owner: iuc revisions: - d943081510da - - 9058d8943303 - 0a1224c4b781 + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - c4db8c4de66f - dbf1798c0dcc + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -123,8 +123,8 @@ tools: owner: iuc revisions: - 6d364c65c946 - - 6c84982ee6f7 - 654548ae1357 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -136,16 +136,16 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - bd7a9c6efb10 - 6aad8ca3918b - e66ab198ec15 + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - b084117133af - c6676a890f50 + - b084117133af - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -153,8 +153,8 @@ tools: owner: iuc revisions: - 9704f1a3b32d - - 7f208f1eb64f - cad93abecac9 + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -167,53 +167,53 @@ tools: owner: iuc revisions: - 79706f10d680 - - c409a495841f - 31c6d107e7a5 + - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c - 172920f67a84 - d24841f5c3d2 - 71ea608ddfa3 + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - 12fb63b5f63f - 4137b492233e - - d7e9a3c41657 - a4d7148ccee4 - - 12fb63b5f63f + - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - 75bedfb2078b - - e2c71b852aba - 6fcb8ac37a3e - cf87759761eb + - e2c71b852aba - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - 4033827c76b8 - c82508e76ad1 - 080ea153677c + - 4033827c76b8 + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 2cd76b089570 - - 95bf7479d53c - 6b7622dda516 + - 95bf7479d53c + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -287,8 +287,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 3d6570bffdb1 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -342,15 +342,15 @@ tools: - 2cff76cf35c6 - 0270541aaf46 - 4fd3b5d8706b - - 27250f92a01a - e073891b2afc + - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -423,13 +423,13 @@ tools: - name: metaphlan owner: iuc revisions: - - 2131d7dca455 + - 6dee4abadccb - ff8f55893e7d - - 1a6cdf55390f - - a92a632c4d9b - b89b0765695d - - 6dee4abadccb + - a92a632c4d9b + - 2131d7dca455 - a16313517e55 + - 1a6cdf55390f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -478,8 +478,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 3bd5f5afb9b1 - 2e62e32d4f33 + - 3bd5f5afb9b1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -497,10 +497,10 @@ tools: - name: staramr owner: nml revisions: - - 4b9a8031ab74 - - 2fd4d4c9c5c2 - 4d83eccf5f81 - aeaa20b96ef2 + - 2fd4d4c9c5c2 + - 4b9a8031ab74 - be818ae858e4 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 3a4bc2787..9b6a140d4 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 @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 9710e4d42..fcffedbce 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,34 +2,34 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - bdfbaf0c10aa - 9baa871cb1d1 - - cd07731e4434 - 48c13389050d + - 80f03df2e2ce + - cd07731e4434 + - 6ae5a7b5a0a2 - 2263989660f5 - - 9422c5a87ee2 - 8b67dd48fec1 - - 80f03df2e2ce + - 9422c5a87ee2 - a74dbfee5a86 - - bdfbaf0c10aa - - 6ae5a7b5a0a2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - bc3831dd65c1 - - d390fe1567dc - 2e093badc689 + - f0af8936ed41 + - aaa0d6a8b808 - f14193ec1f50 - 5abf2c2249aa - - f0af8936ed41 - - 4a60927aaca5 + - d390fe1567dc - fc2e49f91e52 - - aaa0d6a8b808 - - '764845535798' - c18157c68134 - - d7ce0ec78e51 - be78f13134e2 + - bc3831dd65c1 + - '764845535798' + - 4a60927aaca5 + - d7ce0ec78e51 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -48,8 +48,8 @@ tools: - name: clustalw owner: devteam revisions: - - 4daabc25df00 - d6694932c5e0 + - 4daabc25df00 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -61,25 +61,25 @@ tools: - name: mafft owner: rnateam revisions: - - f1a5908ea2cb + - f0d493f8f84f + - 15974dd17515 - a65296ffb4a0 + - f1a5908ea2cb - c5908940967d - - 15974dd17515 - - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - c9685bc0407c + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -106,7 +106,7 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 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 9b2536b56..57c90a507 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,33 +2,33 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 72b5e9dda577 + - 79e9a869f40e - a7228a7ea146 - - 0e9e7fcdd543 - cb34f00cc10f - - 79e9a869f40e + - 72b5e9dda577 + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - fa11aa8103b2 - db25ec99c3ea - d6cddc06aeae - 682d1e2c8be4 - - fa11aa8103b2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 222669c4afb6 - - edf6d4003fad + - cc36773a3681 - 0f5f4a208660 - - ec699520444c - - 19f3b583a9b3 + - edf6d4003fad + - 222669c4afb6 - 2bf63b38ee9b - 43815fa60f3a - - cc36773a3681 + - 19f3b583a9b3 + - ec699520444c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -47,10 +47,10 @@ tools: - name: nanoplot owner: iuc revisions: - - 0f1c34698076 - - edbb6c5028f5 - a3c4fe6f49ab + - 0f1c34698076 - 645159bcee2d + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -63,8 +63,8 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya @@ -77,23 +77,23 @@ tools: - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - de5b3d8f5b90 + - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - 5f76b20953e5 - - 93d623d9979c - 543cbeef3949 + - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -105,8 +105,8 @@ 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 @@ -118,8 +118,8 @@ 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 @@ -131,8 +131,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 4fe6b96aff72 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle @@ -169,8 +169,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 63eab2449..4d33f580c 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -20,16 +20,16 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - adfd6bf710bd - 3e73c97f025d + - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 83da94c0e4a6 - 9dd107db92c2 - 1586b111d2a3 - - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -68,9 +68,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 38ccd4589990 - 5711fc06a63e - 48a42ca61006 - - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -83,22 +83,22 @@ tools: - 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 owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -118,9 +118,9 @@ tools: owner: iuc revisions: - 52b6a4d98009 + - b4b2b284230a - 27a6a256cd23 - 172815da3d41 - - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -132,8 +132,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -192,33 +192,33 @@ tools: - 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: - - 29c738066906 - - df30a2f1db55 - - ed7a967cb11b - 6e24e79d3d69 + - ed7a967cb11b + - df30a2f1db55 + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - 1865e693d8b2 - ad90c2da4f38 - 3e4d45aca422 - - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -230,17 +230,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - - d63c1442407f - 64deddb6a8ec + - d63c1442407f + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - - 9946bc39c834 - 94a50db37d1a + - 9946bc39c834 + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index aff02fd68..630dc1fcd 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,60 +20,60 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_absrel owner: iuc revisions: + - 3f59ebfbfe3d + - cce7b18495e4 + - 3b8b5bde0bd9 - 5a7c56a5cc08 - d7c7ef3353fe - - 107d3ba7024a - - 6a457678efcb + - c78f3d7dd1db + - a6619171428e + - d033ffc1c161 - 8834daeb9892 + - b89cac5156ec + - '841557158611' + - 6a457678efcb + - 107d3ba7024a - f73435dc282b - - a6619171428e - 26de3a7b1cb9 - - 3b8b5bde0bd9 - - b89cac5156ec - - d033ffc1c161 - - 81e66674859e - - c78f3d7dd1db - - 3f59ebfbfe3d - f04a1264e2a2 - - '841557158611' - - cce7b18495e4 + - 81e66674859e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - df47d4845b62 + - 6283babe736e - a185b079b095 - - 659517798cc4 - - 88c4aa435ded - - 6a726db04d4b + - e75442c7f4da - 5fcd1ece3a6e - 3b96e92e8ec3 - - df47d4845b62 - - b0af57c1a968 - - e75442c7f4da - - aa8cc71438cf - - 7a2092844346 + - 4755f52427c4 - 5b777002c2de + - 7a2092844346 - 6223845127ea + - b0af57c1a968 + - aa8cc71438cf + - 88c4aa435ded - 02b8758214b0 - - 6283babe736e - - 4755f52427c4 + - 659517798cc4 + - 6a726db04d4b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - - 9b892d7f82cc - c1d53e95327f - b8476e82ac20 + - d1c340a5664b + - 9b892d7f82cc - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu @@ -81,32 +81,32 @@ tools: owner: iuc revisions: - 9e10ba792be2 + - 128ba8da994f - feb40665d7cd - daddf188c13f - - 128ba8da994f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - abf6dbe8c9d7 - - 5f8727ff21e7 - - 03ed9524dcd1 - - ca0d8cf80567 + - ca337cce3888 + - 9d61d3fa046c - 36912871ccdc - - a2099fb98cdb - - 81804a978fc0 - 42a174224817 + - 2fa9d4f1b48f - b6abccb1f25b - - b7e297c2ede6 - - 437e28791761 + - 83a69484cb87 + - 5f8727ff21e7 - 3a43c3982401 + - 81804a978fc0 + - 437e28791761 + - ca0d8cf80567 + - 03ed9524dcd1 + - abf6dbe8c9d7 - 14ae456b8cc5 + - b7e297c2ede6 + - a2099fb98cdb - 7bb8726be37c - - 2fa9d4f1b48f - - 83a69484cb87 - - 9d61d3fa046c - - ca337cce3888 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -118,21 +118,21 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - - 73a469f7dc96 - ea30d3089354 + - a4b71be30c3c - ba29b5e2a4be + - 73a469f7dc96 - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 809e42326fc2 - - f1ccc8a6eb05 - e88a7de55d6e - dbe2b2204555 + - f1ccc8a6eb05 - 15ac71df11a0 - 91887494eb97 + - 809e42326fc2 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 278976150..1481ae6cd 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - a1f0b3f4b781 - f6ced08779c4 - fc288950c3b7 - - b502c227b5e6 + - 7d34178f2812 + - a1f0b3f4b781 - 881d7645d1bf - 1aac2a13842a + - b502c227b5e6 - 585027e65f3b - - 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 39ac5d69e..d4ca6d7c4 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,13 +2,13 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - c0e71cb2bd1b - - ca90d17ff51b - 7fbec959cf2b - 3bd420ec162d - eb085b3dbaf8 - - 5b85006245f3 - d00e15139065 + - 5b85006245f3 - a58f7eb0df2c + - ca90d17ff51b + - c0e71cb2bd1b 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 50221183e..3b1b8d15a 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,21 +2,21 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - f28ad96b76dc - - b574b84afc4d - - b18329a8ac14 - 0a18ac48ac53 - 277dc652246e + - b574b84afc4d - ece627528a78 + - b18329a8ac14 + - f28ad96b76dc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - - b41107d8fe89 - bf06d196e23d + - b41107d8fe89 - e215f71d7983 + - 525f201b86c1 - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -40,47 +40,47 @@ tools: - name: cardinal_mz_images owner: galaxyp revisions: - - 25b83cbd596a - - a95a82eb4d50 - 59e85306eae5 + - a95a82eb4d50 - a69865da6f80 + - 25b83cbd596a - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - e0669b1854b1 - - ed9ed1e6cca2 - - 611d80c0e29d - - f1897eb07081 - 798da6bdff3d + - f1897eb07081 + - 611d80c0e29d + - ed9ed1e6cca2 + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - 5a35e3a8d013 - - a7fb9b395ddf - 74b61bf5bc4b + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 10566783d718 - - d2483487e077 - - 043f9c91f686 - c5aa9fca18c6 + - 043f9c91f686 + - 10566783d718 - 1693b2126f30 + - d2483487e077 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -111,9 +111,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: + - 4081e4faa4ab - 0fa397f4f40b - 1c5cbf8f79ce - - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -125,8 +125,8 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - ce1a157a41bd - d6a4dfdad269 + - ce1a157a41bd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -160,32 +160,32 @@ tools: - name: maxquant owner: galaxyp revisions: - - 4d17fcdeb8ff - - 37d669de2828 + - e42225f8a659 + - 7f432d87c82c + - 8934bc76bb52 - 1f39c833f65f - - 837224ad1694 + - 37d669de2828 + - f522c08e900c - 97a7f34fcb6a - - 8934bc76bb52 - 2133b0be850a - - f522c08e900c - - 7f432d87c82c - - e42225f8a659 + - 837224ad1694 + - 4d17fcdeb8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - '860429737408' - - a72ac2c7cc5b - 0ed07016d668 + - a72ac2c7cc5b + - '860429737408' - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - 352b37c66d97 + - 990b4560ead7 - 1974224d63c2 - 4187b6df1a40 tool_panel_section_label: Proteomics @@ -193,17 +193,17 @@ tools: - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - - 99450519d727 - - a1daafbf5233 - 4f359549383c + - a1daafbf5233 + - 99450519d727 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c7745841de24 - 40ca115438d2 + - c7745841de24 - e79958768a2c - c1343e3389ca tool_panel_section_label: Proteomics @@ -211,9 +211,9 @@ tools: - name: metaquantome_stat owner: galaxyp revisions: - - b648e45fd3cf - - d2eac53666f0 - da986f83631b + - d2eac53666f0 + - b648e45fd3cf - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -221,9 +221,9 @@ tools: owner: galaxyp revisions: - 944b43462104 - - eb811f3018ea - - 9bf325045235 - 1199751329b0 + - 9bf325045235 + - eb811f3018ea tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -241,10 +241,10 @@ tools: - name: msstats owner: galaxyp revisions: - - b7034eff0db1 - - 28434abe6c5c - 593839e1f2c3 - 8212e342e482 + - b7034eff0db1 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -257,9 +257,9 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - - 8960fb791701 - 01dbaf6a57e0 + - 8960fb791701 + - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -271,50 +271,50 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 518b1730cf2a - - c9eff69a7c62 - f7fef900f5b2 - 9cdf15d3cfc8 + - 518b1730cf2a + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - 5e948629bc73 + - ca88bd28f116 - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 890025d6e426 - - 658494a2cb00 - 41859bbdc16e + - 658494a2cb00 + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - 6634cad7d797 - - 5ad0b5bf1deb - 9b7977080f6d + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 0bb5056cb775 - - d6878d27f051 - 05d5e1ddc985 + - d6878d27f051 + - 0bb5056cb775 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: + - 5ad830edc021 - 52ba9695e752 - febd569ad26f - - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger @@ -328,26 +328,26 @@ tools: - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - d413dc49d650 - - 0efbc235f314 - 9e26f5c770f8 + - 0efbc235f314 + - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 3720e349ba2a - - 8a04ed1c1d1b - c28f13cab67a + - 8a04ed1c1d1b + - 3720e349ba2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - c427a8628cbe - - 382cde407f81 - - ca799a7246e7 - c55dddc5844a + - ca799a7246e7 + - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper @@ -371,38 +371,38 @@ tools: owner: galaxyp revisions: - 111c3a00136d - - 5d9f175dff81 - c69f69d7867a + - 5d9f175dff81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - 0e52c85f3b15 + - be74a8cd7d66 - 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 owner: galaxyp revisions: - - c18d8efa4474 - - 2b2a7551a857 - a407b6790342 + - 2b2a7551a857 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 4e66c4e73909 - d0304fb829c0 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter @@ -416,22 +416,22 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - a2a6e9551046 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 8c01da82292c - 2a9ff56cb279 + - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - e8f64a7dc470 - 1bf940c18d93 + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator @@ -444,22 +444,22 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 89254095cbf6 - 8b814eafce2c + - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - 05ec9fb05ed1 - f9ed7e074900 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer @@ -472,25 +472,25 @@ tools: - name: openms_openswathworkflow owner: galaxyp revisions: - - bc63b4d12779 - 2aebe58de46e + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 3d8d4ada5405 - 5ae104d0da6e - decc397c3b7e + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - dd173849c3d8 - - 5182338d5e7c - e039cc5c7aed - 539a3a4dcc9e + - dd173849c3d8 + - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -522,36 +522,36 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: + - fb52e95a370c - 7f6a1f27553e - c8b225c69a7f - - fb52e95a370c 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: 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: - - 1beff3ddce58 - - 7fdd9119cc4f - - a72c48001f7c - 943a34df6047 - 3634c90301af + - a72c48001f7c + - 1beff3ddce58 - da885ca16cb2 - - 3ec27b4cee7c + - 7fdd9119cc4f - 07ff622ec007 + - 3ec27b4cee7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -605,8 +605,8 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa - 1a5690a5eedc + - 265c35540faa - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 02de2d8d9..e5d430425 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -3,33 +3,33 @@ tools: owner: iuc revisions: - 2f1d464ebfd2 + - cd5f98911089 - e345aadf914f + - 42201b90e3f4 - 289b7d6b69a4 - - cd5f98911089 - 110a346daf36 - - 42201b90e3f4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 0cd2df8af811 - - 0345dbaaa79b - 8501601a118d - - c207119ba5f6 - fcce77c09289 + - c207119ba5f6 + - 0cd2df8af811 + - 0345dbaaa79b - 42d9087b4789 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 04db7fd6b238 - - ad5ab22ffe24 + - 89eb29319bf4 - 421c33b8bf17 + - 04db7fd6b238 - 405a212b32ab - 33486216eec0 - - 89eb29319bf4 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -37,97 +37,97 @@ tools: revisions: - f6e91108b7b1 - fa51dc5e8386 - - 7370bb65bad4 + - eb784fa07f80 - 1d839ead7ad3 + - 7370bb65bad4 - 7b72fde3d27e - - eb784fa07f80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - 3d70c2996730 - - 8a55d29c8fcf - - 1544278c272e - - a3e86cd9cac7 - d30e36c48c93 + - a3e86cd9cac7 - c9b77ced9a78 + - 8a55d29c8fcf + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: + - a5969aa9347e - e2db212d64ad - - 7b881f5f5ad5 - 564c33e5c3e3 - - a5969aa9347e - - 887cf585cafc - b242deb58952 + - 7b881f5f5ad5 + - 887cf585cafc tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 9a171f9a450b - bd5ff77e2036 - e897c74a48bb - b4bab607eb05 - 8cff84759bf6 + - 9a171f9a450b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - 33f0793edf93 - - 887e0991eb24 - - 6dafad990086 - - adc7a7610d4f - 4f65e343ecdf + - 6dafad990086 - 5e10f396979e + - 887e0991eb24 + - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: + - 97575d01f06b + - c287418eb288 - 17d39bf0a63a - 43e3eeb2e0ec - - c287418eb288 - 4e280b27a831 - c5d7050e4ad7 - - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - d9bf483266a1 + - a819ec3b362d - 09b8edb56d80 - cd034465d4a4 - - d9bf483266a1 - - 9586f08634c0 - 0b8c84a7fdb5 - - a819ec3b362d + - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 69842dd5aa48 - - a4b4bd84f69e - - a9c34a289493 - - bf0e43ab0416 - 95351dd0fd3f - 2645575d1bf2 + - a9c34a289493 + - bf0e43ab0416 + - 69842dd5aa48 + - a4b4bd84f69e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - 912f904a6e1e - - bb0475c884ff - - d1fda11e602f - cfb504394ae1 + - d1fda11e602f - 8a35a3bc6752 - d033e1ccb386 + - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - - 95286af4139b - d504d945a655 + - 95286af4139b + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index e937ca3bc..eb57e33fa 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,15 +2,15 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 2d4e3aff9dc7 - 31f8063eedea + - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 32e542c2a773 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -46,15 +46,15 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - e66b9b5b8580 + - f648e5180e40 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -93,42 +93,42 @@ tools: - name: describe_samples owner: iuc revisions: - - 57f477b57c35 - e3b16fd7dd08 - - 8f0181aacb7a + - 57f477b57c35 - 0693ccd171c4 + - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 24a09ca67621 - cd9874cb9019 - - d027d1f4984e + - 8fe98f7094de + - 24a09ca67621 - 0696db066a5b + - d027d1f4984e - 6a3a025714d3 - - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 62adf13b86ea + - 2872c633f07e - b47c006d90c5 + - 62adf13b86ea - df929f257179 - - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 9bdff28ae1b1 - - 334ce9b1bac5 - df0c8d0a5992 - - f2843df56434 + - 334ce9b1bac5 - 6e53e565fc6a - - 555659de7321 - 3d89af8a44f0 + - 555659de7321 + - f2843df56434 + - 9bdff28ae1b1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -147,16 +147,16 @@ tools: - name: featurecounts owner: iuc revisions: - - f3a5f075498f - - ea04b737afa0 - - 90d16db017d7 - a37612abf7f9 - - 7db9d3ea71c9 - af814359d244 - - a56fbe2d6ba7 + - 7db9d3ea71c9 + - 90d16db017d7 - e6a2a912677a - - 38b6d12edc68 - 6f66ae7c5f7a + - 38b6d12edc68 + - a56fbe2d6ba7 + - f3a5f075498f + - ea04b737afa0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -174,8 +174,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 + - 0f710191a66d - f99dd58de04f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,20 +188,20 @@ tools: - name: hisat2 owner: iuc revisions: - - a86e80d3c09c - - f4af63aaf57a - - 26371a1df031 - - 3fb01a8c902d - - 6c19daec423d - 6ab42baa56e9 + - 6c19daec423d + - 3fb01a8c902d + - f4af63aaf57a - d4b55e2beb12 + - 26371a1df031 + - a86e80d3c09c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -213,32 +213,32 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 5ae5c312d718 - 1c75aa5de15e - - 87c11c05d238 - 01247aaf0a10 + - 5ae5c312d718 - ce5d418183c5 + - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - 40985510cd98 - - c971db6f0fe5 - 10c98fab6c5a + - c971db6f0fe5 - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - e827f9aae031 - - 0921444c832d - - d6f5fa4ee473 - 708348a17fa1 - 97e06a4c7c75 + - 0921444c832d - 58c35179ebf0 + - d6f5fa4ee473 - 32511f586472 + - e827f9aae031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -250,8 +250,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -287,18 +287,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 0a563fd2f22e - - 4df95e2d7f61 + - e132e7d02a3e - 7ed2edc1337f - - 3ea5a2a63fa2 - - c772497b2c32 + - 0a563fd2f22e - b9e04854e2bb - - 5ec75f5dae3c - - c7c55b694974 - 980d2a2e1180 + - 4df95e2d7f61 - 4074fc1940e2 - - e132e7d02a3e + - c7c55b694974 + - c772497b2c32 + - 5ec75f5dae3c - 99b17b74a8cd + - 3ea5a2a63fa2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -310,33 +310,33 @@ tools: - name: salmon owner: bgruening revisions: - - e3d32471da11 - - ebab418107f5 - - 49121db48873 - - 2c0ca397d302 - cc05793bb896 + - ebab418107f5 - 53e9709776a0 + - e3d32471da11 + - 2c0ca397d302 + - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - c0fd285eb553 - fab6ff46e019 - - 56242ff81c84 + - c0fd285eb553 - 8c28affc7c48 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 76d290331481 - - 1ebd14235b92 - - ae618321f34a - - cef79931dda5 - 258d696dbd7e + - ae618321f34a - dd4df992d93d - 914cfcba0ec8 + - 1ebd14235b92 + - cef79931dda5 + - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -360,9 +360,9 @@ tools: - name: transdecoder owner: iuc revisions: + - 0db979fead3a - c6334cb383ff - ffd1300599a1 - - 0db979fead3a - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -370,17 +370,17 @@ tools: owner: iuc revisions: - a009c96c5c18 + - bcc5f03f1900 - d6a479fd4281 - 74217fbfba4d - - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - - c2b82a94493e - 75f4e1859ed7 + - c2b82a94493e + - 478f36effca1 - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -395,69 +395,69 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - be3f26533209 - 34a018cbee9c - 41db7569b4ba + - 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: - - 05ab8d5e04a2 - c5fbddcac63a - 33406f5a445c - - ae501908a17f - 5192f657f305 + - 05ab8d5e04a2 + - ae501908a17f 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 - e406ac71165d - aa38fa8c5815 - - 1fdb25a8384d + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - c2c039e421af - - 37a1129c89d2 - ba460ccf0006 + - 37a1129c89d2 - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: + - 047c22569787 - c63338cf419f - - 1d689e4e1caf - eafea3083352 - - 047c22569787 + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: + - 3a4ac03d1266 - 9871104ea630 - - 1812dbc5bb7b - 1b1a25f93f80 - - 3a4ac03d1266 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - d84caa5a98ad - d2bc35f3d1c5 + - c9cfec002f71 + - db1f362cca3e - 77cf519a812e + - cee61b3fcf78 - 48636f857c4b + - d84caa5a98ad - 32b86cd8eb50 - - db1f362cca3e - - c9cfec002f71 - - cee61b3fcf78 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 b41c54fe8..ee91e8906 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 080fd5739bb4 - 1a052c827e88 - 473382134e56 + - 080fd5739bb4 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index 802217af2..56f9ddab9 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -9,9 +9,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - 1dfd95ee241e - 108db6635177 + - 1dfd95ee241e + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -41,9 +41,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - - 19ece8afbaab - e7fd6754d093 + - 19ece8afbaab + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -111,43 +111,43 @@ tools: owner: iuc revisions: - b3d99709fe1a - - 720217c23995 - a8d69aee190e + - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - 22970df7a40e + - fe34990e5ce7 - db17d5321bad + - 22970df7a40e - cc61ade70eb8 - - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7a6034296ae9 + - 88b8c2916784 - 7def34e6cf4d + - 7a6034296ae9 - 811fc2d75ad4 - - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: + - 36677f429310 - b40e2d865d52 - 740ce0a18f0d - - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 9da0311ab1dd + - 583abf29fc8e - 329deb17a9f7 + - 9da0311ab1dd - 8da515fbc1bf - - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -174,46 +174,46 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - 344fc91e1bfd + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - - e613c1ad4c4c - cab3f8d35989 + - e613c1ad4c4c + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 5d9ae78f34d3 - 135c85f4cfaf - bcedabb53ddf - b7f7826ef1cd + - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e - - 1cc79f49b8d5 - 5a08c09b9311 - - 3a0efe14891f - 24c5d43cb545 + - 145f6d74ff5e + - 3a0efe14891f + - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - 5826298f6a73 - 350bbc5c2ffd - - c370440f901e + - b72793637686 - b01db2684fa5 - - 5826298f6a73 - bf328cec6a42 - 0dbf49c414ae - - b72793637686 + - c370440f901e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index afceefb71..a98b99579 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,10 +2,10 @@ tools: - name: ena_upload owner: iuc revisions: - - 6f6537780379 - - 4aab5ae907b6 - a62c4a11a67d - d147d6455873 - 59bb6d34fca6 + - 4aab5ae907b6 + - 6f6537780379 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 32b662477..6b4d140fa 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -2,40 +2,40 @@ tools: - name: anndata_import owner: iuc revisions: + - 32e547223c9e + - cfc3f5a57dc6 - fb9e030ffae4 - 55e35e9203cf - - cfc3f5a57dc6 - 00712416fdaa - - 32e547223c9e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 688357ad5e61 - 038e32885fec - b9fac48532eb - ee98d611afc6 - - 688357ad5e61 - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 43cb7b5a6fe7 - - 9bd945a03d7b - 3d748954434b - - b85871dd69f9 - d4af736e7b83 + - 9bd945a03d7b + - b85871dd69f9 + - 43cb7b5a6fe7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: - - cdf4443d5625 - 2c1200fba922 - - 8855361fcfc5 - a9caad671439 + - cdf4443d5625 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -74,15 +74,15 @@ tools: - name: raceid_clustering owner: iuc revisions: - - 0bff0ee0683a - f911a64454fb + - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - - f3eb2291da05 - 2b0d3e2f402a + - f3eb2291da05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -95,24 +95,24 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - 2af7c5086a96 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - aaa5da8e73a9 - b2df381a6004 + - aaa5da8e73a9 - 77b91b9bdf52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: + - b409c2486353 - 3c86f71498bc - a97abb8cd15b - - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -125,25 +125,25 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 3bcd5445cd7a - - a407e7f8bdc1 - ab55fe8030b6 + - a407e7f8bdc1 + - 3bcd5445cd7a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: + - dbbe1ea8ecb1 - aa0c474463c2 - 6adf98e782f3 - - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - bf2017df9837 - - 215733a383f2 - f2f6c703da06 + - 215733a383f2 + - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -165,9 +165,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: + - ef4c80837bc5 - 2e41b35b5bdd - 81e5bdff4853 - - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 79b22b7ca..65a4e8f9b 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -33,10 +33,10 @@ tools: owner: iuc revisions: - 4c07ddedc198 - - 419027d822d6 - 746e8e4bf929 - - 2f3c6f2dcf39 - 562f3c677828 + - 419027d822d6 + - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,8 +49,8 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - cb1c59d69557 - - 6c29c7e347e8 - 7a15159140d1 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,33 +120,33 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 9c3e1d3235c8 - - b1eda492f063 - 840f29aad145 - aef56d0e7a61 + - 9c3e1d3235c8 + - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 375bbd555f4a - d0352e8b4c10 - 07843f917990 + - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - 2c58b83c9bad - - 4cc980df6265 - cd02bf168d23 + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - ad7e0b4291ee - 1dd433d2c92c + - ad7e0b4291ee - 4bbaf77573ef - 7dd3fb35904f tool_panel_section_label: Statistics diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index a8b3e424b..9606986e5 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -20,20 +20,20 @@ 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: - - 02026300aa45 - - 6e8d94597139 - - 464b9305180e - - 9cd341095afd - 13b6f0007d9e - - 6595517c2dd8 - be25c075ed54 + - 464b9305180e + - 6595517c2dd8 + - 9cd341095afd + - 02026300aa45 + - 6e8d94597139 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -70,9 +70,9 @@ tools: - name: filter_tabular owner: iuc revisions: - - 34d29339abab - 37cde8134c6a - 4d5aae46f850 + - 34d29339abab - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -104,20 +104,20 @@ tools: - name: query_tabular owner: iuc revisions: - - 33d61c89fb8d - 1ea4e668bf73 - - cf34c344508d - - 83069b38aa85 - - 2e8f945f7285 - 623f3eb7aa48 + - 2e8f945f7285 + - 83069b38aa85 + - 33d61c89fb8d + - cf34c344508d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - ae8c4b2488e7 - 503bcd6ebe4b - 399da6b5ec21 - - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -130,25 +130,25 @@ tools: owner: iuc revisions: - bce29ec10b78 - - c29d2f80a066 - b722161a845a + - c29d2f80a066 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - d698c222f354 - - a6f147a050a2 - ddf54b12c295 + - 9ff72e942410 - f46f0e4f75c4 + - d698c222f354 - 74a8bef53a00 - - 9ff72e942410 + - a6f147a050a2 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 87d267282..04d726f93 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -18,55 +18,55 @@ tools: revisions: - a5937157062f - ef2c525bd8cd + - 04fa42777df9 - 156b60c1530f - 57def2d7c093 - - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 09d6e4693887 + - 435b157bed6d - e61c9ac190ad - 791f73caa0c8 - - 435b157bed6d - - 09d6e4693887 tool_panel_section_label: Variant Calling 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