From ce4caac37e222788535181bfb2800facab6a41c2 Mon Sep 17 00:00:00 2001 From: admin Date: Tue, 31 Oct 2023 00:28:05 +0000 Subject: [PATCH] Jenkins install build 1343. --- automated_tool_installation_log.tsv | 1 + requests/requested_tool.yml | 7 - staging.gvl.org.au/annotation.yml | 66 +++--- staging.gvl.org.au/assembly.yml | 212 ++++++++--------- staging.gvl.org.au/bacterial_typing.yml | 6 +- staging.gvl.org.au/bb_tools.yml | 2 +- staging.gvl.org.au/bed.yml | 14 +- staging.gvl.org.au/blast.yml | 8 +- staging.gvl.org.au/chemicaltoolbox.yml | 54 ++--- staging.gvl.org.au/chip_seq.yml | 12 +- staging.gvl.org.au/collection_operations.yml | 8 +- staging.gvl.org.au/convert_formats.yml | 32 +-- staging.gvl.org.au/deeptools.yml | 124 +++++----- staging.gvl.org.au/dna_metabarcoding.yml | 4 +- staging.gvl.org.au/emboss.yml | 2 +- staging.gvl.org.au/epigenetics.yml | 4 +- staging.gvl.org.au/fastafastq.yml | 80 +++---- staging.gvl.org.au/fastq_quality_control.yml | 26 +- staging.gvl.org.au/filter_and_sort.yml | 2 +- staging.gvl.org.au/gemini_tools.yml | 22 +- staging.gvl.org.au/genome_editing.yml | 4 +- staging.gvl.org.au/get_data.yml | 24 +- staging.gvl.org.au/graphdisplay_data.yml | 60 ++--- staging.gvl.org.au/hca_single_cell.yml | 4 +- staging.gvl.org.au/hicexplorer.yml | 14 +- staging.gvl.org.au/imaging.yml | 26 +- staging.gvl.org.au/ivar.yml | 66 +++--- .../join_subtract_and_group.yml | 10 +- staging.gvl.org.au/machine_learning.yml | 26 +- staging.gvl.org.au/mapping.yml | 40 ++-- staging.gvl.org.au/metagenomic_analysis.yml | 78 +++--- staging.gvl.org.au/mothur.yml | 4 +- staging.gvl.org.au/multiple_alignments.yml | 40 ++-- staging.gvl.org.au/nanopore.yml | 40 ++-- staging.gvl.org.au/none.yml | 38 +-- staging.gvl.org.au/phylogenetics.yml | 82 +++---- staging.gvl.org.au/picard.yml | 8 +- staging.gvl.org.au/proteomic_ai.yml | 8 +- staging.gvl.org.au/proteomics.yml | 138 +++++------ staging.gvl.org.au/rad_seq.yml | 68 +++--- staging.gvl.org.au/rna_seq.yml | 158 ++++++------- staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 66 +++--- staging.gvl.org.au/send_data.yml | 4 +- staging.gvl.org.au/single_cell.yml | 46 ++-- staging.gvl.org.au/statistics.yml | 24 +- staging.gvl.org.au/text_manipulation.yml | 40 ++-- staging.gvl.org.au/variant_calling.yml | 42 ++-- staging.gvl.org.au/vcfbcf.yml | 222 +++++++++--------- usegalaxy.org.au/annotation.yml | 78 +++--- usegalaxy.org.au/assembly.yml | 184 +++++++-------- usegalaxy.org.au/bacterial_typing.yml | 4 +- usegalaxy.org.au/bb_tools.yml | 2 +- usegalaxy.org.au/bed.yml | 14 +- usegalaxy.org.au/blast.yml | 8 +- usegalaxy.org.au/chemicaltoolbox.yml | 54 ++--- usegalaxy.org.au/chip_seq.yml | 4 +- usegalaxy.org.au/collection_operations.yml | 10 +- usegalaxy.org.au/convert_formats.yml | 32 +-- usegalaxy.org.au/deeptools.yml | 114 ++++----- usegalaxy.org.au/dna_metabarcoding.yml | 14 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 86 +++---- usegalaxy.org.au/fastq_quality_control.yml | 28 +-- usegalaxy.org.au/gemini_tools.yml | 28 +-- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 30 +-- usegalaxy.org.au/graphdisplay_data.yml | 54 ++--- usegalaxy.org.au/hca_single_cell.yml | 4 +- usegalaxy.org.au/hicexplorer.yml | 10 +- usegalaxy.org.au/imaging.yml | 30 +-- usegalaxy.org.au/ivar.yml | 70 +++--- usegalaxy.org.au/join_subtract_and_group.yml | 6 +- usegalaxy.org.au/machine_learning.yml | 38 +-- usegalaxy.org.au/mapping.yml | 42 ++-- usegalaxy.org.au/metagenomic_analysis.yml | 96 ++++---- usegalaxy.org.au/mothur.yml | 8 +- usegalaxy.org.au/multiple_alignments.yml | 48 ++-- usegalaxy.org.au/nanopore.yml | 32 +-- usegalaxy.org.au/none.yml | 34 +-- usegalaxy.org.au/phylogenetics.yml | 84 +++---- usegalaxy.org.au/picard.yml | 6 +- usegalaxy.org.au/proteomic_ai.yml | 10 +- usegalaxy.org.au/proteomics.yml | 154 ++++++------ usegalaxy.org.au/rad_seq.yml | 74 +++--- usegalaxy.org.au/rna_seq.yml | 144 ++++++------ usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 48 ++-- usegalaxy.org.au/send_data.yml | 6 +- usegalaxy.org.au/single_cell.yml | 44 ++-- usegalaxy.org.au/statistics.yml | 30 +-- usegalaxy.org.au/text_manipulation.yml | 24 +- usegalaxy.org.au/variant_calling.yml | 32 +-- usegalaxy.org.au/vcfbcf.yml | 220 ++++++++--------- 95 files changed, 2051 insertions(+), 2069 deletions(-) delete mode 100644 requests/requested_tool.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 3be4176a1..13c30cbd2 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -5807,3 +5807,4 @@ Update 169 18/10/23 22:08:29 rna_starsolo False Tests failed iuc 5ef7ec16b04f 5e Update 169 18/10/23 22:39:31 shovill False Installed iuc ee17a294d3a3 ee17a294d3a3 7/7 7/7 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_169/install_log.txt Install 1340 20/10/23 09:30:06 kraken_biom True Installed iuc 65eb9962d272 65eb9962d272 5/5 5/5 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1340/install_log.txt Install 1340 20/10/23 09:55:14 krakentools_extract_kraken_reads True Installed iuc f329328da134 f329328da134 11/11 11/11 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1340/install_log.txt +Install 1343 31/10/23 10:27:46 rgi True Tests failed card 84bd24ac33fd 84bd24ac33fd Production Testing 0/1 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1343/install_log.txt diff --git a/requests/requested_tool.yml b/requests/requested_tool.yml deleted file mode 100644 index b683ff1e5..000000000 --- a/requests/requested_tool.yml +++ /dev/null @@ -1,7 +0,0 @@ -tools: -- name: rgi - owner: card - revisions: - - 84bd24ac33fd - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 42e947c88..f86ad52cd 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - - 6e9aea89e388 - - 78c75f134c16 - 4efdca267d51 + - 78c75f134c16 - c2ef298da409 + - 3f3e247c053d + - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: + - 1aae04680c4b + - 44018dd6b447 + - f29602ae449e - 133f36c29579 + - 4f2967b27e67 + - b5d8e5475247 - 3e1f6f6d557e - fe3ca740a485 - - f29602ae449e - - b5d8e5475247 - cd2480f35935 - - 1aae04680c4b - - 4f2967b27e67 - - 44018dd6b447 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -57,17 +57,17 @@ tools: - name: augustus_training owner: bgruening revisions: + - 7be22100e5e1 - 6519ebe25019 - dc027fa56d55 - - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - ca6d970d931c - 09855551d713 - 28433faa6e42 + - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,8 +79,8 @@ tools: - name: barrnap owner: iuc revisions: - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -118,9 +118,9 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 14f588312c56 - 582fd74dc2a1 - 9f2455341fac - - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean @@ -135,24 +135,24 @@ tools: owner: iuc revisions: - 563a19373357 - - 30f08d74024f - 494f0bb4a993 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 - f31125bb85ea - 7abc5f6dd595 + - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - b3cf4684e9c7 - d3af38b9c7e1 - 52af33194019 - - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -164,9 +164,9 @@ tools: - name: gff_to_prot owner: iuc revisions: + - 07d7991bf205 - 79261884facd - 2aea122fbd25 - - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -178,10 +178,10 @@ tools: - name: goseq owner: iuc revisions: - - 8b3e3657034e - - 43798b4caee0 - ef2ad746b589 + - 8b3e3657034e - 602de62d995b + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -199,15 +199,15 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -241,8 +241,8 @@ tools: - name: mitos2 owner: iuc revisions: - - 033755194fe9 - 624606f7c996 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -266,11 +266,11 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - d643e3b03500 - bf68eb663bc3 - a17498c603ec - eaee459f3d69 - - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -293,12 +293,6 @@ tools: - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: rgi - owner: card - revisions: - - 84bd24ac33fd - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training owner: iuc revisions: @@ -308,21 +302,21 @@ tools: - name: snpeff owner: iuc revisions: + - 8f92c2b26e6d + - cfcf33df7fc0 - 5a29ab10dba6 - 68693743661e - - 8f92c2b26e6d - - 5c7b70713fb5 - - 5b80f544c67f - 268d162b9c49 - - cfcf33df7fc0 + - 5b80f544c67f + - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - 09d6806c609e - 5fab4f81391d + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -346,14 +340,14 @@ tools: - name: tbprofiler owner: iuc revisions: - - e1a9d6fd258d - - 37213cf56392 - ac8250086ac3 - 45083d070fb8 + - 37213cf56392 - 200c378d85f3 - ba6f87115e13 - - 037a11682176 + - e1a9d6fd258d - 809dfc93d593 + - 037a11682176 - 2c68b0c38785 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 81fb93285..2547e9175 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,41 +2,41 @@ tools: - name: abyss owner: iuc revisions: - - 0e93176640ac - - 841084c5fc46 - - fa5259cc561b - - 553bfe8bd0b5 - 8f1b150a2487 + - 841084c5fc46 - 890b794c997d + - 553bfe8bd0b5 + - fa5259cc561b - a929ce596a34 - 7547fcab5d19 + - 0e93176640ac tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - 067592b6b312 - ddddce450736 - - b9e31c5c01c7 + - 94fe43e75ddc - b2860df42e16 - 21e491ad532a - - 94fe43e75ddc - - 067592b6b312 + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - a7f16f24e9a1 + - faee8629b460 - 22286dab5aa1 + - a7f16f24e9a1 - 5258e18bbe23 - - faee8629b460 - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,29 +49,29 @@ tools: - name: busco owner: iuc revisions: - - 41030a6c03b7 - - 602fb8e63aa7 - - cf13a1e03e5b - - 4048d82f0c88 - - 5ecdeca79a0d - - e4bd1e99bacf - 94170eee0ad8 - - 1e62c28ba91d + - 4048d82f0c88 + - e824f5d958d0 + - 602fb8e63aa7 + - 1440ae06552f + - f18f0b887c31 - bb935709506a - 2dd755c1c6ff - - f18f0b887c31 - - 0d243f458b53 - - 1440ae06552f - 46ae58b1d792 - - e824f5d958d0 + - 5ecdeca79a0d + - cf13a1e03e5b + - 1e62c28ba91d + - e4bd1e99bacf + - 41030a6c03b7 + - 0d243f458b53 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 86f150c8019d - 5732f959936a - c5b7390290b1 - - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -83,27 +83,27 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 - - 3ee0ef312022 - - e27815e82dd4 - 8d4f03b5fe9d - 1ce9b1d72ec3 + - 276f5d8712d5 + - 3ee0ef312022 - cb8dfd28c16f + - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 01210c4e9144 - 3169a38c2656 + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 611219887a48 - 06bcf65179fb + - 611219887a48 - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -112,8 +112,8 @@ tools: revisions: - 3fba9c77550a - 5127a713de83 - - 690c2caa367e - 3ef480892a9f + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -125,19 +125,19 @@ tools: - name: hifiasm owner: bgruening revisions: - - 9ef6920c3089 - - ec9e21e9c71b - 71740308d412 + - 6505bd37670d + - 5f625c63b8bc + - 5bec28269d95 - 60024a528cbd - - 2061fb3b81b4 - f3c89da3af16 - - 6505bd37670d + - 3f7be05a1597 + - da9d8bf98802 + - 9ef6920c3089 - 366a11d316a7 - - 5bec28269d95 - 045c7c3d8e59 - - 5f625c63b8bc - - da9d8bf98802 - - 3f7be05a1597 + - ec9e21e9c71b + - 2061fb3b81b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -155,37 +155,37 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - de387b2b2803 + - 14ddfc8ffb93 - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - - f8113c25bc6b - 9d79beb19ac3 + - f8113c25bc6b + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 3ca2d2a9068c - - eb7a370f6588 + - fd128c111ab0 - 2ecf5a570907 + - f338e9942b27 + - eb7a370f6588 + - 3ca2d2a9068c - 606b09cc9860 - e731ea24e48d - - fd128c111ab0 - - f338e9942b27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -199,8 +199,8 @@ tools: revisions: - 73a3846701e1 - 8dee0218ac7d - - a7b889b90140 - 80d1250bd5fd + - a7b889b90140 - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -227,11 +227,11 @@ tools: - name: pretext_map owner: iuc revisions: - - 2b16ba799da9 - - 02831bf9e95f + - d256a51a656b - bbe19ef04a74 + - 02831bf9e95f + - 2b16ba799da9 - dfb8a4497339 - - d256a51a656b - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,62 +239,62 @@ tools: owner: iuc revisions: - 76d4cbefff85 - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 72472698a2df - - ebb0dcdb621a - - 59db8ea8c845 - - 342a1d1fed7b + - 675488238c96 - 875d0f36d66f - - 3061c8b029e5 - - 7594365c546b - 6fcbee531de6 - - 675488238c96 + - 7594365c546b + - 3061c8b029e5 + - ebb0dcdb621a + - 342a1d1fed7b + - 72472698a2df + - 59db8ea8c845 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - 39bed8de8017 - - d865b62f501c - - aa39b19ca11e - - 936f0b5e7fcc - a199cd7ac344 - cd06929b224b + - 936f0b5e7fcc + - d865b62f501c + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - f11b994b7eb2 - - 3edba9afc9bc - 2b2a352488fa - f8564b2d7f63 - 33b7d8481a76 + - 3edba9afc9bc + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - 1d06c8b38e77 - - 53c2bc8c2ae3 - - 378e55aeeb25 - e122f9101584 + - 378e55aeeb25 + - 53c2bc8c2ae3 - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - ab5b7f6b7198 + - 9a22227bb6d0 - ba7b0f11e470 + - ab5b7f6b7198 - f77f7a7f3b83 - - 9a22227bb6d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -306,39 +306,39 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - - 196a599ec43d - 83ead2be47b2 - f698c7604b3b - - ee17a294d3a3 - 865119fcb694 - ad80238462c1 + - 196a599ec43d + - ee17a294d3a3 + - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 5a0ddb4dc3a4 - 24e471d13fe9 - 5e0825476fb7 - - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - 1fc82fe7ebef - 7490b213baa9 - - 1bb12736175c - 051fd2db8a27 - 904bf932cf78 - - 1fc82fe7ebef + - 1bb12736175c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - d6e617c4e338 - ad8b536d1caa - fee85957cebe - - d6e617c4e338 - 808b3a0a6716 - 34305b013402 tool_panel_section_label: Assembly @@ -346,82 +346,82 @@ tools: - name: spades_metaplasmidspades owner: iuc revisions: - - 6b5a5842531e - - b8002c3f7141 + - e5a3b75a271f - 21da31ed41a1 - 8d4b90bf9caf - - e5a3b75a271f + - b8002c3f7141 + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - 2a10645aeadd + - f1532cb33c75 + - 86f66ab58e14 - 328aa71f0f3c - 9de69775f512 - - 86f66ab58e14 - - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 1708851f8804 - - 6aad515a5270 - - e41dcb0e913b - 340bc17f49cf + - e41dcb0e913b + - 1708851f8804 - 85fb02c43042 + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d159735a6a9f - 249f6a28c751 - - d5fb354f745d - - b3490b036c5a - b65a43f70b99 + - d159735a6a9f + - b3490b036c5a + - d5fb354f745d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - 9006e5836729 + - 33368fec3b70 + - b7829778729f - dd7ad84f3943 - 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 - 8f631679571f + - 6f4c8ad6ea01 + - 189e837009c9 - ced385aa976d + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 19bdfd1e6fe3 - 356afed970b4 + - d40ed4eb0c0e - e59bee4565b3 - 9ded6109434a - - d40ed4eb0c0e + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b - - 4688ae3b49b5 - - ebd801e712bc - 80a17897564d + - 4688ae3b49b5 + - 6dd935e4984b - b23249f81bc4 + - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa @@ -429,48 +429,48 @@ tools: revisions: - b5e35a2ca4f3 - b64696992ee9 - - cb1e3db43020 - - 59bd28f6265d - 937ea677d437 + - 59bd28f6265d + - cb1e3db43020 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b - - 383bb5ad32e2 - - 6015aa0303f2 - 05bd7504fdb2 + - cb4768eeca3b - 2628f6790eda + - 6015aa0303f2 + - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - - 0a3a602cd1e3 + - d10bdad2fd17 - 9e3e80cc4ad4 + - 0a3a602cd1e3 + - 6e26c9afd301 - e92675014ac9 - - d10bdad2fd17 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 8d09f8be269e - 920677cd220f + - 08256557922f - 5da9a0e2fb2d + - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 + - 0e2b4e3f9ca1 - d81360ea69d8 - - 37d88f41c810 - 82398ba86ba7 - - 0e2b4e3f9ca1 + - 37d88f41c810 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 2e9178e81..e088cbd6b 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: - - 1f5641a52664 - ded48b36f3b7 - - 8e8dc9a1e3e5 - 31812e7a1315 + - 8e8dc9a1e3e5 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 17fcac7ddf54 - 24a7a95867b0 - 5c8ff92e38a9 - - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 434a88153..70adf3e9d 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: + - 204a131e47db - 159b04e36791 - a9c9d768b751 - - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 13d494f2d..18dece3a8 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - 07e8b80f278c - - a68aa6c1204a - - 87ee588b3d45 + - 589e7e57fd6d - b28e0cfa7ba1 - - a8eabd2838f6 - - e19bebe96cd2 - - ce3c7f062223 - dde39ba9c031 - - 589e7e57fd6d + - 87ee588b3d45 - 0a5c785ac6db + - a8eabd2838f6 + - 07e8b80f278c + - a68aa6c1204a - a1a923cd89e8 + - ce3c7f062223 + - e19bebe96cd2 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 759a775bc..d3c46732c 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: + - 1e3323a44643 - 54f751e413f4 - f921014aba5a - 62c9df8382c2 - - 1e3323a44643 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -24,10 +24,10 @@ tools: owner: devteam revisions: - 0e3cf9594bb7 - - e25d3acf6e68 + - 6f386c5dc4fb - 2889433c7ae1 - acf4e47b734c - - 6f386c5dc4fb + - e25d3acf6e68 - 5edc472ec434 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -40,8 +40,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index c029c0854..ee1eae5dc 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - 6ca543ec1bf8 - f4230f116196 - - 710301bc46fa - 095ad4d096d1 - da6bd1975a71 - - 27ee142314a9 - - 6ca543ec1bf8 - c8cdde00b105 + - 710301bc46fa + - 27ee142314a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -74,15 +74,15 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -100,11 +100,11 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - bfb65cb551d8 + - 88076940fa94 - 0fac8e2afc13 - - 3b8a9d5ced85 - 79cfd9ead848 + - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em @@ -112,79 +112,79 @@ tools: revisions: - 715cd0e87781 - b46d4b4d995c + - f5d979cb4b54 - 55918daa5651 - d532b7e5f64b - eb6564a60136 - - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - 97872d87ba80 - - fdf2cc80adb5 - - d2f955aea23a - f26afd1b7104 - 5579659312e6 + - fdf2cc80adb5 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - bc31d02be922 + - 319a28774da9 - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - cac1886249a2 - ed736e6eee39 - - 2c349b027a01 - 4da9ee404eab + - cac1886249a2 + - 2c349b027a01 - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 525ca7c8065f - - 807aa4c9293d - f197e34c33a9 - - c0c9a5024177 + - 807aa4c9293d - d1f803b5943c - - da8753545526 - 73008ef1f487 + - c0c9a5024177 + - 525ca7c8065f - 2e219a2d9327 + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 - 7568ae18908a - - 2c8ed1b52bf7 + - 27ea4e1a3f95 - 1809414a9454 - - c4fbab8e03c5 - 61094e01eff9 + - 2c8ed1b52bf7 + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - ccfbd956a2d3 - - 79e8ab8f1e81 - - ba83f0923369 - - 730ef07b90ae - d7ec25187599 + - 730ef07b90ae + - ba83f0923369 + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -197,8 +197,8 @@ tools: owner: bgruening revisions: - e6011617c748 - - b59c91adeac1 - 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: - d4c67ced6abc - - 85fad59f8168 - - 9b48456a96fe - bf99565cec1f + - 9b48456a96fe + - 85fad59f8168 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index b7dc00baf..97f0848c1 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - fa56d93f7980 - c97a786e8fb5 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -22,17 +22,17 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - f5d67c722d67 - - 495a4173006f - 640d3af5d833 + - 495a4173006f - 424aefbd7777 + - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -51,9 +51,9 @@ tools: - name: sicer owner: devteam revisions: - - 4a14714649b4 - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 + - 4a14714649b4 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 0ca7b4089..bd3d36103 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -9,10 +9,10 @@ tools: - name: collapse_collections owner: nml revisions: - - 830961c48e42 - - 90981f86000f - 25136a2b0cfe - 33151a38533a + - 830961c48e42 + - 90981f86000f 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: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 0826b6a8b..db51037e2 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -8,35 +8,35 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a - - 0b3c3ad92827 - - 367b1ed91207 + - f3a19509108a - a3b86937ead6 + - 4a6ee918c13a + - 6ef0b5664c69 - 5e1240a87bcb - e3cbd2287f63 - - 6ef0b5664c69 - - f3a19509108a + - 367b1ed91207 + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 501c21cce614 - 72ed72122deb + - bd46669113b9 - e177a8ea0bf1 + - e525f9ffb9ac - 584008e574b2 - 54ccb7e1f49a - - 1b5fc03380d4 - - e525f9ffb9ac + - 501c21cce614 - 33c99804a32f - - bd46669113b9 + - 1b5fc03380d4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - a0d092f27fdf - 11c3eb512633 + - a0d092f27fdf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -55,9 +55,9 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 186b8d913e6c - 77b41c89d856 - 8979c288aefb + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -115,25 +115,25 @@ tools: - 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: - - 2dcfbbf9071a - 68f57cc8fad0 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - 92ac8e086317 - - 63769c4217a7 - - 26c6706bfb07 - b9b385097f13 + - 26c6706bfb07 + - 63769c4217a7 + - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 64de0df0a..1825e0e6c 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,95 +2,95 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 268e91e540ee + - de72ba3ed6f2 - c929a006727f + - 29451af70c52 - 5f6d123679f4 + - 268e91e540ee - e821645ef8fc - - 29451af70c52 - a1ca9bccc7f2 - - de72ba3ed6f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - - 0e49b109abc2 - 0e143b4c3987 - - 7a7fd0f5f15d - - 12af64f93288 - - 2d2cf5c1ea8a - 5d11599b8a7d + - 2d2cf5c1ea8a + - 12af64f93288 + - 0e49b109abc2 + - 7a7fd0f5f15d + - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - c06951d10364 - dc059492a995 - 195e98217334 - 1d848bc4585f - 81b1e3e1fc6c - 7c1beb6d6eca + - c06951d10364 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 26e7304d6737 - - 93eb012d9eed - a67ac707496a - - 07418a30ed01 - - 3d211717a775 + - 93eb012d9eed - 71aa86af6762 + - 26e7304d6737 - bfff7454b59a + - 3d211717a775 + - 07418a30ed01 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 5be24eba848d - - dd0b7398bb96 - - b8858746dc1f - 56d5b797ce84 + - 26983857c91a - 2bc10a9ca58b + - b8858746dc1f + - dd0b7398bb96 - 29fcfd36e90a - - 26983857c91a + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - e6d0bff01239 - - ee3a1b0f45f1 - - 7e6bcd2e5128 - - c3e012dfe21f - 72bfafe3330b + - 7e6bcd2e5128 - 7ef978dc1b8a - 9384cd033f30 + - c3e012dfe21f + - ee3a1b0f45f1 + - e6d0bff01239 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - 9470f29702f8 + - a60c359ec43c + - 514fa53b5efb - fd1275e01605 - - fb9cf9c97ec4 - b73e213add0c - d9a637e83828 - 167788df3b46 - - 9470f29702f8 - - a60c359ec43c - - 514fa53b5efb + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - e479c7ca5570 - - ca0616bb2cdf - a02cfa31e9cb - - 2c37ce318bc3 - 5bffaa8354a1 + - e479c7ca5570 + - 2c37ce318bc3 + - ca0616bb2cdf - 86febdcc4283 - c34d11ea4ba6 tool_panel_section_label: DeepTools @@ -98,108 +98,108 @@ tools: - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 + - 78f405266706 + - 2d466b530754 + - 69a8621ca2f0 - 1fcb7adc39b8 - 192ef85c0b0b - - 2d466b530754 + - 01fb6a7654e6 - 004aea905d4d - - 69a8621ca2f0 - - 78f405266706 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 - - 2f9e4843f480 + - 9ecba5e225a6 - 137c4beed34b + - db940c262830 - d580d6acd1df + - d9ce4897dbb2 - 459cfa861f0b - 3c9f0c486cca - - 9ecba5e225a6 - - db940c262830 + - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - 2c66e43f1c86 - - 32e451def88c - - fbe773640707 - fd408d755394 + - 2c66e43f1c86 - bd7db9e2f2cb + - fbe773640707 + - 32e451def88c + - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 7fda5607e777 - 56bce3c82278 - - 7e361d147872 - - 231994413f89 - - 9368fbc49c8b - 4e12ea27f788 - - 7fda5607e777 + - 9368fbc49c8b + - 231994413f89 - 3b9d990a0a0e + - 7e361d147872 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 - - e65d16fb2724 + - ce4ce3316f74 + - b1779366c8e9 - c03c3384cd81 + - d9114ef1c8a5 - 94ca68515826 - 4431f39ede55 - - ce4ce3316f74 - - b1779366c8e9 + - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 23f7c5f1fdaf - - 793665fff0f8 - - d57251071381 - b88ebb3672a1 + - d57251071381 + - 793665fff0f8 + - 23f7c5f1fdaf + - f8fc4e5aff9d - 2da482e408b8 - 4ed32329e0ed - - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - a4dfb122e52b - e4c7985d4585 - - ba6efa77fb79 + - 25d830337d31 - c60570fa602f - - 010e58e9d822 - 512155688d98 - a7849312d328 - - a4dfb122e52b - - 25d830337d31 + - 010e58e9d822 + - ba6efa77fb79 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 443d9a9d6d11 - c899e0ccff8c - 00d869ea03a1 - - 69264da0ce77 - - 4d678170d29b + - 443d9a9d6d11 - 38e3f226248b - aa200e4f3939 + - 69264da0ce77 + - 4d678170d29b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - c361b12d207a - - d806504e96d9 - - 6662b1a8d326 - 10301d137111 + - 6662b1a8d326 + - d806504e96d9 - a2d70c4fd406 + - aac8444d6681 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index 22d56e08f..2ec9a7e41 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -16,8 +16,8 @@ tools: - name: obi_convert owner: iuc revisions: - - 374fd9feb032 - 4d705e3443a7 + - 374fd9feb032 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -30,8 +30,8 @@ tools: - 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 diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 2bdbfb936..42a614fb1 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - ce385837c160 - dba489bfcd62 - 832c20329690 - - ce385837c160 - 63dd26468588 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index a49902aae..f868cc534 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: + - 29bdbc353f20 - 6da3972210ee - - d82648ad25a3 - 62f5fab76dfb - - 29bdbc353f20 + - d82648ad25a3 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 52127fa52..651f5812b 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -9,21 +9,21 @@ tools: owner: lparsons revisions: - 49370cb85f0f - - 48f587c13075 - - 8c0175e03cee - - e4691e1589d3 - - de6cebe3c043 - - 4e5056fefd88 + - 8665bcc8b847 - 288f97432497 - 660cffd8d92a - - 8665bcc8b847 - - 5915ea1ec9b1 - - 44e2cc14f75b + - e4691e1589d3 + - c5e2e5902201 - c053d4cad713 - 093678460093 - c4b82dce8335 + - 8c0175e03cee + - 48f587c13075 - 135b80fb1ac2 - - c5e2e5902201 + - 5915ea1ec9b1 + - 4e5056fefd88 + - 44e2cc14f75b + - de6cebe3c043 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -35,9 +35,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: + - f666895cbebd - 8889eb864cef - 9db07fd39f85 - - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -49,8 +49,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -76,9 +76,9 @@ tools: - name: fasta_formatter owner: devteam revisions: + - 9457a20156db - 516b97a23d7e - 859422bcb689 - - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -97,9 +97,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: + - f773e98b26cf - ec0b5076173a - f81d4362b6c1 - - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -111,9 +111,9 @@ tools: - name: fasta_stats owner: iuc revisions: - - cd0874854f51 - 56022eb50bbd - 9c620a950d3a + - cd0874854f51 - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,9 +126,9 @@ tools: - name: fastp owner: iuc revisions: + - 65b93b623c77 - 1d8fe9bc4cb0 - dbf9c561ef29 - - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -140,15 +140,15 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - 10b75444feae + - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -161,22 +161,22 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 03d57fea6482 - f3936d0632cb + - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -196,9 +196,9 @@ tools: - 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_paired_end_splitter @@ -210,9 +210,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - - 54053ea6c77e - 045f0e1043f7 + - 54053ea6c77e + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -224,8 +224,8 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -244,10 +244,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 + - d5e9e83cd3d8 - 529bccd5e4a1 + - 567d5b3c52b1 - 09070cacefd8 - - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -259,9 +259,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 - 0b7ec11b3c7c - 8abdedf55101 + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -273,10 +273,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 90858c306551 + - bdf1ce174e39 - cb1e251cac37 + - 90858c306551 - 736b8f6ee456 - - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -288,9 +288,9 @@ tools: - name: fastx_collapser owner: devteam revisions: + - 7ce1891db6f5 - 421f0af4ee95 - 07497255281e - - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -302,8 +302,8 @@ tools: - name: fastx_renamer owner: devteam revisions: - - f984bb114520 - b29d37ca9e41 + - f984bb114520 - 3599f5451ee2 - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ @@ -317,10 +317,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 0c2907307ba4 - - e246088b6e34 - 6027ef51ef91 + - e246088b6e34 - 177f0621c266 + - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -332,8 +332,8 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 61b4cedc8934 - 73194cdd4f57 + - 61b4cedc8934 - 547e8d00f11c - 377ac2829eac tool_panel_section_label: FASTA/FASTQ @@ -372,8 +372,8 @@ 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 @@ -398,8 +398,8 @@ tools: - 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 @@ -413,9 +413,9 @@ tools: revisions: - e654095ab143 - a535cf1e5da4 + - b557acca0b56 - 24013bf85a6f - 8250ea3a1501 - - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -434,11 +434,11 @@ tools: owner: iuc revisions: - 27ac32a22ad2 - - f3759eec3018 - 9fa7803d1c51 - 6a675c3aa610 - - 828dba98cdb4 - 7accf7407811 + - 828dba98cdb4 + - f3759eec3018 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 4c9fac632..f26e84718 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -3,28 +3,28 @@ tools: owner: devteam revisions: - 64e9a6afdd0c - - 7b4468117008 - ce9cd02d5b88 - e41385662e5e + - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - 9da02be9c6cc - - ff9530579d1f - 5ec9f6bceaee + - 2b0c9d9fc6ca - 3d0c7bdf12f5 - f2e8552cf1d0 - e7b2202befea - - 2b0c9d9fc6ca + - ff9530579d1f tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -37,46 +37,46 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: + - b6b54ba71bd8 - 18a51655db17 - ad116ae3f4d9 - - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - 7306ec78632a - 59003d0543cd + - cc0fd298cc17 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: - - 1c2db0054039 - - 5e33b465d8d5 - - f7985e0479b9 + - 3d93dd18d9f8 + - 9a913cdee30e - bf675f34b056 - 75c93c70d094 - - 9a913cdee30e + - 1c2db0054039 - b2f1f75d49c4 - - 3d93dd18d9f8 + - f7985e0479b9 - abfd8a6544d7 + - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 084bbd8ba7b8 - cd7e644cae1d - 949f01671246 - - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index 5b44a1c25..7946b577d 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index ffd3084c6..a251273e2 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,23 +2,23 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: + - 0c8f7322f8fc - 8f53b238a360 - f2f3bc622a16 - - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,16 +86,16 @@ tools: - name: gemini_load owner: iuc revisions: + - b2c25142267e - cf61daf064fe - 45296e47d565 - - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -115,16 +115,16 @@ 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 + - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -158,8 +158,8 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index aade5505c..c5b84e945 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 6dd4890ca..3215a1993 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,9 +2,9 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - e9df53a75f3c - b39347891609 - c1b437242fee - - e9df53a75f3c - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -12,44 +12,44 @@ tools: owner: iuc revisions: - 1c58de56d587 - - 28587613264f - e063168e0a81 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 69ebb7f46e45 - - f5ea3ce9b9b0 + - 4df8de2d0e48 - 5e6237d58b0c - 653e89d73fc4 - - 4df8de2d0e48 - aad3885b3216 + - 1790dcf3c32d - 4317d3cb6cba - - 6ea73833cf67 - - 734abc7ac21d - - e08a7ad4378b - 7068f48d0ef9 + - 69ebb7f46e45 + - 734abc7ac21d - 9a776b080193 - - 1790dcf3c32d - 83c7d564b128 - c441583adae5 + - 6ea73833cf67 + - f5ea3ce9b9b0 + - e08a7ad4378b tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 75b3b3d0adbf + - 34758ab8aaa4 - 9aaa46d45472 - 7863f1abcdda - - 34758ab8aaa4 - - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a - af5eccf83605 - 054483e27a35 + - bfdc6a7ffd3a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 7d5e4bff8..df024c498 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: + - a64dc31ab7f2 - df7356989ac1 + - 4b519282a05b - 290a11559985 - - c4bde687c846 - 7f13dc906cb9 - - a64dc31ab7f2 + - c4bde687c846 + - ae9994cf526f - fd59d783248a - 740057a5126d - - 4b519282a05b - - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,38 +34,38 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - f95284aa2946 - - 7cf5b1d072b5 - 867ab348287d + - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: + - '566197475670' + - 3b37b1b1c3a7 - 53460afd5115 - ca7cb0eaad62 - - 3b37b1b1c3a7 - - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 391a4cc45fea + - da4c086cff5b - d3a9e32672ec - - 10515715c940 - 3d059e9c2fba - - da4c086cff5b + - 391a4cc45fea + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - e3a675da7fd0 + - 299307abd804 - 3b12bf9b4b87 + - 1acf88921176 - 5fe1dc76176e - - 299307abd804 + - e3a675da7fd0 - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -99,17 +99,17 @@ tools: - name: jbrowse owner: iuc revisions: + - 836d1aa3e89a + - 112eb40ba6cf + - 17359b808b01 - a6e57ff585c0 - - 6cd09d7b5f37 - - ca2def38369c - - 667e17248bfe + - 4542035c1075 - 2bb2e07a7a21 - 1cfc579079a6 + - ca2def38369c + - 667e17248bfe + - 6cd09d7b5f37 - fd5dbf0f732e - - 836d1aa3e89a - - 4542035c1075 - - 112eb40ba6cf - - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -127,9 +127,9 @@ tools: - name: pathview owner: iuc revisions: + - fe154a7af404 - f1691de443a7 - 03c13085aecc - - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -141,15 +141,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -161,8 +161,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - 44c66e8d21e6 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -174,22 +174,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 2824d77cd8f8 - 59fd173ac850 + - 7dd841a32245 - 14e7c35f3d00 - - 360df4999907 - - 326a3db8d9d1 - a1abfa420d9d + - 360df4999907 - 4ac4e7083b7e - - 7dd841a32245 + - 326a3db8d9d1 + - 2824d77cd8f8 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 73b8cb5bddcd - 83c573f2e73c + - 44608d0193ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 73010e498..dceb99ab4 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -82,8 +82,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - 0f98603d0116 + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 08fa44981..20cc3d920 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,40 +2,40 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 921a2da49a0c - - 9edf8894a22d - 29f66c353bcb + - 9edf8894a22d + - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 5746d61f0a91 - d404277cc87a - 78fb5e286609 - - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - 4d511437b1e5 - 03dd3c16ae4e + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - 41dbf4d162a2 + - 3b5b54ed6392 - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 7babd8a46fe0 - - 5308ca68ef3d - 9939786dd9c9 + - 5308ca68ef3d + - 7babd8a46fe0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 35e7b5534..f466b8361 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,8 +2,8 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - 81f0cbca04a7 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -33,9 +33,9 @@ tools: - name: bfconvert owner: imgteam revisions: - - 10eed33aa9b2 - f3360fbeda64 - b07f4839ca77 + - 10eed33aa9b2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -54,8 +54,8 @@ 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 @@ -88,8 +88,8 @@ tools: - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - 11f177b1a59e + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -102,15 +102,15 @@ tools: - name: cp_gray_to_color owner: bgruening revisions: - - ad271f78a87a - 31d195bedf6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - b6eec6087271 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -123,8 +123,8 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity @@ -137,22 +137,22 @@ tools: - 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: - - 5499dc6f8ac1 - 8536b1ae0254 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -172,8 +172,8 @@ tools: - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -192,8 +192,8 @@ 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 @@ -217,7 +217,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index dcd4e0b08..d6d6a3c32 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - a38934e303b9 + - e4ee04da1c19 + - 3e4f434a69c6 - d6e72da3ec35 - e319b5b65879 - - 17f911830a8c - f362150bef41 - - 3e4f434a69c6 - - e4ee04da1c19 - - 78bbd17d0703 - 1069f6db0a0e + - a38934e303b9 + - 17f911830a8c + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - f91cfb73d369 + - 0135f1d487a0 - 9537184d421f - - 2b95d5c04908 - - 72ddd32392cd - - 7fe36019c073 - c88553ec696e - - f91cfb73d369 - - 8f8df367470d - 1ef5b6e3e09d - - 0135f1d487a0 + - 7fe36019c073 + - 72ddd32392cd + - 8f8df367470d + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - 2cf4a1cafc16 - ad0dc9f4c9e2 - fafb3d685fa9 - d7e79eb3bcb3 - - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - bd2a7d1316b9 + - 28a6f1908fcc - 8c05afb547fa + - ee29337f905c + - 94df24c6bc00 - 9eaadf03e0df - 69797fa273c3 - - 28a6f1908fcc + - ee2beb764a7b + - bd2a7d1316b9 - 3d18f8c3c0f6 - - 8d36959b000d + - 7f1cfa4c0e32 - 6a1515bb0687 - - ee2beb764a7b + - 8d36959b000d - 43aac8d29685 - - 94df24c6bc00 - - 7f1cfa4c0e32 - - ee29337f905c tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - 5671e1d3d5ee + - cb903c9dc33d + - bcaa0d571ce2 + - 364f4ffec275 - e3bb03cf207a - - 9f978da6528a - - 0893a1dbb807 - 8858fa037a15 - - db536ad45f28 - - 364f4ffec275 - - bcaa0d571ce2 - - cb903c9dc33d - - d37ede8589b2 - c092052ed673 + - 5d6ed46cc101 + - d37ede8589b2 + - 0893a1dbb807 + - 9f978da6528a + - db536ad45f28 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - f95f403841ad - - 584beffa972b - 12d66d0d05ac - - 49236b03e4fd + - ed28dd32141c - 38b91a3190cd + - 584beffa972b + - f95f403841ad + - 045d6d00f606 + - e1a015876aa9 - 3b6a16d82c1b + - 49236b03e4fd - 230b05597996 - - e1a015876aa9 - c5c9f02b6167 - - 045d6d00f606 - - ed28dd32141c tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index d426d972a..6f5e9ff89 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,18 +2,18 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - - 0f1724dd59d2 - f198773344e4 - 17e3b698dd52 + - b8a457820315 + - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf - - 22c2a1ac7ae3 - - 374cb875d38a - ac092723240d + - 374cb875d38a + - 22c2a1ac7ae3 + - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index fff07de56..574b3845c 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,62 +2,62 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - 66d7efc06000 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 8a794e6d3388 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - b6ef6d0cb6b7 + - e1317b5502fa - f1b9a42d6809 - 818f9b69d8a0 - - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: + - 947c2eacccb8 - 1588f9076e32 - 05143043ca13 - - 947c2eacccb8 - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 9991c4ddde14 + - 1552b8cb4a94 - 83228baae3c5 - 29e4122c90de - - 1552b8cb4a94 + - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - a07ab242b0b5 + - 53616c8b0865 - 841a6cc5fc58 - 1a53edc4b438 - - a07ab242b0b5 - f3dfa4bdf87e - - 53616c8b0865 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 + - 91c4e3331208 - 40f4447733b2 - - 927586a18553 + - 2fc89dcd41c8 - dc4b5fd604a6 - - 91c4e3331208 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv @@ -66,17 +66,17 @@ tools: - 25ab6b4e376e - e5a5ad882f1f - 301e07345c93 - - c6ae57f774c6 - 36e8d6d5d01b + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - 0630258dcf35 - - 02d2be90dedb - f9639b488779 - 4ed102b922cb + - 02d2be90dedb - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 6c944a793..3ab7df1a7 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - 17062a0decb7 - - 3ba8d4563129 - - 937aa69e715f - f6877ad76b00 - - cd659e8cc5fa - - a6d65b0c67af + - 937aa69e715f + - 17062a0decb7 - 749c918495f7 + - 3ba8d4563129 - 017aba02828d - 03e9b2fbc005 + - cd659e8cc5fa + - a6d65b0c67af tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -29,10 +29,10 @@ tools: owner: devteam revisions: - 64f11cf59c6e - - dfd8b7f78c37 - - 3fe632431b68 - 53646aaaafef + - dfd8b7f78c37 - e188dc7a68e6 + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -44,42 +44,42 @@ tools: - name: lastz owner: devteam revisions: - - 3e1ea2facca6 - - e7f19d6a9af8 - 2ff111fac1d7 - 37b497aa133f + - e7f19d6a9af8 + - 3e1ea2facca6 - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - be1d967337e4 - - b3eab4b67562 - - f54f5baedfdd - 3f4d6399997b - 53c0b7a1a0c3 - - 77b2770508f6 + - b3eab4b67562 + - c0c2d0941de8 - 09b53c1d4ab1 + - 11a0d50a54e6 - 6b1e195506a3 + - be1d967337e4 - 037c6e54df11 - - 11a0d50a54e6 - - c0c2d0941de8 - 8c6cd2650d1f + - f54f5baedfdd + - 77b2770508f6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - 9ee34ba73ebf + - 178bdbdb6d24 + - 1cd2511a396e - 00fbfac99d39 - - 13022c3d3076 - ec9cbd6b9a49 - - 79b885ce78d7 - - 1cd2511a396e - b8f5f6e87f5c + - 13022c3d3076 - e403d27e8f24 - - 178bdbdb6d24 - - 9ee34ba73ebf + - 79b885ce78d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 2a270f98c..eb9571dfd 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -34,16 +34,16 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 5b5a7af9fbb4 - - 63f86089423e - 76d3d2b10738 + - 63f86089423e + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - 1c35dadbe76f + - 18a502a9d287 - 96336c6a2bb7 - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis @@ -51,44 +51,44 @@ tools: - name: dada2_filterandtrim owner: iuc revisions: - - 34e55239e68b - addaf9d22850 - - a9f4a217dcd6 + - 34e55239e68b - f732237754fc + - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 75403243703a - 0776d824d896 - 8c202e741d68 - 04c15826a0b8 - - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - 8470de786d47 - - 43c99742158b - - e96bbb9e24ea - 1c9b3bcd4261 + - e96bbb9e24ea + - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - 1d75bd0595e2 - - 5c865a382933 - 84743da21318 + - 5c865a382933 - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 78faebd0879c - ac72310b038a + - 78faebd0879c - 555ccac8a4c5 - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis @@ -96,19 +96,19 @@ tools: - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - a58e4a43f49c - 7b8cb2b02978 - d60df8727f59 + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 7f3b59dee073 - 1bc3657cd694 - - 04144473e59e - 7136e9ab70db - - 7f3b59dee073 + - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts @@ -159,9 +159,9 @@ 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 @@ -189,56 +189,56 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - - c409a495841f - 79706f10d680 + - c409a495841f + - 31c6d107e7a5 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 - - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - a293a742194f + - d7e9a3c41657 - a4d7148ccee4 - 4137b492233e - - d7e9a3c41657 - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - 64bc7acc22a9 - - e2c71b852aba - - cf87759761eb + - 97f7bb0851e7 - 75bedfb2078b + - cf87759761eb + - e2c71b852aba - 6fcb8ac37a3e - - 97f7bb0851e7 + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: + - 2d35528d2141 + - 5e5a999ffaa9 + - 080ea153677c - c82508e76ad1 - 4033827c76b8 - - 080ea153677c - - 5e5a999ffaa9 - - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 6b7622dda516 - 2cd76b089570 + - 6b7622dda516 - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -305,9 +305,9 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - - e674066930b2 - 328c607150ff + - e674066930b2 + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -332,8 +332,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1902d3de4a4f + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -384,9 +384,9 @@ tools: owner: iuc revisions: - 2cff76cf35c6 + - 4fd3b5d8706b - e073891b2afc - 0270541aaf46 - - 4fd3b5d8706b - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -467,13 +467,13 @@ tools: - name: metaphlan owner: iuc revisions: + - 2131d7dca455 + - a92a632c4d9b + - 6dee4abadccb - 1a6cdf55390f - - ff8f55893e7d - a16313517e55 + - ff8f55893e7d - b89b0765695d - - 6dee4abadccb - - 2131d7dca455 - - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -545,8 +545,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 9168545e09df + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -595,13 +595,13 @@ tools: - name: staramr owner: nml revisions: - - 4d83eccf5f81 - - be818ae858e4 - - 141afacabcfa - 3b22de20bd4b - 2fd4d4c9c5c2 - aeaa20b96ef2 + - 141afacabcfa - 4b9a8031ab74 + - 4d83eccf5f81 + - be818ae858e4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -631,8 +631,8 @@ tools: - name: vsearch owner: iuc revisions: + - 9495df9dd6ef - b3c7199d8786 - 576963db5f1b - - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 1aef0a352..0ee576bb4 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - de3cfb122105 - 12e856482d26 + - de3cfb122105 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index e5073500d..03eed4ba1 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - a74dbfee5a86 - cd07731e4434 - 9eeb13a92d79 - - 48c13389050d - - 8b67dd48fec1 - - 94b8c6013083 - - bdfbaf0c10aa - - 9422c5a87ee2 - 2263989660f5 - - 6ae5a7b5a0a2 - 9baa871cb1d1 + - 9422c5a87ee2 + - 6ae5a7b5a0a2 + - a74dbfee5a86 + - 48c13389050d + - 94b8c6013083 + - 8b67dd48fec1 - 80f03df2e2ce + - bdfbaf0c10aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - d7ce0ec78e51 - - '764845535798' - c18157c68134 - - f14193ec1f50 + - 3ff17bad4006 - be78f13134e2 - - d390fe1567dc - - f0af8936ed41 - - 2e093badc689 - fc2e49f91e52 + - d390fe1567dc + - 5abf2c2249aa - 4a60927aaca5 - - 3ff17bad4006 + - f14193ec1f50 + - f0af8936ed41 + - '764845535798' - bc3831dd65c1 - aaa0d6a8b808 - - 5abf2c2249aa + - 2e093badc689 + - d7ce0ec78e51 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,8 +44,8 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -66,9 +66,9 @@ tools: revisions: - c5908940967d - f1a5908ea2cb + - 15974dd17515 - a65296ffb4a0 - f0d493f8f84f - - 15974dd17515 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -95,21 +95,21 @@ 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: - - 636b049e6141 - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - 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/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index bfc6fa864..bf9ea628c 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,12 +8,12 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - - a7228a7ea146 - - 0e9e7fcdd543 - cb34f00cc10f - - 79e9a869f40e - 72b5e9dda577 + - 79e9a869f40e + - a7228a7ea146 + - fc8804320156 + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus @@ -21,22 +21,22 @@ tools: revisions: - fa11aa8103b2 - db25ec99c3ea - - 18505fe2bdb1 - d6cddc06aeae + - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: + - cc36773a3681 + - 222669c4afb6 - ec699520444c - eb746fa6f514 - - edf6d4003fad - - 0f5f4a208660 - - 222669c4afb6 - - cc36773a3681 - - 2bf63b38ee9b - 43815fa60f3a + - 0f5f4a208660 - 19f3b583a9b3 + - 2bf63b38ee9b + - edf6d4003fad tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -55,10 +55,10 @@ 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 @@ -78,8 +78,8 @@ 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 @@ -92,16 +92,16 @@ tools: - name: porechop owner: iuc revisions: - - 543cbeef3949 - - 93d623d9979c - 5f76b20953e5 + - 93d623d9979c + - 543cbeef3949 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 @@ -113,8 +113,8 @@ 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 @@ -126,8 +126,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 338d15b8d6fb + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -139,15 +139,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index cc76fc8a8..457dac0a4 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -14,8 +14,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 4e85a3a5dbd1 - 71186bb66ca2 + - 4e85a3a5dbd1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -60,9 +60,9 @@ tools: - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 9dd107db92c2 - 1586b111d2a3 - 83da94c0e4a6 - - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -74,9 +74,9 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - 2f27f3b86827 - edacc4bcd3cb - ed1518ce2237 - - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -101,16 +101,16 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - - 5711fc06a63e - 48a42ca61006 + - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -123,15 +123,15 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - b1bc53e9bbc5 - 4d3eff1bc421 + - b1bc53e9bbc5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -178,16 +178,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - fea85c467896 - 87febc68b45b + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -225,33 +225,33 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 0db22932bc39 - aec831b54a5b - 9d09724f2bf1 - - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - 29c738066906 - 6e24e79d3d69 + - 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: - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -263,17 +263,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - - 64deddb6a8ec - c520a52b5174 + - 64deddb6a8ec + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 625fd9476402 - 9946bc39c834 - 94a50db37d1a - - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1024,16 +1024,16 @@ tools: - name: rdock_rbcavity owner: bgruening revisions: - - 744a777e9f90 - 7e5c2e4bc227 + - 744a777e9f90 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock owner: bgruening revisions: - c362398df83b - - e4b7d1507a75 - a22969b08177 + - e4b7d1507a75 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 81578a16c..2a396b6a1 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -33,51 +33,51 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - 6a457678efcb + - 3f59ebfbfe3d + - 26de3a7b1cb9 - b89cac5156ec - - 3b8b5bde0bd9 - - d033ffc1c161 - - 8834daeb9892 - - '841557158611' - d7c7ef3353fe - - 6a457678efcb - - 107d3ba7024a - c78f3d7dd1db + - f73435dc282b + - d033ffc1c161 + - 8834daeb9892 - cce7b18495e4 - - f04a1264e2a2 - - 3f59ebfbfe3d + - '841557158611' - 5a7c56a5cc08 - - f73435dc282b + - f04a1264e2a2 + - 3b8b5bde0bd9 - 81e66674859e + - 107d3ba7024a - a6619171428e - - 26de3a7b1cb9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 5b777002c2de + - 5fcd1ece3a6e - b0af57c1a968 - 4755f52427c4 - - a185b079b095 - - 6283babe736e + - 88c4aa435ded + - 7a2092844346 - aa8cc71438cf + - e75442c7f4da - 3b96e92e8ec3 - - 659517798cc4 - - df47d4845b62 + - 5b777002c2de - 02b8758214b0 + - 6283babe736e - 6223845127ea - - e75442c7f4da + - df47d4845b62 - 6a726db04d4b - - 88c4aa435ded - - 5fcd1ece3a6e - - 7a2092844346 + - a185b079b095 + - 659517798cc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 524d31add34a - 9b892d7f82cc + - 524d31add34a - b8476e82ac20 - d1c340a5664b - f97743d52b87 @@ -86,34 +86,34 @@ tools: - name: nextclade owner: iuc revisions: - - feb40665d7cd - 128ba8da994f - 9e10ba792be2 - daddf188c13f + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 3a43c3982401 - - 03ed9524dcd1 - - b7e297c2ede6 + - ca0d8cf80567 - 7bb8726be37c - - 2fa9d4f1b48f - - 81804a978fc0 - - 5f8727ff21e7 - - 9d61d3fa046c + - a2099fb98cdb + - 36912871ccdc + - b7e297c2ede6 - abf6dbe8c9d7 - - b6abccb1f25b + - 9d61d3fa046c + - 5f8727ff21e7 + - 437e28791761 + - 14ae456b8cc5 - 42a174224817 + - 03ed9524dcd1 - 2f1019071464 - - 36912871ccdc - - 14ae456b8cc5 - - 83a69484cb87 + - b6abccb1f25b + - 3a43c3982401 - ca337cce3888 - - a2099fb98cdb - - 437e28791761 - - ca0d8cf80567 + - 81804a978fc0 + - 83a69484cb87 + - 2fa9d4f1b48f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -125,21 +125,21 @@ tools: - name: raxml owner: iuc revisions: + - 29ff6a849eac - 73a469f7dc96 + - a4b71be30c3c - ea30d3089354 - ba29b5e2a4be - - 29ff6a849eac - - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - e88a7de55d6e - - 809e42326fc2 - 15ac71df11a0 - - dbe2b2204555 - - 91887494eb97 - f1ccc8a6eb05 + - 91887494eb97 + - dbe2b2204555 + - e88a7de55d6e + - 809e42326fc2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 086b0f53c..3098484a7 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - - fc288950c3b7 - a1f0b3f4b781 - - 881d7645d1bf - 7d34178f2812 - - f6ced08779c4 - b502c227b5e6 + - 881d7645d1bf + - fc288950c3b7 + - f6ced08779c4 + - 1aac2a13842a - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index a3c36d2a0..6b1f8446f 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,13 +2,13 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - d00e15139065 - c0e71cb2bd1b - - 5b85006245f3 - eb085b3dbaf8 + - d00e15139065 + - a58f7eb0df2c - 7fbec959cf2b - - ca90d17ff51b - 3bd420ec162d - - a58f7eb0df2c + - 5b85006245f3 + - ca90d17ff51b tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index ba7635085..cb6d0a4e7 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,22 +2,22 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - f28ad96b76dc - - b574b84afc4d + - 277dc652246e - b18329a8ac14 - - ece627528a78 - 0a18ac48ac53 - - 277dc652246e + - f28ad96b76dc + - ece627528a78 + - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - e988563cc6e5 - - 525f201b86c1 - - e215f71d7983 - bf06d196e23d - b41107d8fe89 + - 525f201b86c1 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter @@ -31,56 +31,56 @@ tools: - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - f23d67e28cc8 - - b8c79e70516d + - 528fb09022be - a8157342d9a3 + - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 - - 80600735685d - - 25b83cbd596a - a95a82eb4d50 - 59e85306eae5 + - 80600735685d + - 25b83cbd596a + - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - - ed9ed1e6cca2 - - e0669b1854b1 - 798da6bdff3d - f1897eb07081 + - e0669b1854b1 + - 611d80c0e29d + - ed9ed1e6cca2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - 74b61bf5bc4b + - a7fb9b395ddf - 5a35e3a8d013 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: - - 043f9c91f686 - - 1693b2126f30 - d2483487e077 - - 10566783d718 - c5aa9fca18c6 + - 10566783d718 + - 043f9c91f686 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -118,9 +118,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - - 1c5cbf8f79ce - 4081e4faa4ab + - 1c5cbf8f79ce + - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -132,8 +132,8 @@ 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 @@ -145,8 +145,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,59 +160,59 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: + - e42225f8a659 - 7f432d87c82c - - 4d17fcdeb8ff - - f522c08e900c - 8934bc76bb52 - - 2133b0be850a - 837224ad1694 - - e42225f8a659 + - f522c08e900c - 37d669de2828 - - 1f39c833f65f - 97a7f34fcb6a + - 2133b0be850a + - 4d17fcdeb8ff + - 1f39c833f65f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: + - a72ac2c7cc5b + - '860429737408' - 85b8866f06d7 - 0ed07016d668 - - '860429737408' - - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 352b37c66d97 + - 1974224d63c2 - 990b4560ead7 + - 352b37c66d97 - 4187b6df1a40 - - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - deaf035bbe9f - 99450519d727 - a1daafbf5233 + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - c7745841de24 - - e79958768a2c + - c1343e3389ca - 40ca115438d2 + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat @@ -227,10 +227,10 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - eb811f3018ea - - 9bf325045235 - 1199751329b0 - 944b43462104 + - eb811f3018ea + - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -250,8 +250,8 @@ tools: revisions: - 28434abe6c5c - 8212e342e482 - - 593839e1f2c3 - b7034eff0db1 + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -278,10 +278,10 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - c9eff69a7c62 + - 518b1730cf2a - 9cdf15d3cfc8 - f7fef900f5b2 - - 518b1730cf2a + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex @@ -295,25 +295,25 @@ tools: - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 658494a2cb00 + - 41859bbdc16e - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 9b7977080f6d - 6634cad7d797 + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 0bb5056cb775 - - 05d5e1ddc985 - d6878d27f051 + - 05d5e1ddc985 + - 0bb5056cb775 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo @@ -327,34 +327,34 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 - - 39e8fde08881 - 92352a475eed + - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 9e26f5c770f8 - 0efbc235f314 + - 9e26f5c770f8 - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - 8a04ed1c1d1b - 3720e349ba2a - c28f13cab67a - - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - 382cde407f81 - - c55dddc5844a - ca799a7246e7 + - 382cde407f81 - c427a8628cbe + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper @@ -368,26 +368,26 @@ tools: - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c + - 18f93351f8b6 - f817513840a9 + - 8d4db262964c - 1c5f31b8d632 - - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - c69f69d7867a - 111c3a00136d - 5d9f175dff81 - - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 476b5e296979 - be74a8cd7d66 - 0e52c85f3b15 + - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -408,8 +408,8 @@ tools: - name: openms_multiplexresolver owner: galaxyp revisions: - - d0304fb829c0 - 4e66c4e73909 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter @@ -444,22 +444,22 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - 89254095cbf6 + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher @@ -472,8 +472,8 @@ tools: - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 18826fb8e5db - 6e8cc5ed2a9b + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -496,8 +496,8 @@ tools: revisions: - e039cc5c7aed - 539a3a4dcc9e - - 5182338d5e7c - dd173849c3d8 + - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -516,8 +516,8 @@ 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 @@ -529,9 +529,9 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e - - c8b225c69a7f - fb52e95a370c + - c8b225c69a7f + - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -551,14 +551,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 07ff622ec007 - - 3ec27b4cee7c - - 7fdd9119cc4f + - 1beff3ddce58 - 3634c90301af - 943a34df6047 + - 7fdd9119cc4f + - 3ec27b4cee7c - da885ca16cb2 - a72c48001f7c - - 1beff3ddce58 + - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -613,9 +613,9 @@ tools: owner: galaxyp revisions: - a371252a2cf6 + - 1a5690a5eedc - 12692567c7f9 - 265c35540faa - - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index ff9864fd2..09e1c73fe 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - cd5f98911089 - - 110a346daf36 - e345aadf914f - - 2f1d464ebfd2 - 42201b90e3f4 + - 110a346daf36 - 289b7d6b69a4 + - 2f1d464ebfd2 + - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - fcce77c09289 - - 0345dbaaa79b - - 0cd2df8af811 - c207119ba5f6 - 42d9087b4789 - 8501601a118d + - fcce77c09289 + - 0cd2df8af811 + - 0345dbaaa79b 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: - - ad5ab22ffe24 - - 04db7fd6b238 + - 89eb29319bf4 - 33486216eec0 - - 405a212b32ab + - ad5ab22ffe24 - 421c33b8bf17 - - 89eb29319bf4 + - 405a212b32ab + - 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: + - eb784fa07f80 - f6e91108b7b1 - - 7370bb65bad4 - - 7b72fde3d27e - 1d839ead7ad3 + - 7b72fde3d27e - fa51dc5e8386 - - eb784fa07f80 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: + - 1544278c272e + - a3e86cd9cac7 - 8a55d29c8fcf - d30e36c48c93 - c9b77ced9a78 - 3d70c2996730 - - a3e86cd9cac7 - - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -89,10 +89,10 @@ tools: revisions: - 564c33e5c3e3 - 887cf585cafc - - 7b881f5f5ad5 - - a5969aa9347e - b242deb58952 + - 7b881f5f5ad5 - e2db212d64ad + - a5969aa9347e 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: - - 9a171f9a450b - bd5ff77e2036 - e897c74a48bb - - b4bab607eb05 + - 9a171f9a450b - 8cff84759bf6 + - b4bab607eb05 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: + - 4f65e343ecdf - adc7a7610d4f + - 887e0991eb24 - 5e10f396979e - 6dafad990086 - 33f0793edf93 - - 4f65e343ecdf - - 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: + - c287418eb288 + - c5d7050e4ad7 + - 43e3eeb2e0ec - 17d39bf0a63a - - 4e280b27a831 - 97575d01f06b - - 43e3eeb2e0ec - - c5d7050e4ad7 - - c287418eb288 + - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: + - a819ec3b362d - d9bf483266a1 - cd034465d4a4 - 09b8edb56d80 - - 9586f08634c0 - 0b8c84a7fdb5 - - a819ec3b362d + - 9586f08634c0 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: + - a4b4bd84f69e - bf0e43ab0416 - 2645575d1bf2 - - 95351dd0fd3f - - a4b4bd84f69e - 69842dd5aa48 + - 95351dd0fd3f - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: + - 8a35a3bc6752 + - bb0475c884ff - d033e1ccb386 - - 912f904a6e1e - cfb504394ae1 - - bb0475c884ff - d1fda11e602f - - 8a35a3bc6752 + - 912f904a6e1e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - d504d945a655 - d1fad35bdb4a - 95286af4139b - - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 0d80a79fb..ea6bd9276 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,8 +2,8 @@ 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 @@ -46,8 +46,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -60,9 +60,9 @@ tools: - name: cuffmerge owner: devteam revisions: + - 86285ddd4512 - cf747d1bd79a - 6a6717a5f421 - - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -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: - - 3b36efd62b3e - - 8f0181aacb7a - - e3b16fd7dd08 - 0693ccd171c4 + - e3b16fd7dd08 + - 8f0181aacb7a + - 3b36efd62b3e 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: - - 24a09ca67621 + - 8fe98f7094de - 0696db066a5b - cd9874cb9019 - - 6a3a025714d3 - - 8fe98f7094de - d027d1f4984e + - 6a3a025714d3 + - 24a09ca67621 - 9a882d108833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -132,10 +132,10 @@ tools: - name: dexseq owner: iuc revisions: - - 62adf13b86ea - 2872c633f07e - - df929f257179 + - 62adf13b86ea - b47c006d90c5 + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -147,16 +147,16 @@ tools: - name: edger owner: iuc revisions: - - df0c8d0a5992 + - 3d89af8a44f0 - 9bdff28ae1b1 - - 070900306913 - - 0cb907a2a810 - 334ce9b1bac5 - - 6e53e565fc6a + - 0cb907a2a810 + - a8305cf0c951 - 555659de7321 - f2843df56434 - - 3d89af8a44f0 - - a8305cf0c951 + - 070900306913 + - df0c8d0a5992 + - 6e53e565fc6a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -168,8 +168,8 @@ tools: - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -187,16 +187,16 @@ tools: - name: featurecounts owner: iuc revisions: - - e6a2a912677a - - 7db9d3ea71c9 - - f3a5f075498f - - 90d16db017d7 - a37612abf7f9 - - a56fbe2d6ba7 + - e6a2a912677a - ea04b737afa0 + - 6f66ae7c5f7a + - a56fbe2d6ba7 - af814359d244 + - 7db9d3ea71c9 + - f3a5f075498f - 38b6d12edc68 - - 6f66ae7c5f7a + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -220,9 +220,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 0f710191a66d - f99dd58de04f - 3c97c841a443 - - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -240,13 +240,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 3fb01a8c902d - - f4af63aaf57a - - 6ab42baa56e9 + - 26371a1df031 - a86e80d3c09c + - 6ab42baa56e9 + - f4af63aaf57a + - 3fb01a8c902d - d4b55e2beb12 - 6c19daec423d - - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -264,8 +264,8 @@ tools: - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -283,9 +283,9 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - ce5d418183c5 - 1c75aa5de15e + - 87c11c05d238 - 01247aaf0a10 - 5ae5c312d718 tool_panel_section_label: RNA-seq @@ -299,10 +299,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - - 10c98fab6c5a - 4f9c4e6566e5 + - c971db6f0fe5 - 40985510cd98 + - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -314,12 +314,12 @@ tools: - name: limma_voom owner: iuc revisions: - - 97e06a4c7c75 - - 708348a17fa1 - - 0921444c832d - e827f9aae031 - 58c35179ebf0 + - 0921444c832d + - 708348a17fa1 - d6f5fa4ee473 + - 97e06a4c7c75 - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -338,8 +338,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -381,18 +381,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - c7c55b694974 - - 5ec75f5dae3c - - 99b17b74a8cd - - e132e7d02a3e - - 0a563fd2f22e - - c772497b2c32 - 3ea5a2a63fa2 - 7ed2edc1337f + - 4074fc1940e2 - 980d2a2e1180 + - 0a563fd2f22e + - e132e7d02a3e + - 5ec75f5dae3c - 4df95e2d7f61 - - 4074fc1940e2 - b9e04854e2bb + - 99b17b74a8cd + - c772497b2c32 + - c7c55b694974 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -416,13 +416,13 @@ tools: - name: salmon owner: bgruening revisions: + - 2c0ca397d302 - cc05793bb896 - - 49121db48873 - - ebab418107f5 - e3d32471da11 - - 15cd64d7c58b - - 2c0ca397d302 + - ebab418107f5 - 53e9709776a0 + - 49121db48873 + - 15cd64d7c58b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -435,8 +435,8 @@ tools: owner: iuc revisions: - 56242ff81c84 - - fab6ff46e019 - 8c28affc7c48 + - fab6ff46e019 - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -444,12 +444,12 @@ tools: owner: iuc revisions: - 914cfcba0ec8 - - 258d696dbd7e - - cef79931dda5 + - 1ebd14235b92 - dd4df992d93d - ae618321f34a + - 258d696dbd7e + - cef79931dda5 - 76d290331481 - - 1ebd14235b92 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -479,10 +479,10 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - 0db979fead3a - - c6334cb383ff + - d0d4cef4f967 - ffd1300599a1 + - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -494,10 +494,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - ba3720d7e68b - d6a479fd4281 - bcc5f03f1900 - 74217fbfba4d - - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -509,10 +509,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - - 56162e446004 - c2b82a94493e + - 478f36effca1 - 2fb4ee002432 + - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -525,8 +525,8 @@ tools: owner: iuc revisions: - fab23c3b5258 - - 9ff3765e7172 - 3f4094b6a565 + - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -538,10 +538,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - - 34a018cbee9c - be3f26533209 + - 870ac06dff8e - 4687ecf0eb2d + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -553,11 +553,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 5192f657f305 - - 65e7dea767ea + - 05ab8d5e04a2 - c5fbddcac63a + - 65e7dea767ea - 33406f5a445c - - 05ab8d5e04a2 + - 5192f657f305 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -569,10 +569,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - - e406ac71165d - 6f0fb35b799c + - 1fdb25a8384d - a35cba31d904 + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -584,10 +584,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - - 37a1129c89d2 - - 7c7fbf13aadd - c2c039e421af + - 7c7fbf13aadd + - 37a1129c89d2 + - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -599,9 +599,9 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: + - eafea3083352 - 1d689e4e1caf - 24e94d84adc9 - - eafea3083352 - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -614,10 +614,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - - 3a4ac03d1266 - 9871104ea630 + - 04bb8bb7c198 - 1812dbc5bb7b + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -629,15 +629,15 @@ tools: - name: trinity owner: iuc revisions: - - 48636f857c4b - - d84caa5a98ad - c9cfec002f71 + - d84caa5a98ad - cee61b3fcf78 - - 32b86cd8eb50 + - d2bc35f3d1c5 - 8f1c3df4dd49 - - 9fa24d5aac68 - db1f362cca3e - - d2bc35f3d1c5 + - 48636f857c4b + - 9fa24d5aac68 + - 32b86cd8eb50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -649,10 +649,10 @@ tools: - name: trinotate owner: iuc revisions: + - 4383070d29ed - 9e61bc67866f - - 6fd16fad465d - 2b093007fab9 - - 4383070d29ed + - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index b41c54fe8..ee91e8906 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.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/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 5bcd51abb..c131e6d02 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,8 +2,8 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 88eedb4abea0 + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -15,8 +15,8 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - 1dfd95ee241e + - cb20f99fd45b - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -35,8 +35,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -54,9 +54,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - 19ece8afbaab - 5f8e69cc4c6e + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -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 @@ -81,15 +81,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - cf1ffd88f895 - 9bd1568619cd + - cf1ffd88f895 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: - - 56c31114ad4a - - dc6ff68ea5e8 - 649a225999a5 + - dc6ff68ea5e8 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 - - 12749212f61b - 9149ad20699a + - 12749212f61b + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -130,8 +130,8 @@ tools: owner: devteam revisions: - 33208952b99d - - 92ec40abcdcf - 06dc50b7b711 + - 92ec40abcdcf 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: - - a8d69aee190e - b3d99709fe1a - 720217c23995 + - a8d69aee190e 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: - - fe34990e5ce7 - cc61ade70eb8 - - db17d5321bad + - fe34990e5ce7 - 22970df7a40e + - db17d5321bad 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: - - 88b8c2916784 - - 7def34e6cf4d - - 7a6034296ae9 - 811fc2d75ad4 + - 7a6034296ae9 + - 7def34e6cf4d + - 88b8c2916784 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: - - 9da0311ab1dd - - 329deb17a9f7 - fa7ad9b89f4a + - 329deb17a9f7 - 583abf29fc8e + - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -210,8 +210,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -223,9 +223,9 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - - 30388d878f81 - bb8cfc6f6e0c + - 30388d878f81 + - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -243,8 +243,8 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - a4a10c7924d1 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -257,8 +257,8 @@ tools: owner: devteam revisions: - cab3f8d35989 - - e613c1ad4c4c - 6c2c1836728b + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -271,9 +271,9 @@ tools: owner: devteam revisions: - 5d9ae78f34d3 - - 135c85f4cfaf - bcedabb53ddf - b7f7826ef1cd + - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -285,11 +285,11 @@ tools: - name: samtools_stats owner: devteam revisions: - - 1cc79f49b8d5 - 145f6d74ff5e + - 5a08c09b9311 - 24c5d43cb545 + - 1cc79f49b8d5 - 3a0efe14891f - - 5a08c09b9311 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -301,13 +301,13 @@ tools: - name: samtools_view owner: iuc revisions: - - c370440f901e - - 0dbf49c414ae - - 350bbc5c2ffd - - 5826298f6a73 - bf328cec6a42 + - 5826298f6a73 - b01db2684fa5 + - 350bbc5c2ffd - b72793637686 + - 0dbf49c414ae + - c370440f901e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index 5e937390d..0ee71983f 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,10 +2,10 @@ tools: - name: ena_upload owner: iuc revisions: - - 6f6537780379 - - a62c4a11a67d - d147d6455873 + - 6f6537780379 - 4aab5ae907b6 + - a62c4a11a67d - 59bb6d34fca6 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index f908b06c7..d009b76e8 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -2,11 +2,11 @@ tools: - name: anndata_import owner: iuc revisions: + - 32e547223c9e - 00712416fdaa - 55e35e9203cf - - fb9e030ffae4 - - 32e547223c9e - cfc3f5a57dc6 + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -18,11 +18,11 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - ee98d611afc6 - - 038e32885fec - 688357ad5e61 + - 39e945f0b2c1 - b9fac48532eb + - 038e32885fec 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: - - d4af736e7b83 - - 3d748954434b - - 9bd945a03d7b - b85871dd69f9 - 43cb7b5a6fe7 + - d4af736e7b83 + - 9bd945a03d7b + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -50,9 +50,9 @@ tools: - name: dropletutils owner: iuc revisions: - - 8855361fcfc5 - - a9caad671439 - cdf4443d5625 + - a9caad671439 + - 8855361fcfc5 - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,8 +78,8 @@ tools: - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -99,8 +99,8 @@ tools: owner: iuc revisions: - 0bff0ee0683a - - 7e014059a88d - f911a64454fb + - 7e014059a88d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -118,9 +118,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - f3eb2291da05 - - 37a47c4fd84d - 2b0d3e2f402a + - 37a47c4fd84d + - f3eb2291da05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -132,9 +132,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - a6821f856a1e - 69018f285aa3 - df8e4e54d367 - - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -147,8 +147,8 @@ tools: owner: iuc revisions: - 2af7c5086a96 - - c92d0f9338c5 - 44b935f2271b + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -160,8 +160,8 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - aaa5da8e73a9 + - b2df381a6004 - 77b91b9bdf52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -175,8 +175,8 @@ tools: owner: iuc revisions: - 3c86f71498bc - - b409c2486353 - a97abb8cd15b + - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -189,8 +189,8 @@ tools: owner: iuc revisions: - 6c145a6868cc - - c5d3684f7c4c - 5e9171dc8244 + - c5d3684f7c4c - cc0deb593fc8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -217,9 +217,9 @@ tools: - name: scanpy_plot owner: iuc revisions: - - dbbe1ea8ecb1 - 6adf98e782f3 - aa0c474463c2 + - dbbe1ea8ecb1 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: - - f2f6c703da06 - 215733a383f2 - bf2017df9837 + - f2f6c703da06 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: + - 8f333f90d8d6 - b834074a9aff - fd808de478b1 - - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -259,9 +259,9 @@ tools: - name: scater_filter owner: iuc revisions: + - 652923ce664f - 7a365ec81b52 - b7ea9f09c02f - - 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: - - 81e5bdff4853 - ef4c80837bc5 - 2e41b35b5bdd + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 90c954e29..48f3e4157 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - - 562f3c677828 - 419027d822d6 - - 4c07ddedc198 - 746e8e4bf929 + - 2f3c6f2dcf39 + - 4c07ddedc198 + - 562f3c677828 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 @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: + - cb1c59d69557 - 6c29c7e347e8 - 7a15159140d1 - - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,39 +120,39 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 840f29aad145 - 7442b94d6a1e - 9c3e1d3235c8 - aef56d0e7a61 - - 840f29aad145 - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - - 375bbd555f4a - 9fda0b82f419 + - 375bbd555f4a + - d0352e8b4c10 - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad - cd02bf168d23 - - 7ae443e6217d - 4cc980df6265 + - 2c58b83c9bad + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 4bbaf77573ef - - bb9fc9d46ea4 - ad7e0b4291ee - 1dd433d2c92c + - 4bbaf77573ef - 7dd3fb35904f + - bb9fc9d46ea4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index 3d124cc5a..d058bb78b 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -8,8 +8,8 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -28,14 +28,14 @@ tools: - name: column_maker owner: devteam revisions: - - 464b9305180e - - 6595517c2dd8 - - 13b6f0007d9e - - be25c075ed54 - 02026300aa45 + - 9cd341095afd + - be25c075ed54 - 6e8d94597139 + - 464b9305180e + - 13b6f0007d9e - 626658afe4cb - - 9cd341095afd + - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -47,8 +47,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -74,8 +74,8 @@ tools: revisions: - 557ec8d7087d - 9cc411a62277 - - 37cde8134c6a - 34d29339abab + - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -99,29 +99,29 @@ tools: - name: merge_cols owner: devteam revisions: - - f2aac0c5c60d - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f + - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 1ea4e668bf73 + - 3a6b78c39dca - cf34c344508d + - 83069b38aa85 + - 1ea4e668bf73 + - 623f3eb7aa48 - 2e8f945f7285 - 33d61c89fb8d - - 623f3eb7aa48 - - 3a6b78c39dca - - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: + - 503bcd6ebe4b - ae8c4b2488e7 - 399da6b5ec21 - - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -133,27 +133,27 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - f768f6183386 - b722161a845a + - f768f6183386 - bce29ec10b78 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: - - 9ff72e942410 + - 74a8bef53a00 - f46f0e4f75c4 + - 0a8c6b61f0f4 - d698c222f354 + - 9ff72e942410 - ddf54b12c295 - - 74a8bef53a00 - - 0a8c6b61f0f4 - a6f147a050a2 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index 2ca50c3e4..3bfb39880 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -2,9 +2,9 @@ tools: - name: breseq owner: iuc revisions: + - 82fb5e3bb93e - 0d18a3ba2d1c - 85c57cc9b558 - - 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: - - a5937157062f + - 156b60c1530f - 04fa42777df9 - 57def2d7c093 - - 156b60c1530f - ef2c525bd8cd + - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 - e61c9ac190ad - - 435b157bed6d - 791f73caa0c8 + - 435b157bed6d + - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - - 3b4b2121842f - - 03627f24605f + - 074d44697036 - dfadc322b065 - - 65432c3abf6c - 4805fe3d8fda - - 074d44697036 + - 3b4b2121842f + - 65432c3abf6c + - 03627f24605f + - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 701d134358ad - - 9cb929f21cfa - 7dfca164d2e3 + - 9cb929f21cfa + - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - - 971e07ca4456 - f4473557ffc7 - c27549b9aa1f + - 426d707dfc47 + - 971e07ca4456 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: - - fa016f1eea1a - d220115f882b + - fa016f1eea1a + - c9a8ef2aa380 - 9bccc8404a3c - 5bbf9eada9c2 - - c9a8ef2aa380 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -130,19 +130,19 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 3b1e7c170b10 + - ee4a90760848 + - 40f0591deda0 - 32f14a2723ec - e7aff4a85df5 - - 40f0591deda0 - - ee4a90760848 + - 3b1e7c170b10 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - - 02d81b994ef5 - 4934c0ac6197 + - 02d81b994ef5 + - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 636708288..3d7e881bf 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -3,12 +3,12 @@ tools: owner: iuc revisions: - 8a2e296c07ef + - b7ea370b8f5d - e075b1be5abb - - ebe5fc018e72 - 6a88248893c4 - 265fe0f9ea64 + - ebe5fc018e72 - 3f62d4939d54 - - b7ea370b8f5d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -20,12 +20,12 @@ tools: - name: bcftools_call owner: iuc revisions: - - 544cb432072b + - b03984136ce4 - 21687e35f066 + - 544cb432072b + - 0fba2c15b40d - 22637b1a55bf - - b03984136ce4 - c37b684e7f4e - - 0fba2c15b40d - f0d44631365f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 01d6b7d6365e - - 8627b2b383b4 - 0238f68ad641 - bf1f4994f104 - - 6d35a3780bfd - - 8ca3647c90fd - 8408bffd5616 - 3a7084316a6e + - 01d6b7d6365e + - 6d35a3780bfd + - 8627b2b383b4 + - 8ca3647c90fd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -58,13 +58,13 @@ tools: owner: iuc revisions: - 9b5abbf50d23 + - 08296952d12f + - 03e0645395d2 - f430a1ec7ee4 - 62ca6da715bf - d144af39073a - - 03e0645395d2 - 81426b3cf18b - 6b6c992d3a14 - - 08296952d12f 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: - - d37e313a41be - 95c6f3f4c77f - - 147de996e34f + - e522022137f6 - d3081540d175 - - 2363ef414c9b + - d37e313a41be - 1829900b5dcd - - e522022137f6 + - 2363ef414c9b + - 147de996e34f 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: + - b14ff40958cb + - 9b29129fb491 - 1137ce8efc1e + - 348cd212dbad + - cacc9970727a - 09f37afb3621 - - 9b29129fb491 - 92c0aff8b53e - - cacc9970727a - - b14ff40958cb - - 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: + - 367ba501b6eb + - 55c0e906c14c - 4935320a59a8 - - ecc9192912b8 - 1f2183a23823 - - 55c0e906c14c - - 367ba501b6eb - de68c11034f6 + - ecc9192912b8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -129,11 +129,11 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 64a8f7dae3ad - 6c790a091c7c - - 039ea3f1dea9 - - ae68ceb4cca3 + - 64a8f7dae3ad - f01b2c9506b9 + - ae68ceb4cca3 + - 039ea3f1dea9 - 7cbf3c66d4ad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -146,13 +146,13 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 6ea7170a016d - - 33bd9301568c + - 277719af4dd7 - e7452697afd9 - cdb7b4927742 - - 963a3635b2e1 - - 277719af4dd7 + - 33bd9301568c - 656a916779fe + - 963a3635b2e1 + - 6ea7170a016d 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: + - 501bfb078342 - 3eac729e66c9 - - a1213a0b7b66 + - b7f0f59baa7e + - 26d97cdd5410 - a29a2f40b665 + - a1213a0b7b66 - 5a321fab1fe4 - - 26d97cdd5410 - - b7f0f59baa7e - - 501bfb078342 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -183,13 +183,13 @@ tools: owner: iuc revisions: - 81e4014fa809 - - 5f27e814a119 - 63aabc920911 - 709dd8291b83 - - c803c34361e0 - - d7d1663559e9 - 768d04526638 + - 5f27e814a119 - 97d19c008d15 + - d7d1663559e9 + - c803c34361e0 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: + - 2215287d5cc9 - 7ba36babba2d - - b1eba148b35b - - b931e65638b8 - - 86296490704e - af163c712539 - - 2215287d5cc9 - 85ee7e6c4204 + - b931e65638b8 + - b1eba148b35b + - 86296490704e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,14 +219,14 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 4e1d23e5c691 - - ce9396ddcb2b - - f506df85c652 - 9c711df3258d - - 37757ffb4c5f - - 5660b21a0dbd - 03191140c66a - cf06b44624c7 + - 5660b21a0dbd + - ce9396ddcb2b + - 37757ffb4c5f + - f506df85c652 + - 4e1d23e5c691 - 31ea13dfe5e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,12 +239,12 @@ tools: - name: bcftools_norm owner: iuc revisions: + - 48291658fdf6 - 6deb4d549bc9 - a404f786a94c - - 19905c025d2a - - 48291658fdf6 - 021693fdadaa - ebb2e12a6de1 + - 19905c025d2a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -256,12 +256,12 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - be6b217710af - - 97e8145d7e30 - - 5ad5d4243987 - - 71c78e0eea52 - f7879f1e77f9 + - 71c78e0eea52 - c450406f722b + - 5ad5d4243987 + - 97e8145d7e30 + - be6b217710af - 69d8b7567281 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 79f7a1acc2cd - cc7f9a4e186b + - d31a2e310a52 - 0fe007201caf + - 79f7a1acc2cd - 89720ec3d58e - - 52f9e4a660e3 - - d31a2e310a52 - 2514e684f8a3 + - 52f9e4a660e3 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: - - 80e6e399ccd0 - 1411bef27a75 - - 75ddd081f608 + - 026a989b7cee - 230e424bde67 - 0a62420cb9cd - - 026a989b7cee + - 80e6e399ccd0 - 99f4a81a47be + - 75ddd081f608 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -311,12 +311,12 @@ tools: owner: iuc revisions: - bca7ce81688f - - c01be0ab9806 - 444e6a756c35 - - e493702b19eb - - ba20340426fe - 5808f77b2bb6 - 5acfca5a76af + - ba20340426fe + - 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: + - f2482aa4862e + - 68fec03a63b7 + - 12152af85697 - 4d236c696844 - 157ffcdd3fa7 - - 12152af85697 - - 68fec03a63b7 - - 7fe09ad6a939 - d52b8947b269 - - f2482aa4862e + - 7fe09ad6a939 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: - - 0e5d11004815 - - 27e2611639a9 - 29ba253e2e05 + - 0e5d11004815 + - 6f8e223f78f3 - 8f2fc0ab30fb - 8dbce095986c - cbe39e530cbf - - 6f8e223f78f3 + - 27e2611639a9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,9 +364,9 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - a8630d4fbaf8 - - 88bb477f45f7 - e0a856def0b0 + - 88bb477f45f7 + - a8630d4fbaf8 - 3ff5654b4e7d - a367a15c6de5 - af36eb5418fe @@ -382,13 +382,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 03e30f06f15f - 4ed46189d6c6 + - 2f4eef1f0d22 + - 03e30f06f15f - 31c096c6b156 - - 96d0145c041a - 6ce175385dd9 - 5c9729d54721 - - 2f4eef1f0d22 + - 96d0145c041a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -401,12 +401,12 @@ tools: owner: iuc revisions: - 2c4941386820 - - 262bba5b90ef - - 11af7fce71cf + - a1aad8b559c6 - 46eb13bc2c73 - - 40daf124be88 - 09f5e45a8212 - - a1aad8b559c6 + - 11af7fce71cf + - 40daf124be88 + - 262bba5b90ef 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: - - 12038f59c0f4 + - 4b796b58938b - 743cd1472aeb - - 882b2e649602 - - 8cb121b6a1d2 - 0594ea1417c8 - - 4b796b58938b - - 6cbb9c47795c - f272b8ba0983 + - 12038f59c0f4 + - 8cb121b6a1d2 + - 6cbb9c47795c + - 882b2e649602 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: + - 8c3ff4ef1190 + - eccb508bb678 - cced6715f926 - 18cf9de1cf73 - dba06328556a - adee7e8b746f - - eccb508bb678 - - 8c3ff4ef1190 - 238f78e38a8b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -456,12 +456,12 @@ tools: owner: iuc revisions: - e53501abf992 - - 9f36041495a3 - e0ad88dec40d - - c9935c9e8a24 - - a850902cac64 + - 9f36041495a3 - f64e7ca2efd2 - 3ce32adc55b2 + - a850902cac64 + - c9935c9e8a24 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: - - b7be725976b6 - - d68c43202172 - 8057cf55fa41 - - d43eb39b989e - - 4db0695a6fc7 - 79489d5685dd - fd3539749127 + - 4db0695a6fc7 + - d68c43202172 + - d43eb39b989e + - b7be725976b6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -492,11 +492,11 @@ tools: owner: iuc revisions: - 78cd8b69da4c - - 6a636d58dfc2 - - 58091e1be01b - 5296d26b0373 - bdc67eeb0bc9 + - 58091e1be01b - b0d39ef600a7 + - 6a636d58dfc2 - 1ccf0e7fb4f6 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: - - 4d3ce9dc1525 + - baa8823f8073 - e8af591435d1 - - b641062a2587 - b17394940c7a - - baa8823f8073 - - '388983871932' - a2f8dc22d7c0 + - 4d3ce9dc1525 + - '388983871932' + - b641062a2587 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: - - abc3ced31cd1 - - 59fa8742285e - e6b5cbbf449b - - d1f8f55f564d - - 38d75661c235 - 3a233c8eb814 - 3ca3de4e5291 + - d1f8f55f564d + - 38d75661c235 + - 59fa8742285e + - abc3ced31cd1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -545,8 +545,8 @@ tools: - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo @@ -559,15 +559,15 @@ tools: - name: vcfallelicprimitives owner: devteam revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -580,8 +580,8 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti @@ -594,8 +594,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -623,15 +623,15 @@ tools: owner: devteam revisions: - fa24bf0598f4 - - eae7c08ebb6f - 6b935ab36d7b + - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -651,8 +651,8 @@ tools: - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -665,8 +665,8 @@ tools: - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -686,15 +686,15 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 958b6484a7f1 - 2ba3b87f904f + - 958b6484a7f1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - dd44c3f416c3 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index c4ad6e46a..a5891e90c 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,9 +2,9 @@ tools: - name: abricate owner: iuc revisions: - - 6e9aea89e388 - - 78c75f134c16 - c2ef298da409 + - 78c75f134c16 + - 6e9aea89e388 - 3f3e247c053d - 4efdca267d51 tool_panel_section_label: Annotation @@ -36,38 +36,38 @@ tools: - name: annotatemyids owner: iuc revisions: - - 4f2967b27e67 - 44018dd6b447 - cd2480f35935 + - f29602ae449e + - 4f2967b27e67 - fe3ca740a485 - - 3e1f6f6d557e - 1aae04680c4b - 133f36c29579 + - 3e1f6f6d557e - b5d8e5475247 - - f29602ae449e 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 - - 7be22100e5e1 - 6519ebe25019 + - 7be22100e5e1 + - dc027fa56d55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - ca6d970d931c - - 09855551d713 - 28433faa6e42 + - 09855551d713 + - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,9 +79,9 @@ tools: - name: barrnap owner: iuc revisions: - - 8fd427007e93 - 7355bbf5e05f - fe48aa4ccd5e + - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -124,41 +124,41 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 9f2455341fac - 14f588312c56 - 582fd74dc2a1 + - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 73428a792541 - 30fb23d4c31c - a230ea445788 - - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - 30f08d74024f - - 494f0bb4a993 - 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: - b3cf4684e9c7 - - d3af38b9c7e1 - 52af33194019 + - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -184,9 +184,9 @@ tools: - name: goseq owner: iuc revisions: + - 43798b4caee0 - 8b3e3657034e - ef2ad746b589 - - 43798b4caee0 - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -212,8 +212,8 @@ tools: - name: interproscan owner: bgruening revisions: - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -232,23 +232,23 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - 370c210d9541 - 3c1a01127868 + - 370c210d9541 - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 033755194fe9 - 624606f7c996 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -272,10 +272,10 @@ tools: - name: prokka owner: crs4 revisions: - - a17498c603ec + - bf68eb663bc3 - 8a22554cdde2 + - a17498c603ec - d643e3b03500 - - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -287,15 +287,15 @@ 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: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training @@ -307,27 +307,21 @@ tools: - name: snpeff owner: iuc revisions: - - 68693743661e - 5c7b70713fb5 - - 8f92c2b26e6d - - 268d162b9c49 + - 5a29ab10dba6 - cfcf33df7fc0 - 5b80f544c67f - - 5a29ab10dba6 + - 268d162b9c49 + - 68693743661e + - 8f92c2b26e6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - 5fab4f81391d - 09d6806c609e - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: snptools - owner: rreumerman - revisions: - - 8de0ffc2166f + - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -346,14 +340,14 @@ tools: owner: iuc revisions: - 037a11682176 - - e1a9d6fd258d - - 45083d070fb8 - - ac8250086ac3 - - 200c378d85f3 - - 2c68b0c38785 - - 809dfc93d593 - 37213cf56392 + - 2c68b0c38785 - ba6f87115e13 + - 200c378d85f3 + - ac8250086ac3 + - 45083d070fb8 + - 809dfc93d593 + - e1a9d6fd258d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index b1f8f7832..6ecba3306 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - 553bfe8bd0b5 + - fa5259cc561b - 841084c5fc46 + - 7547fcab5d19 - a929ce596a34 + - 553bfe8bd0b5 + - 890b794c997d - 0e93176640ac - 8f1b150a2487 - - 890b794c997d - - fa5259cc561b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - b9e31c5c01c7 - 21e491ad532a - - 067592b6b312 - 94fe43e75ddc - - b9e31c5c01c7 - b2860df42e16 - ddddce450736 + - 067592b6b312 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - a7f16f24e9a1 - - faee8629b460 + - 22286dab5aa1 - 5258e18bbe23 + - faee8629b460 - 3371c5bdc17a - - 22286dab5aa1 + - a7f16f24e9a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,28 +49,28 @@ tools: - name: busco owner: iuc revisions: - - 94170eee0ad8 - 41030a6c03b7 - - e824f5d958d0 - - 4048d82f0c88 - - 1e62c28ba91d + - 46ae58b1d792 + - bb935709506a - 602fb8e63aa7 - - 5ecdeca79a0d - - 2dd755c1c6ff - e4bd1e99bacf - - cf13a1e03e5b - 1440ae06552f - - bb935709506a - - 46ae58b1d792 + - 4048d82f0c88 + - 5ecdeca79a0d - 0d243f458b53 + - cf13a1e03e5b + - 1e62c28ba91d + - 94170eee0ad8 + - 2dd755c1c6ff + - e824f5d958d0 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 @@ -84,17 +84,17 @@ tools: revisions: - cb8dfd28c16f - 3ee0ef312022 + - 276f5d8712d5 - e27815e82dd4 - 8d4f03b5fe9d - 1ce9b1d72ec3 - - 276f5d8712d5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 3169a38c2656 + - b2f674562a18 - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -110,9 +110,9 @@ tools: owner: bgruening revisions: - 3fba9c77550a - - 3ef480892a9f - 5127a713de83 - 690c2caa367e + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -124,19 +124,19 @@ tools: - name: hifiasm owner: bgruening revisions: - - 045c7c3d8e59 + - 366a11d316a7 + - f3c89da3af16 + - da9d8bf98802 - 5f625c63b8bc - - 6505bd37670d - - 9ef6920c3089 - ec9e21e9c71b - - 3f7be05a1597 + - 2061fb3b81b4 + - 71740308d412 + - 6505bd37670d - 5bec28269d95 - - 366a11d316a7 + - 045c7c3d8e59 - 60024a528cbd - - f3c89da3af16 - - 71740308d412 - - 2061fb3b81b4 - - da9d8bf98802 + - 3f7be05a1597 + - 9ef6920c3089 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -154,8 +154,8 @@ tools: - name: megahit owner: iuc revisions: - - de387b2b2803 - 7518ee87b53d + - de387b2b2803 - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -170,21 +170,21 @@ tools: - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - eadfd71dde37 - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 2ecf5a570907 - f338e9942b27 + - eb7a370f6588 - e731ea24e48d + - 606b09cc9860 - 3ca2d2a9068c - fd128c111ab0 - - 606b09cc9860 - - eb7a370f6588 + - 2ecf5a570907 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -196,10 +196,10 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d - a7b889b90140 - 8b6d0d85252b - 73a3846701e1 + - 8dee0218ac7d - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -213,8 +213,8 @@ tools: owner: iuc revisions: - 7c2f5268d01c - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -226,74 +226,74 @@ tools: - name: pretext_map owner: iuc revisions: - - dfb8a4497339 - - 2b16ba799da9 - d256a51a656b - - bbe19ef04a74 - 02831bf9e95f + - bbe19ef04a74 + - 2b16ba799da9 + - dfb8a4497339 - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - e9bd16ba5ebd + - 76d4cbefff85 - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 875d0f36d66f + - 6fcbee531de6 + - 342a1d1fed7b - 3061c8b029e5 + - 59db8ea8c845 - 72472698a2df - 7594365c546b - ebb0dcdb621a - 675488238c96 - - 342a1d1fed7b - - 6fcbee531de6 - - 59db8ea8c845 + - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - d865b62f501c + - a199cd7ac344 - 936f0b5e7fcc - - aa39b19ca11e - cd06929b224b + - aa39b19ca11e + - d865b62f501c - 39bed8de8017 - - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - f11b994b7eb2 + - 2b2a352488fa - 33b7d8481a76 - 3edba9afc9bc - f8564b2d7f63 - - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 53c2bc8c2ae3 + - 378e55aeeb25 - ef69617ecb42 - 1d06c8b38e77 - - 53c2bc8c2ae3 - e122f9101584 - - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - 9a22227bb6d0 + - f77f7a7f3b83 - ba7b0f11e470 - ab5b7f6b7198 - - f77f7a7f3b83 + - 9a22227bb6d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -306,130 +306,130 @@ tools: owner: iuc revisions: - f698c7604b3b + - 865119fcb694 - 83ead2be47b2 + - ad80238462c1 - ee17a294d3a3 - - d9f6a00b6db7 - 196a599ec43d - - ad80238462c1 - - 865119fcb694 + - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - 5a0ddb4dc3a4 - 5e0825476fb7 + - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 - - 1fc82fe7ebef + - 904bf932cf78 - 7490b213baa9 + - 1fc82fe7ebef + - 051fd2db8a27 - 1bb12736175c - - 904bf932cf78 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - 34305b013402 - - ad8b536d1caa - fee85957cebe - - 808b3a0a6716 - d6e617c4e338 + - ad8b536d1caa + - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - - 6b5a5842531e - - 21da31ed41a1 - - e5a3b75a271f - b8002c3f7141 + - e5a3b75a271f + - 21da31ed41a1 + - 6b5a5842531e + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 86f66ab58e14 - 2a10645aeadd - 9de69775f512 - - 328aa71f0f3c - f1532cb33c75 + - 328aa71f0f3c + - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - e41dcb0e913b - - 85fb02c43042 - 340bc17f49cf - - 1708851f8804 - 6aad515a5270 + - 85fb02c43042 + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 + - d159735a6a9f - b3490b036c5a - 249f6a28c751 - d5fb354f745d - - d159735a6a9f + - b65a43f70b99 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d2d1df21dfb9 - - 7897763d14ec - 33368fec3b70 - 9006e5836729 - - dd7ad84f3943 - b7829778729f + - dd7ad84f3943 + - d2d1df21dfb9 + - 7897763d14ec tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - - 8f631679571f - - ced385aa976d - 6f4c8ad6ea01 + - ced385aa976d + - 8f631679571f - 189e837009c9 + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - d40ed4eb0c0e - - 19bdfd1e6fe3 - 356afed970b4 - 9ded6109434a + - 19bdfd1e6fe3 - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b - 4688ae3b49b5 - b23249f81bc4 - ebd801e712bc - 80a17897564d + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - 937ea677d437 + - 59bd28f6265d - b5e35a2ca4f3 - b64696992ee9 - - 59bd28f6265d - - 937ea677d437 - cb1e3db43020 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -437,28 +437,28 @@ tools: owner: iuc revisions: - 6015aa0303f2 + - 383bb5ad32e2 - 2628f6790eda - - 05bd7504fdb2 - cb4768eeca3b - - 383bb5ad32e2 + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 9e3e80cc4ad4 - e92675014ac9 - - d10bdad2fd17 - 6e26c9afd301 + - 9e3e80cc4ad4 + - d10bdad2fd17 - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 920677cd220f - 8d09f8be269e - 5da9a0e2fb2d + - 920677cd220f - 08256557922f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -466,14 +466,14 @@ tools: owner: simon-gladman revisions: - 82398ba86ba7 - - 37d88f41c810 - 4a53b89fa703 + - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs owner: iuc revisions: - - 425e63adcc5d - 39495e107274 + - 425e63adcc5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index f077c344e..116fc6df8 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -9,10 +9,10 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - - 1f5641a52664 - 31812e7a1315 - ded48b36f3b7 + - 1f5641a52664 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 70adf3e9d..26700f340 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -3,7 +3,7 @@ tools: owner: iuc revisions: - 204a131e47db - - 159b04e36791 - a9c9d768b751 + - 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 4093b9b6e..25f6f164d 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - 07e8b80f278c - - a1a923cd89e8 - - 589e7e57fd6d - - 0a5c785ac6db - a8eabd2838f6 - - 87ee588b3d45 - a68aa6c1204a - - ce3c7f062223 - - dde39ba9c031 + - 87ee588b3d45 - b28e0cfa7ba1 + - 0a5c785ac6db + - ce3c7f062223 - e19bebe96cd2 + - dde39ba9c031 + - a1a923cd89e8 + - 589e7e57fd6d + - 07e8b80f278c 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 7eaf0640d..f52768ff6 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -9,20 +9,20 @@ tools: owner: bgruening revisions: - 1e3323a44643 - - f921014aba5a - 54f751e413f4 - 62c9df8382c2 + - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - 2889433c7ae1 - - acf4e47b734c - 5edc472ec434 - - 0e3cf9594bb7 + - 6f386c5dc4fb - e25d3acf6e68 + - 0e3cf9594bb7 + - acf4e47b734c tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 926ffafd2..e7757a9e2 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 + - f4230f116196 - da6bd1975a71 - - 710301bc46fa - 27ee142314a9 - - f4230f116196 - - 095ad4d096d1 - c8cdde00b105 + - 095ad4d096d1 + - 6ca543ec1bf8 + - 710301bc46fa 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: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -102,89 +102,89 @@ tools: revisions: - 88076940fa94 - 0fac8e2afc13 - - 79cfd9ead848 - - 3b8a9d5ced85 - bfb65cb551d8 + - 3b8a9d5ced85 + - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - eb6564a60136 - b46d4b4d995c - 55918daa5651 - d532b7e5f64b - - 715cd0e87781 - f5d979cb4b54 - - eb6564a60136 + - 715cd0e87781 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - d2f955aea23a + - dae135dfd519 + - f26afd1b7104 - fdf2cc80adb5 - 5579659312e6 - - f26afd1b7104 - - 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 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - 2c349b027a01 - cac1886249a2 - 4da9ee404eab - 070e3ecc3fda + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - da8753545526 - - 73008ef1f487 - - d1f803b5943c - - 525ca7c8065f - - f197e34c33a9 - 2e219a2d9327 - - 807aa4c9293d + - 525ca7c8065f + - d1f803b5943c - c0c9a5024177 + - 807aa4c9293d + - f197e34c33a9 + - 73008ef1f487 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 61094e01eff9 - - c4fbab8e03c5 - 7568ae18908a - 2c8ed1b52bf7 - 1809414a9454 + - 61094e01eff9 + - c4fbab8e03c5 - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - ccfbd956a2d3 - - ba83f0923369 - 79e8ab8f1e81 - 730ef07b90ae + - ba83f0923369 + - d7ec25187599 + - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -196,9 +196,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - e6011617c748 - b59c91adeac1 - e2c36f62e22f - - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -228,9 +228,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - d4c67ced6abc - 85fad59f8168 - 9b48456a96fe + - d4c67ced6abc - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 6c81b6015..88d939dbc 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -23,17 +23,17 @@ tools: - name: macs2 owner: iuc revisions: - - 495a4173006f - f5d67c722d67 - 424aefbd7777 - 640d3af5d833 + - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index d18fcc880..3aa10ce48 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,24 +2,24 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 25136a2b0cfe - - 830961c48e42 - 33151a38533a - 90981f86000f + - 25136a2b0cfe + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_to_collection @@ -32,7 +32,7 @@ tools: - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 9121543a0..4d21ef57d 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,14 +8,14 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - a3b86937ead6 - - 5e1240a87bcb - - 4a6ee918c13a - f3a19509108a + - 0b3c3ad92827 + - 6ef0b5664c69 + - 5e1240a87bcb - e3cbd2287f63 + - 4a6ee918c13a - 367b1ed91207 - - 6ef0b5664c69 - - 0b3c3ad92827 + - a3b86937ead6 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert @@ -23,13 +23,13 @@ tools: revisions: - 1b5fc03380d4 - 72ed72122deb - - 33c99804a32f - bd46669113b9 - - e525f9ffb9ac - - 54ccb7e1f49a + - 584008e574b2 - e177a8ea0bf1 + - 33c99804a32f - 501c21cce614 - - 584008e574b2 + - 54ccb7e1f49a + - e525f9ffb9ac tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -47,16 +47,16 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - 186b8d913e6c - - 8979c288aefb - 77b41c89d856 + - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -69,8 +69,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -82,8 +82,8 @@ tools: - name: gffread owner: devteam revisions: - - 154d00cbbf2d - 4dea02886337 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -114,18 +114,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 2dcfbbf9071a - 68f57cc8fad0 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - 63769c4217a7 + - 26c6706bfb07 - 92ac8e086317 - 19e45916daf9 - b9b385097f13 - - 63769c4217a7 - - 26c6706bfb07 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 43bebaa33..d3227fd89 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,204 +2,204 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - e821645ef8fc - - 29451af70c52 + - de72ba3ed6f2 + - 5f6d123679f4 - a1ca9bccc7f2 - c929a006727f - - 5f6d123679f4 - - de72ba3ed6f2 + - e821645ef8fc - 268e91e540ee + - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - 0e143b4c3987 - 12af64f93288 - 0e49b109abc2 + - 7a7fd0f5f15d + - 5d11599b8a7d - bb1e4f63e0e6 - 2d2cf5c1ea8a - - 7a7fd0f5f15d + - 0e143b4c3987 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c - 7c1beb6d6eca - - dc059492a995 - c06951d10364 - - 1d848bc4585f - 195e98217334 + - 1d848bc4585f + - 81b1e3e1fc6c + - dc059492a995 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - bfff7454b59a - - 3d211717a775 + - 26e7304d6737 - 93eb012d9eed + - 3d211717a775 - 71aa86af6762 - a67ac707496a + - bfff7454b59a - 07418a30ed01 - - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 2bc10a9ca58b + - 5be24eba848d + - dd0b7398bb96 - 56d5b797ce84 - b8858746dc1f - - dd0b7398bb96 - 26983857c91a - - 5be24eba848d - 29fcfd36e90a - - 2bc10a9ca58b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - ee3a1b0f45f1 - 7e6bcd2e5128 - - e6d0bff01239 + - ee3a1b0f45f1 - 72bfafe3330b - - c3e012dfe21f + - e6d0bff01239 - 7ef978dc1b8a - 9384cd033f30 + - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: + - 9470f29702f8 + - fb9cf9c97ec4 + - a60c359ec43c - b73e213add0c - fd1275e01605 - - 514fa53b5efb - d9a637e83828 + - 514fa53b5efb - 167788df3b46 - - 9470f29702f8 - - a60c359ec43c - - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - c34d11ea4ba6 - 5bffaa8354a1 + - 86febdcc4283 - e479c7ca5570 + - c34d11ea4ba6 - ca0616bb2cdf - 2c37ce318bc3 - - 86febdcc4283 - a02cfa31e9cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 78f405266706 - 01fb6a7654e6 - - 192ef85c0b0b - - 004aea905d4d + - 2d466b530754 - 69a8621ca2f0 + - 78f405266706 - 1fcb7adc39b8 - - 2d466b530754 + - 192ef85c0b0b + - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 137c4beed34b - d580d6acd1df - - 459cfa861f0b - - db940c262830 - - 2f9e4843f480 - 9ecba5e225a6 + - 2f9e4843f480 - 3c9f0c486cca - - 137c4beed34b + - db940c262830 - d9ce4897dbb2 + - 459cfa861f0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - fd408d755394 - - f264afa9fa6f - 32e451def88c + - f264afa9fa6f + - 2c66e43f1c86 - bd7db9e2f2cb - fbe773640707 - - 2c66e43f1c86 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - 7e361d147872 + - 56bce3c82278 + - 4e12ea27f788 - 3b9d990a0a0e - 231994413f89 - - 7fda5607e777 - 9368fbc49c8b - - 4e12ea27f788 - - 56bce3c82278 + - 7fda5607e777 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 - - e65d16fb2724 + - c03c3384cd81 - 94ca68515826 + - b1779366c8e9 - ce4ce3316f74 + - d9114ef1c8a5 - 4431f39ede55 - - b1779366c8e9 - - c03c3384cd81 + - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - f8fc4e5aff9d - - 2da482e408b8 - 793665fff0f8 + - f8fc4e5aff9d - d57251071381 - 23f7c5f1fdaf - b88ebb3672a1 + - 2da482e408b8 - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 - - e4c7985d4585 - a4dfb122e52b - - 25d830337d31 - - 512155688d98 - - c60570fa602f - 010e58e9d822 - ba6efa77fb79 + - e4c7985d4585 + - 512155688d98 + - 25d830337d31 + - c60570fa602f + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 00d869ea03a1 - - c899e0ccff8c - - 69264da0ce77 - - 4d678170d29b - - aa200e4f3939 - 443d9a9d6d11 - 38e3f226248b + - 4d678170d29b + - 69264da0ce77 + - aa200e4f3939 + - c899e0ccff8c + - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - a2d70c4fd406 + - d806504e96d9 + - 6662b1a8d326 - 10301d137111 - c361b12d207a - - 6662b1a8d326 - - d806504e96d9 - - a2d70c4fd406 - aac8444d6681 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 2082696e5..f5a60a3d6 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 12baadec7809 - 7d16de45c021 + - 12baadec7809 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,36 +23,36 @@ tools: - 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: - - 83fbdf93d51e - 94f412098ac8 + - 83fbdf93d51e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 3bf57dadf7cd + - 76e69de726b2 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: - - 39320fee9d70 - 723a93febe89 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab @@ -65,7 +65,7 @@ tools: - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - ec215ed98831 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 2bdbfb936..e9a6db869 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 - - 832c20329690 - ce385837c160 + - dba489bfcd62 - 63dd26468588 + - 832c20329690 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 a80e93566..685df40a5 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - - d82648ad25a3 - 62f5fab76dfb + - 6da3972210ee - 29bdbc353f20 + - d82648ad25a3 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 7fe346176..db37cac8c 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,37 +8,37 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5915ea1ec9b1 - - 288f97432497 - - 093678460093 - e4691e1589d3 - - 49370cb85f0f - - 8c0175e03cee - c5e2e5902201 - - 48f587c13075 - - 44e2cc14f75b - - 660cffd8d92a - - c4b82dce8335 + - c053d4cad713 - 8665bcc8b847 - - 135b80fb1ac2 + - c4b82dce8335 + - 44e2cc14f75b + - 48f587c13075 + - 5915ea1ec9b1 - de6cebe3c043 - 4e5056fefd88 - - c053d4cad713 + - 49370cb85f0f + - 093678460093 + - 660cffd8d92a + - 8c0175e03cee + - 288f97432497 + - 135b80fb1ac2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - 8889eb864cef - f666895cbebd + - 8889eb864cef - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - - 7d37cfda8e00 - de2db1bdfbf8 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -56,9 +56,9 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 9457a20156db - 516b97a23d7e - 859422bcb689 + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -79,18 +79,18 @@ tools: - name: fasta_stats owner: iuc revisions: + - 56022eb50bbd - 0dbb995c7d35 - cd0874854f51 - 9c620a950d3a - - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: + - 65b93b623c77 - 1d8fe9bc4cb0 - dbf9c561ef29 - - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -117,8 +117,8 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -131,15 +131,15 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 03d57fea6482 - f3936d0632cb + - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -152,31 +152,31 @@ tools: - 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: - - 045f0e1043f7 - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e + - 045f0e1043f7 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 @@ -188,10 +188,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 09070cacefd8 - 567d5b3c52b1 - - 529bccd5e4a1 - d5e9e83cd3d8 + - 529bccd5e4a1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -205,45 +205,45 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 90858c306551 - - bdf1ce174e39 - cb1e251cac37 - 736b8f6ee456 + - 90858c306551 + - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - - b29d37ca9e41 - f984bb114520 + - b29d37ca9e41 + - 3599f5451ee2 - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: + - e246088b6e34 - 0c2907307ba4 - - 177f0621c266 - 6027ef51ef91 - - e246088b6e34 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - 61b4cedc8934 - 547e8d00f11c - 377ac2829eac + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -255,8 +255,8 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -275,8 +275,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -290,10 +290,10 @@ tools: owner: iuc revisions: - 8250ea3a1501 - - b557acca0b56 + - e654095ab143 - 24013bf85a6f - a535cf1e5da4 - - e654095ab143 + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -305,11 +305,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 828dba98cdb4 - - 27ac32a22ad2 - - 9fa7803d1c51 - - 7accf7407811 - 6a675c3aa610 - f3759eec3018 + - 9fa7803d1c51 + - 828dba98cdb4 + - 7accf7407811 + - 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 b1e646177..607cc7298 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 - - ce9cd02d5b88 - - e41385662e5e - 64e9a6afdd0c + - e41385662e5e + - ce9cd02d5b88 + - 7b4468117008 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,28 +18,28 @@ tools: - name: fastqc owner: devteam revisions: - - f2e8552cf1d0 + - ff9530579d1f - 2b0c9d9fc6ca - - 5ec9f6bceaee - 9da02be9c6cc - e7b2202befea - - ff9530579d1f + - f2e8552cf1d0 + - 5ec9f6bceaee - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - 18a51655db17 - ad116ae3f4d9 + - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics @@ -53,30 +53,30 @@ tools: - name: filtlong owner: iuc revisions: - - 41b2ad601cf0 - - a72af9de6bf5 - 8880fb74ef56 + - a72af9de6bf5 + - 41b2ad601cf0 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 1c2db0054039 - - b2f1f75d49c4 - - 5e33b465d8d5 - 75c93c70d094 - 9a913cdee30e - 3d93dd18d9f8 + - b2f1f75d49c4 + - 5e33b465d8d5 - bf675f34b056 - abfd8a6544d7 - c1a4b5f3b432 + - 1c2db0054039 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - 949f01671246 - - cd7e644cae1d - 084bbd8ba7b8 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 0f74fede6..608c16441 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,15 +2,15 @@ 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 @@ -24,29 +24,29 @@ tools: - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,8 +59,8 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -79,8 +79,8 @@ 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 @@ -94,22 +94,22 @@ tools: - 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 owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -123,15 +123,15 @@ tools: owner: iuc revisions: - 666f60a9331a - - da74170c55c7 - 840fb4850be3 + - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -144,8 +144,8 @@ 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 diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index eb150e512..ba4164156 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,15 +2,15 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index dbdb9bfa7..0405a2271 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,45 +2,45 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - 983bf725dfc2 - e9df53a75f3c - 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: - - 4df8de2d0e48 - - 1790dcf3c32d + - f5ea3ce9b9b0 + - 7068f48d0ef9 + - 9a776b080193 + - e08a7ad4378b + - 734abc7ac21d - c441583adae5 - - 83c7d564b128 + - 1790dcf3c32d + - 653e89d73fc4 + - 6ea73833cf67 + - 4df8de2d0e48 - 5e6237d58b0c - - 734abc7ac21d - 69ebb7f46e45 - - 9a776b080193 - - 6ea73833cf67 - - 7068f48d0ef9 - - f5ea3ce9b9b0 - 4317d3cb6cba - aad3885b3216 - - e08a7ad4378b - - 653e89d73fc4 + - 83c7d564b128 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - 7863f1abcdda + - 75b3b3d0adbf - 9aaa46d45472 - 34758ab8aaa4 tool_panel_section_label: Get Data @@ -48,8 +48,8 @@ tools: - name: uniprot_rest_interface owner: bgruening revisions: + - bfdc6a7ffd3a - 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 e95ee4cbe..94c24e943 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -5,12 +5,12 @@ tools: - fd59d783248a - a64dc31ab7f2 - 290a11559985 - - 7f13dc906cb9 + - df7356989ac1 - 740057a5126d - c4bde687c846 - - 4b519282a05b - ae9994cf526f - - df7356989ac1 + - 4b519282a05b + - 7f13dc906cb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -29,38 +29,38 @@ tools: owner: devteam revisions: - 7cf5b1d072b5 - - 867ab348287d - f95284aa2946 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - ca7cb0eaad62 - - 3b37b1b1c3a7 - '566197475670' + - 3b37b1b1c3a7 + - 53460afd5115 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - 391a4cc45fea - - d3a9e32672ec + - 3d059e9c2fba - da4c086cff5b + - d3a9e32672ec - 10515715c940 - - 3d059e9c2fba tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e + - e3a675da7fd0 - 3b12bf9b4b87 + - 5fe1dc76176e - 299307abd804 - d0fc8b746d57 - 1acf88921176 - - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -72,15 +72,15 @@ 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 @@ -93,16 +93,16 @@ tools: owner: iuc revisions: - 4542035c1075 - - 17359b808b01 - - 667e17248bfe - - fd5dbf0f732e - - a6e57ff585c0 - - 1cfc579079a6 - - 6cd09d7b5f37 - - 836d1aa3e89a - ca2def38369c + - fd5dbf0f732e + - 667e17248bfe - 2bb2e07a7a21 - 112eb40ba6cf + - 17359b808b01 + - 836d1aa3e89a + - 1cfc579079a6 + - a6e57ff585c0 + - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -120,9 +120,9 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - - f1691de443a7 - 03c13085aecc + - f1691de443a7 + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -167,22 +167,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 360df4999907 - - 326a3db8d9d1 - - 7dd841a32245 - 59fd173ac850 - - 2824d77cd8f8 - 4ac4e7083b7e - - a1abfa420d9d - 14e7c35f3d00 + - 7dd841a32245 + - 2824d77cd8f8 + - 326a3db8d9d1 + - 360df4999907 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c - 44608d0193ed - 73b8cb5bddcd - - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 98bd5728c..84644b2ba 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -82,8 +82,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index e93f01f44..c40dacf28 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,40 +2,40 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - 921a2da49a0c - 9edf8894a22d - 29f66c353bcb - - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - d404277cc87a - 5746d61f0a91 - 78fb5e286609 - - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 9e357a8b2ec3 - 03dd3c16ae4e - 4d511437b1e5 - - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 3b5b54ed6392 - - 41dbf4d162a2 - 0ba4f56a3613 + - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 5308ca68ef3d - 7babd8a46fe0 + - 5308ca68ef3d - 9939786dd9c9 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 80ce9a786..32a26bea9 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,8 +2,8 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - 81f0cbca04a7 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -34,8 +34,8 @@ tools: owner: imgteam revisions: - 10eed33aa9b2 - - b07f4839ca77 - f3360fbeda64 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -47,15 +47,15 @@ tools: - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - 664232d2a3f7 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - 0e4dccaafef5 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -67,36 +67,36 @@ tools: - name: cp_common owner: bgruening revisions: - - e7273daa5ae2 - 670975e92458 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 2484086dee41 - 6a7da2e5f696 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color @@ -116,29 +116,29 @@ 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 owner: bgruening revisions: - - b178453ea8d1 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - a1a961c46d4b + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - 91e03287f285 + - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity @@ -151,15 +151,15 @@ tools: - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - 980aed9e8fd5 + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 7e89f2f7e..b25e15b2f 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - e319b5b65879 - - 1069f6db0a0e - - f362150bef41 - - 17f911830a8c - - d6e72da3ec35 - 78bbd17d0703 + - 3e4f434a69c6 - e4ee04da1c19 + - e319b5b65879 - a38934e303b9 - - 3e4f434a69c6 + - d6e72da3ec35 + - 17f911830a8c + - 1069f6db0a0e + - f362150bef41 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - c88553ec696e - - 8f8df367470d + - 7fe36019c073 + - 1ef5b6e3e09d - 0135f1d487a0 - - 9537184d421f - f91cfb73d369 - - 2b95d5c04908 - - 1ef5b6e3e09d + - 9537184d421f - 72ddd32392cd - - 7fe36019c073 + - 2b95d5c04908 + - c88553ec696e + - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 - d7e79eb3bcb3 - - 2cf4a1cafc16 - fafb3d685fa9 + - 2cf4a1cafc16 + - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: + - ee29337f905c + - 69797fa273c3 + - 8c05afb547fa - bd2a7d1316b9 - - 3d18f8c3c0f6 - - 8d36959b000d - - 28a6f1908fcc + - ee2beb764a7b - 6a1515bb0687 - - 9eaadf03e0df - 7f1cfa4c0e32 - - ee29337f905c + - 8d36959b000d - 94df24c6bc00 + - 3d18f8c3c0f6 + - 28a6f1908fcc + - 9eaadf03e0df - 43aac8d29685 - - ee2beb764a7b - - 8c05afb547fa - - 69797fa273c3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - d37ede8589b2 - db536ad45f28 + - cb903c9dc33d + - 8858fa037a15 + - 364f4ffec275 - 9f978da6528a - e3bb03cf207a - - c092052ed673 - - 5d6ed46cc101 + - d37ede8589b2 - 5671e1d3d5ee - - 8858fa037a15 - - cb903c9dc33d - - bcaa0d571ce2 + - 5d6ed46cc101 + - c092052ed673 - 0893a1dbb807 - - 364f4ffec275 + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - f95f403841ad + - e1a015876aa9 + - 045d6d00f606 - 12d66d0d05ac + - c5c9f02b6167 + - 49236b03e4fd + - ed28dd32141c + - f95f403841ad - 230b05597996 - 38b91a3190cd - - 49236b03e4fd - 3b6a16d82c1b - - ed28dd32141c - - 045d6d00f606 - 584beffa972b - - e1a015876aa9 - - c5c9f02b6167 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index 531468c74..0044b8255 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,18 +2,18 @@ tools: - name: datamash_reverse owner: iuc revisions: + - 0f1724dd59d2 - b8a457820315 - - 17e3b698dd52 - f198773344e4 - - 0f1724dd59d2 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - 374cb875d38a - 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 502afa900..9c08b92d3 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,89 +2,89 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 772e0e89fc68 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 8a794e6d3388 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 818f9b69d8a0 - f1b9a42d6809 - - e1317b5502fa - b6ef6d0cb6b7 + - 818f9b69d8a0 + - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 05143043ca13 + - c80db5d6fd8c - 947c2eacccb8 - 1588f9076e32 - - c80db5d6fd8c + - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 1552b8cb4a94 - - 9991c4ddde14 - 29e4122c90de + - 9991c4ddde14 + - 1552b8cb4a94 - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 1a53edc4b438 - - 53616c8b0865 - - f3dfa4bdf87e - 841a6cc5fc58 + - f3dfa4bdf87e + - 53616c8b0865 - a07ab242b0b5 + - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: + - 927586a18553 - 2fc89dcd41c8 - - dc4b5fd604a6 - - 91c4e3331208 - 40f4447733b2 - - 927586a18553 + - 91c4e3331208 + - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - c6ae57f774c6 - - 25ab6b4e376e - 36e8d6d5d01b + - 25ab6b4e376e - e5a5ad882f1f + - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - f9639b488779 + - 0630258dcf35 - 02d2be90dedb - - 4ed102b922cb - b7c3e9a3b954 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - ec69cbe34b73 - - 14180f9c831e - 61634a87efc7 + - 14180f9c831e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index b467a2aba..9a23ca84b 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - 03e9b2fbc005 + - 749c918495f7 + - a6d65b0c67af - cd659e8cc5fa + - 937aa69e715f - f6877ad76b00 - - 3ba8d4563129 - - a6d65b0c67af - - 749c918495f7 - - 17062a0decb7 - 017aba02828d - - 937aa69e715f + - 03e9b2fbc005 + - 17062a0decb7 + - 3ba8d4563129 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -28,10 +28,10 @@ tools: - name: bwa owner: devteam revisions: - - e188dc7a68e6 - - 64f11cf59c6e - 3fe632431b68 + - 64f11cf59c6e - 53646aaaafef + - e188dc7a68e6 - dfd8b7f78c37 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,41 +45,41 @@ tools: owner: devteam revisions: - 3e1ea2facca6 - - 60afcc2c1d05 - - 2ff111fac1d7 - e7f19d6a9af8 + - 2ff111fac1d7 + - 60afcc2c1d05 - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - f54f5baedfdd - - 8c6cd2650d1f - - 3f4d6399997b - 09b53c1d4ab1 + - be1d967337e4 + - f54f5baedfdd - 53c0b7a1a0c3 - - b3eab4b67562 - 77b2770508f6 + - b3eab4b67562 - c0c2d0941de8 - - be1d967337e4 - - 6b1e195506a3 - 11a0d50a54e6 + - 8c6cd2650d1f - 037c6e54df11 + - 6b1e195506a3 + - 3f4d6399997b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 79b885ce78d7 - - 178bdbdb6d24 - b8f5f6e87f5c + - 178bdbdb6d24 + - 79b885ce78d7 + - 9ee34ba73ebf + - 1cd2511a396e - 00fbfac99d39 + - e403d27e8f24 - ec9cbd6b9a49 - 13022c3d3076 - - 1cd2511a396e - - 9ee34ba73ebf - - e403d27e8f24 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 14c3880a4..fe61187d4 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -22,54 +22,54 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 5b5a7af9fbb4 - 63f86089423e - 76d3d2b10738 - - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 96336c6a2bb7 + - 18a502a9d287 - 84fd33a60b35 + - 96336c6a2bb7 - 1c35dadbe76f - - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - 34e55239e68b - - addaf9d22850 - - a9f4a217dcd6 - f732237754fc + - a9f4a217dcd6 + - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 - - 8c202e741d68 - 75403243703a + - 04c15826a0b8 - 0776d824d896 + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - e96bbb9e24ea - - 43c99742158b - - 1c9b3bcd4261 - 8470de786d47 + - 1c9b3bcd4261 + - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - 5c865a382933 + - 306a40d4bb8f - 84743da21318 - 1d75bd0595e2 - - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity @@ -77,26 +77,26 @@ tools: revisions: - 555ccac8a4c5 - ac72310b038a - - 8daf4564ccda - 78faebd0879c + - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - 7b8cb2b02978 - d60df8727f59 - a58e4a43f49c - f947b4bb5107 + - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 7f3b59dee073 - 1bc3657cd694 - - 04144473e59e - 7136e9ab70db - - 7f3b59dee073 + - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts @@ -118,9 +118,9 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - dbf1798c0dcc - c4db8c4de66f - 6501b5b33988 + - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -133,8 +133,8 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6c84982ee6f7 + - 654548ae1357 - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -147,25 +147,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - bd7a9c6efb10 - e66ab198ec15 - 6aad8ca3918b - - bd7a9c6efb10 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: - - 7f208f1eb64f - cad93abecac9 - 9704f1a3b32d + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -177,26 +177,26 @@ tools: - name: humann_regroup_table owner: iuc revisions: + - c409a495841f - 31c6d107e7a5 - 79706f10d680 - - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 - d24841f5c3d2 - 71ea608ddfa3 - 714d5a28cc5c + - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - a4d7148ccee4 - a293a742194f + - a4d7148ccee4 + - d7e9a3c41657 - 4137b492233e - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis @@ -205,29 +205,29 @@ tools: owner: iuc revisions: - 64bc7acc22a9 + - 6fcb8ac37a3e - e2c71b852aba - - cf87759761eb - - 75bedfb2078b - 97f7bb0851e7 - - 6fcb8ac37a3e + - 75bedfb2078b + - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 2d35528d2141 - 4033827c76b8 - 080ea153677c - 5e5a999ffaa9 - c82508e76ad1 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: + - 2cd76b089570 - 6b7622dda516 - 95bf7479d53c - - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -288,8 +288,8 @@ tools: owner: iuc revisions: - e674066930b2 - - 328c607150ff - 4a9da2b6c2e3 + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -307,15 +307,15 @@ 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 owner: devteam revisions: - - 6c09bed3444f - 1902d3de4a4f + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -327,8 +327,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - aec58624706f + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -340,8 +340,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: mash_sketch @@ -365,11 +365,11 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc + - 27250f92a01a - 4fd3b5d8706b + - e073891b2afc - 2cff76cf35c6 - 0270541aaf46 - - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -442,20 +442,20 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - b89b0765695d - a92a632c4d9b - - ff8f55893e7d - - a16313517e55 + - b89b0765695d + - 6dee4abadccb - 1a6cdf55390f + - a16313517e55 - 2131d7dca455 - - 6dee4abadccb + - ff8f55893e7d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -527,8 +527,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 9168545e09df + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -546,8 +546,8 @@ 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 @@ -565,20 +565,20 @@ tools: - name: staramr owner: nml revisions: - - 141afacabcfa - - 3b22de20bd4b - - 4b9a8031ab74 - - 2fd4d4c9c5c2 - be818ae858e4 + - 3b22de20bd4b + - 141afacabcfa - aeaa20b96ef2 - 4d83eccf5f81 + - 4b9a8031ab74 + - 2fd4d4c9c5c2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: + - 9495df9dd6ef - b3c7199d8786 - 576963db5f1b - - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index d82ec3b93..ddadef270 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - de3cfb122105 - 12e856482d26 + - de3cfb122105 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 4e9136c2c4c3 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 2e6ef90bd..ca9b9c73d 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 6ae5a7b5a0a2 - - 9422c5a87ee2 - - bdfbaf0c10aa - - 9eeb13a92d79 - - 80f03df2e2ce - - cd07731e4434 - - 48c13389050d - - 8b67dd48fec1 - 2263989660f5 + - 48c13389050d + - 80f03df2e2ce + - bdfbaf0c10aa - 9baa871cb1d1 - - a74dbfee5a86 + - 8b67dd48fec1 - 94b8c6013083 + - cd07731e4434 + - a74dbfee5a86 + - 9eeb13a92d79 + - 6ae5a7b5a0a2 + - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - c18157c68134 - - fc2e49f91e52 - 3ff17bad4006 + - d390fe1567dc - aaa0d6a8b808 + - '764845535798' + - 4a60927aaca5 + - c18157c68134 + - 5abf2c2249aa + - bc3831dd65c1 - f0af8936ed41 - - f14193ec1f50 + - fc2e49f91e52 - 2e093badc689 - - 5abf2c2249aa - - 4a60927aaca5 - - d390fe1567dc - be78f13134e2 - d7ce0ec78e51 - - bc3831dd65c1 - - '764845535798' + - f14193ec1f50 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -51,8 +51,8 @@ tools: - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 4daabc25df00 + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -64,18 +64,18 @@ tools: - name: mafft owner: rnateam revisions: - - f1a5908ea2cb - - f0d493f8f84f - - c5908940967d - 15974dd17515 + - c5908940967d + - f0d493f8f84f - a65296ffb4a0 + - f1a5908ea2cb 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 @@ -102,14 +102,14 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - 959c1f8dae95 + - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 0f99e15da..d396a565b 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,35 +2,35 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 79e9a869f40e + - fc8804320156 - cb34f00cc10f - 72b5e9dda577 - - a7228a7ea146 - - 79e9a869f40e - 0e9e7fcdd543 - - fc8804320156 + - a7228a7ea146 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - db25ec99c3ea - - d6cddc06aeae - fa11aa8103b2 + - d6cddc06aeae + - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 222669c4afb6 - - 19f3b583a9b3 + - ec699520444c + - eb746fa6f514 - edf6d4003fad + - 0f5f4a208660 - cc36773a3681 - 43815fa60f3a + - 222669c4afb6 + - 19f3b583a9b3 - 2bf63b38ee9b - - ec699520444c - - eb746fa6f514 - - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -50,9 +50,9 @@ tools: owner: iuc revisions: - 645159bcee2d - - 0f1c34698076 - - edbb6c5028f5 - a3c4fe6f49ab + - edbb6c5028f5 + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -107,8 +107,8 @@ 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 @@ -120,8 +120,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 338d15b8d6fb + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -133,15 +133,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 01a23a820..50ca70d5d 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -28,8 +28,8 @@ tools: - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 9dd107db92c2 + - 1586b111d2a3 - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,9 +42,9 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - ed1518ce2237 - - 2f27f3b86827 - 19b6a2f0dbe2 + - 2f27f3b86827 + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -69,30 +69,30 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 48a42ca61006 - 5711fc06a63e - 38ccd4589990 - - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -111,17 +111,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 52b6a4d98009 - 27a6a256cd23 - - 172815da3d41 + - 52b6a4d98009 - b4b2b284230a + - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -133,8 +133,8 @@ 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 @@ -146,9 +146,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - 87febc68b45b - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -179,9 +179,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 4ba60cb14cb0 - 9c43baa60906 - 5fe20c915fa6 - - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -193,16 +193,16 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 9d09724f2bf1 - aec831b54a5b - 0db22932bc39 - - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - df30a2f1db55 + - ed7a967cb11b - 6e24e79d3d69 - 29c738066906 tool_panel_section_label: None @@ -231,9 +231,9 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - - d63c1442407f - c520a52b5174 + - d63c1442407f + - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 9a9b80049..5aad0cf9b 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/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: hybpiper @@ -34,86 +34,86 @@ tools: owner: iuc revisions: - b89cac5156ec - - 81e66674859e - - 3b8b5bde0bd9 + - 3f59ebfbfe3d + - d033ffc1c161 + - d7c7ef3353fe - 6a457678efcb - f73435dc282b - - c78f3d7dd1db - - d7c7ef3353fe + - 8834daeb9892 + - '841557158611' - 26de3a7b1cb9 - - 3f59ebfbfe3d - - d033ffc1c161 + - 5a7c56a5cc08 - f04a1264e2a2 + - c78f3d7dd1db + - 3b8b5bde0bd9 - cce7b18495e4 - - 8834daeb9892 - a6619171428e - 107d3ba7024a - - 5a7c56a5cc08 - - '841557158611' + - 81e66674859e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 5b777002c2de - - 6a726db04d4b + - 3b96e92e8ec3 + - 6223845127ea - 88c4aa435ded - - 7a2092844346 - - 6283babe736e - - 4755f52427c4 - 5fcd1ece3a6e - - 02b8758214b0 - - 6223845127ea - - b0af57c1a968 + - 4755f52427c4 + - 6a726db04d4b + - 6283babe736e - aa8cc71438cf - - 3b96e92e8ec3 - - a185b079b095 + - 5b777002c2de - e75442c7f4da - 659517798cc4 + - a185b079b095 + - 7a2092844346 + - 02b8758214b0 + - b0af57c1a968 - df47d4845b62 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - c1d53e95327f + - 9b892d7f82cc + - f97743d52b87 - d1c340a5664b + - c1d53e95327f - b8476e82ac20 - - f97743d52b87 - - 9b892d7f82cc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd + - daddf188c13f - 128ba8da994f + - feb40665d7cd - 9e10ba792be2 - - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 2fa9d4f1b48f + - ca0d8cf80567 - b7e297c2ede6 - - b6abccb1f25b - - 9d61d3fa046c - - 437e28791761 - - 5f8727ff21e7 + - 83a69484cb87 - 14ae456b8cc5 - - 42a174224817 - - 7bb8726be37c + - a2099fb98cdb - 2f1019071464 - - 3a43c3982401 - - 03ed9524dcd1 + - 7bb8726be37c - 36912871ccdc + - 3a43c3982401 - abf6dbe8c9d7 - - 83a69484cb87 + - 9d61d3fa046c + - 42a174224817 + - b6abccb1f25b - 81804a978fc0 - - a2099fb98cdb + - 2fa9d4f1b48f + - 5f8727ff21e7 + - 03ed9524dcd1 - ca337cce3888 - - ca0d8cf80567 + - 437e28791761 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -125,21 +125,21 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - ea30d3089354 - - 73a469f7dc96 + - a4b71be30c3c - 29ff6a849eac - ba29b5e2a4be + - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - e88a7de55d6e - - 809e42326fc2 - - dbe2b2204555 - 15ac71df11a0 - f1ccc8a6eb05 - 91887494eb97 + - e88a7de55d6e + - 809e42326fc2 + - dbe2b2204555 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 2cfacc684..2938746f8 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -3,12 +3,12 @@ tools: owner: devteam revisions: - 1aac2a13842a + - f6ced08779c4 - fc288950c3b7 - - 7d34178f2812 - 881d7645d1bf - - f6ced08779c4 - - b502c227b5e6 - a1f0b3f4b781 + - b502c227b5e6 - f9242e01365a + - 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 9e523df48..88fdc31db 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: - - 5b85006245f3 - ca90d17ff51b - - d00e15139065 - - 3bd420ec162d - - eb085b3dbaf8 + - 5b85006245f3 - 7fbec959cf2b - - c0e71cb2bd1b - a58f7eb0df2c + - 3bd420ec162d + - c0e71cb2bd1b + - d00e15139065 + - eb085b3dbaf8 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 0fbf7655b..d6866919f 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,29 +2,29 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b574b84afc4d - - b18329a8ac14 - ece627528a78 - - f28ad96b76dc - 277dc652246e + - b18329a8ac14 + - b574b84afc4d + - f28ad96b76dc - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - 525f201b86c1 - - e215f71d7983 - b41107d8fe89 - bf06d196e23d + - e215f71d7983 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - bb6397b94018 + - 4fbffddde8cd - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -32,29 +32,29 @@ tools: owner: galaxyp revisions: - b8c79e70516d - - f23d67e28cc8 - 528fb09022be - a8157342d9a3 + - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - a95a82eb4d50 - 59e85306eae5 + - a69865da6f80 - 80600735685d - 25b83cbd596a - - a95a82eb4d50 - - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: + - e0669b1854b1 - 798da6bdff3d + - f1897eb07081 - ed9ed1e6cca2 - 611d80c0e29d - - e0669b1854b1 - - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report @@ -68,19 +68,19 @@ tools: - name: cardinal_segmentations owner: galaxyp revisions: + - cc430977c8ff - 82f6c2f4332d - df2187f9013b - - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - c5aa9fca18c6 - - 043f9c91f686 - - 1693b2126f30 - 10566783d718 - d2483487e077 + - 1693b2126f30 + - 043f9c91f686 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -111,16 +111,16 @@ 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 + - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -145,9 +145,9 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - e66f552a3c47 - 160538a890a6 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -160,39 +160,39 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 2133b0be850a - - 7f432d87c82c - - 97a7f34fcb6a + - 4d17fcdeb8ff + - e42225f8a659 - 37d669de2828 - f522c08e900c + - 8934bc76bb52 - 837224ad1694 + - 2133b0be850a + - 7f432d87c82c - 1f39c833f65f - - 8934bc76bb52 - - 4d17fcdeb8ff - - e42225f8a659 + - 97a7f34fcb6a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - a72ac2c7cc5b - - 85b8866f06d7 - '860429737408' + - 0ed07016d668 + - 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 @@ -202,25 +202,25 @@ tools: revisions: - 4f359549383c - deaf035bbe9f - - 99450519d727 - a1daafbf5233 + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 40ca115438d2 + - c7745841de24 - c1343e3389ca + - 40ca115438d2 - e79958768a2c - - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - d2eac53666f0 - da986f83631b - b648e45fd3cf - - d2eac53666f0 - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -228,9 +228,9 @@ tools: owner: galaxyp revisions: - 1199751329b0 - - 9bf325045235 - eb811f3018ea - 944b43462104 + - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -248,17 +248,17 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - - 8212e342e482 - - b7034eff0db1 - 593839e1f2c3 + - b7034eff0db1 + - 8212e342e482 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid @@ -278,17 +278,17 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - f7fef900f5b2 - c9eff69a7c62 - 9cdf15d3cfc8 + - f7fef900f5b2 - 518b1730cf2a 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 @@ -303,17 +303,17 @@ tools: - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - - 5ad0b5bf1deb - 9b7977080f6d + - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - d6878d27f051 - 0bb5056cb775 - 05d5e1ddc985 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo @@ -327,42 +327,42 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - 27cba4c5fc42 - - 39e8fde08881 - 92352a475eed + - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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: + - c28f13cab67a - 8a04ed1c1d1b - 3720e349ba2a - - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - ca799a7246e7 - c55dddc5844a - - c427a8628cbe - 382cde407f81 + - ca799a7246e7 + - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - - b5d0905419da - 39caaa778d2e + - b5d0905419da + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger @@ -370,8 +370,8 @@ tools: revisions: - 8d4db262964c - f817513840a9 - - 1c5f31b8d632 - 18f93351f8b6 + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability @@ -385,9 +385,9 @@ tools: - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - - be74a8cd7d66 - 476b5e296979 + - be74a8cd7d66 + - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -400,45 +400,45 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: + - c18d8efa4474 - 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 owner: galaxyp revisions: - - bf32e0bcf554 - - 8098330f6d91 - ee860980edc6 + - 8098330f6d91 + - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - 0ced5bc9f4dd + - a2a6e9551046 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: - - 1bf940c18d93 - e8f64a7dc470 + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator @@ -451,15 +451,15 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 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 @@ -472,39 +472,39 @@ tools: - 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: + - 3d8d4ada5405 - 5ae104d0da6e - decc397c3b7e - - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - dd173849c3d8 + - e039cc5c7aed - 5182338d5e7c + - dd173849c3d8 - 539a3a4dcc9e - - e039cc5c7aed 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 @@ -516,8 +516,8 @@ 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 @@ -529,9 +529,9 @@ 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 @@ -544,21 +544,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: + - 07ff622ec007 + - 3634c90301af + - 1beff3ddce58 - 7fdd9119cc4f - - a72c48001f7c - - da885ca16cb2 - 3ec27b4cee7c - - 3634c90301af - - 07ff622ec007 + - da885ca16cb2 + - a72c48001f7c - 943a34df6047 - - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -613,8 +613,8 @@ tools: owner: galaxyp revisions: - 12692567c7f9 - - 1a5690a5eedc - a371252a2cf6 + - 1a5690a5eedc - 265c35540faa 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 3da89b5f5..be861a0fe 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -3,98 +3,98 @@ tools: owner: iuc revisions: - 110a346daf36 + - e345aadf914f - 289b7d6b69a4 + - 2f1d464ebfd2 - 42201b90e3f4 - - e345aadf914f - cd5f98911089 - - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: + - fcce77c09289 - 8501601a118d - - c207119ba5f6 + - 42d9087b4789 - 0cd2df8af811 - - fcce77c09289 - 0345dbaaa79b - - 42d9087b4789 + - c207119ba5f6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 04db7fd6b238 - 405a212b32ab - 33486216eec0 - - 421c33b8bf17 - ad5ab22ffe24 - 89eb29319bf4 + - 421c33b8bf17 + - 04db7fd6b238 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - 7370bb65bad4 - 7b72fde3d27e + - f6e91108b7b1 + - fa51dc5e8386 - 1d839ead7ad3 - eb784fa07f80 - - fa51dc5e8386 - - f6e91108b7b1 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: + - c9b77ced9a78 - a3e86cd9cac7 + - 1544278c272e + - 8a55d29c8fcf - d30e36c48c93 - 3d70c2996730 - - 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 - - b242deb58952 - - 564c33e5c3e3 - 887cf585cafc + - e2db212d64ad + - a5969aa9347e - 7b881f5f5ad5 + - 564c33e5c3e3 + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - bd5ff77e2036 - - e897c74a48bb - b4bab607eb05 - - 8cff84759bf6 + - e897c74a48bb - 9a171f9a450b + - bd5ff77e2036 + - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 33f0793edf93 + - 5e10f396979e - adc7a7610d4f - 887e0991eb24 - - 6dafad990086 - - 5e10f396979e - 4f65e343ecdf + - 6dafad990086 + - 33f0793edf93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 4e280b27a831 - - c287418eb288 - - 43e3eeb2e0ec - - 97575d01f06b - 17d39bf0a63a + - c287418eb288 - c5d7050e4ad7 + - 97575d01f06b + - 4e280b27a831 + - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -102,32 +102,32 @@ tools: revisions: - a819ec3b362d - 09b8edb56d80 + - 0b8c84a7fdb5 - d9bf483266a1 - - 9586f08634c0 - cd034465d4a4 - - 0b8c84a7fdb5 + - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 69842dd5aa48 + - 95351dd0fd3f + - 2645575d1bf2 - a4b4bd84f69e + - 69842dd5aa48 - bf0e43ab0416 - - 2645575d1bf2 - a9c34a289493 - - 95351dd0fd3f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - 912f904a6e1e - - d1fda11e602f + - bb0475c884ff - d033e1ccb386 - 8a35a3bc6752 - - bb0475c884ff + - cfb504394ae1 + - d1fda11e602f 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: + - d504d945a655 - d1fad35bdb4a - 95286af4139b - - d504d945a655 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: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c 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 2ceaa29b2..c11908e21 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -46,8 +46,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -60,9 +60,9 @@ tools: - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - - cf747d1bd79a - 86285ddd4512 + - cf747d1bd79a + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -93,46 +93,46 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - 3b36efd62b3e - - e3b16fd7dd08 - 8f0181aacb7a + - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - cd9874cb9019 - - d027d1f4984e + - 24a09ca67621 + - 0696db066a5b - 9a882d108833 - 8fe98f7094de - - 0696db066a5b - - 24a09ca67621 + - d027d1f4984e + - cd9874cb9019 - 6a3a025714d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: + - 2872c633f07e - b47c006d90c5 - 62adf13b86ea - df929f257179 - - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 070900306913 - - df0c8d0a5992 - - a8305cf0c951 - - 3d89af8a44f0 - - 9bdff28ae1b1 - 6e53e565fc6a - - 334ce9b1bac5 - - f2843df56434 - 0cb907a2a810 + - 9bdff28ae1b1 + - f2843df56434 - 555659de7321 + - 334ce9b1bac5 + - 3d89af8a44f0 + - a8305cf0c951 + - 070900306913 + - df0c8d0a5992 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -152,15 +152,15 @@ tools: owner: iuc revisions: - af814359d244 - - ea04b737afa0 - - a56fbe2d6ba7 - - 38b6d12edc68 - - 7db9d3ea71c9 - f3a5f075498f - - 90d16db017d7 - a37612abf7f9 - - e6a2a912677a + - 7db9d3ea71c9 + - a56fbe2d6ba7 + - 38b6d12edc68 - 6f66ae7c5f7a + - ea04b737afa0 + - e6a2a912677a + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -179,8 +179,8 @@ tools: owner: iuc revisions: - 0f710191a66d - - 3c97c841a443 - f99dd58de04f + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -192,13 +192,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6ab42baa56e9 - 26371a1df031 - a86e80d3c09c - - 3fb01a8c902d - - d4b55e2beb12 - - f4af63aaf57a + - 6ab42baa56e9 - 6c19daec423d + - f4af63aaf57a + - d4b55e2beb12 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -217,32 +217,32 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 01247aaf0a10 - - ce5d418183c5 + - 5ae5c312d718 - 87c11c05d238 + - ce5d418183c5 - 1c75aa5de15e - - 5ae5c312d718 + - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - 10c98fab6c5a + - 40985510cd98 - 4f9c4e6566e5 - c971db6f0fe5 - - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - d6f5fa4ee473 - - e827f9aae031 + - 97e06a4c7c75 - 0921444c832d - - 32511f586472 + - d6f5fa4ee473 - 708348a17fa1 - - 97e06a4c7c75 - 58c35179ebf0 + - 32511f586472 + - e827f9aae031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -254,8 +254,8 @@ 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 @@ -291,18 +291,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 99b17b74a8cd + - 4074fc1940e2 + - 3ea5a2a63fa2 + - 7ed2edc1337f - b9e04854e2bb + - 99b17b74a8cd + - 980d2a2e1180 - e132e7d02a3e - - c7c55b694974 - 5ec75f5dae3c - 4df95e2d7f61 - - 4074fc1940e2 - - 3ea5a2a63fa2 - - 7ed2edc1337f - c772497b2c32 + - c7c55b694974 - 0a563fd2f22e - - 980d2a2e1180 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -314,34 +314,34 @@ tools: - name: salmon owner: bgruening revisions: - - 15cd64d7c58b - 53e9709776a0 - - 49121db48873 - 2c0ca397d302 - - cc05793bb896 - e3d32471da11 + - 15cd64d7c58b - ebab418107f5 + - 49121db48873 + - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: + - c0fd285eb553 - fab6ff46e019 - - 8c28affc7c48 - 56242ff81c84 - - c0fd285eb553 + - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - ae618321f34a - - dd4df992d93d - - 258d696dbd7e - - 1ebd14235b92 + - cef79931dda5 - 914cfcba0ec8 + - dd4df992d93d - 76d290331481 - - cef79931dda5 + - 1ebd14235b92 + - ae618321f34a + - 258d696dbd7e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -365,9 +365,9 @@ tools: - name: transdecoder owner: iuc revisions: + - d0d4cef4f967 - 0db979fead3a - ffd1300599a1 - - d0d4cef4f967 - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -376,16 +376,16 @@ tools: revisions: - d6a479fd4281 - 74217fbfba4d - - bcc5f03f1900 - ba3720d7e68b + - 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 - - 56162e446004 - 2fb4ee002432 + - 56162e446004 + - 478f36effca1 - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -400,70 +400,70 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c - be3f26533209 - - 870ac06dff8e - 4687ecf0eb2d + - 870ac06dff8e + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 05ab8d5e04a2 - 5192f657f305 - - 65e7dea767ea - 33406f5a445c - c5fbddcac63a - - 05ab8d5e04a2 + - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - e406ac71165d - 1fdb25a8384d - a35cba31d904 - 6f0fb35b799c + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - 964b7efe2639 - - 37a1129c89d2 - c2c039e421af - 7c7fbf13aadd + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 - - eafea3083352 - 1d689e4e1caf - 24e94d84adc9 + - eafea3083352 + - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - 1812dbc5bb7b - - 9871104ea630 - 04bb8bb7c198 - 3a4ac03d1266 + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - 48636f857c4b - - db1f362cca3e - - 32b86cd8eb50 - - c9cfec002f71 - - d84caa5a98ad - - cee61b3fcf78 - d2bc35f3d1c5 - 9fa24d5aac68 + - c9cfec002f71 - 8f1c3df4dd49 + - d84caa5a98ad + - 32b86cd8eb50 + - cee61b3fcf78 + - 48636f857c4b + - db1f362cca3e 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 ba833d62f..ad071beec 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -3,7 +3,7 @@ tools: owner: nilesh revisions: - 473382134e56 - - 1a052c827e88 - 080fd5739bb4 + - 1a052c827e88 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index 2201d86c2..cf938c395 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -9,8 +9,8 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - 108db6635177 + - cb20f99fd45b - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,8 +42,8 @@ tools: owner: iuc revisions: - 19ece8afbaab - - 5f8e69cc4c6e - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -67,15 +67,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - 9bd1568619cd - cf1ffd88f895 + - 9bd1568619cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -94,25 +94,25 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 - 12749212f61b - 9149ad20699a + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - - 92ec40abcdcf - 33208952b99d + - 92ec40abcdcf + - 06dc50b7b711 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx owner: iuc revisions: - - 720217c23995 - - a8d69aee190e - b3d99709fe1a + - a8d69aee190e + - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -127,27 +127,27 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - 7a6034296ae9 - - 88b8c2916784 + - 811fc2d75ad4 - 7def34e6cf4d + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 36677f429310 - 740ce0a18f0d - b40e2d865d52 + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e + - 329deb17a9f7 - 9da0311ab1dd - 8da515fbc1bf - - 329deb17a9f7 + - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -160,8 +160,8 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - 30388d878f81 + - bb8cfc6f6e0c - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,15 +174,15 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - a4a10c7924d1 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - cab3f8d35989 + - 6c2c1836728b - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -191,29 +191,29 @@ tools: revisions: - 5d9ae78f34d3 - 135c85f4cfaf - - b7f7826ef1cd - bcedabb53ddf + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: + - 5a08c09b9311 + - 3a0efe14891f - 24c5d43cb545 - 1cc79f49b8d5 - - 5a08c09b9311 - 145f6d74ff5e - - 3a0efe14891f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - c370440f901e + - b72793637686 + - 0dbf49c414ae - 5826298f6a73 + - b01db2684fa5 - bf328cec6a42 - 350bbc5c2ffd - - 0dbf49c414ae - - b72793637686 - - b01db2684fa5 - - 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 6412f5d1e..8f47af79f 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: - - 59bb6d34fca6 - d147d6455873 - - 4aab5ae907b6 - - a62c4a11a67d - 6f6537780379 + - 59bb6d34fca6 + - a62c4a11a67d + - 4aab5ae907b6 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 d4b2658e6..4b98983a4 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 - - 55e35e9203cf - fb9e030ffae4 - - cfc3f5a57dc6 - 00712416fdaa + - 55e35e9203cf + - 32e547223c9e + - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 688357ad5e61 - - b9fac48532eb - - 038e32885fec - ee98d611afc6 + - 038e32885fec + - 688357ad5e61 - 39e945f0b2c1 + - b9fac48532eb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - b85871dd69f9 - - 43cb7b5a6fe7 - 9bd945a03d7b - - d4af736e7b83 - 3d748954434b + - 43cb7b5a6fe7 + - d4af736e7b83 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 @@ -47,22 +47,22 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 7705cc75ac18 - 8c64a2da3869 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -74,8 +74,8 @@ 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 @@ -88,8 +88,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - a6821f856a1e + - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -102,16 +102,16 @@ tools: - 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 - a97abb8cd15b + - b409c2486353 - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -125,9 +125,9 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - ab55fe8030b6 - a407e7f8bdc1 - 3bcd5445cd7a + - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -141,9 +141,9 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - f2f6c703da06 - 215733a383f2 - bf2017df9837 + - f2f6c703da06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -157,24 +157,24 @@ tools: - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - 652923ce664f - b7ea9f09c02f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter owner: iuc revisions: + - 81e5bdff4853 - ef4c80837bc5 - 2e41b35b5bdd - - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca owner: iuc revisions: + - 9e5c0bb18d08 - 46fc6751d746 - c99ba278dfa9 - - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 5ae3dc477..a2047bc6b 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,25 +32,25 @@ tools: - name: datamash_ops owner: iuc revisions: - - 419027d822d6 + - 746e8e4bf929 - 562f3c677828 - 2f3c6f2dcf39 - - 746e8e4bf929 + - 419027d822d6 - 4c07ddedc198 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 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 + - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -122,37 +122,37 @@ tools: revisions: - b1eda492f063 - 840f29aad145 - - 7442b94d6a1e - - aef56d0e7a61 - 9c3e1d3235c8 + - aef56d0e7a61 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 + - 375bbd555f4a - 9fda0b82f419 + - d0352e8b4c10 - 07843f917990 - - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 2c58b83c9bad - - cd02bf168d23 - 4cc980df6265 + - 2c58b83c9bad - 7ae443e6217d + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 4bbaf77573ef - - bb9fc9d46ea4 - - 7dd3fb35904f - 1dd433d2c92c - ad7e0b4291ee + - 7dd3fb35904f + - bb9fc9d46ea4 + - 4bbaf77573ef tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 483a0fa1d..e1648df4e 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -8,8 +8,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -28,13 +28,13 @@ tools: - name: column_maker owner: devteam revisions: - - 13b6f0007d9e - 6e8d94597139 - - 6595517c2dd8 - be25c075ed54 + - 02026300aa45 + - 6595517c2dd8 - 464b9305180e - 9cd341095afd - - 02026300aa45 + - 13b6f0007d9e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -72,9 +72,9 @@ tools: owner: iuc revisions: - 9cc411a62277 - - 37cde8134c6a - 557ec8d7087d - 34d29339abab + - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -105,13 +105,13 @@ tools: - name: query_tabular owner: iuc revisions: - - 2e8f945f7285 - - 83069b38aa85 - - 3a6b78c39dca - 623f3eb7aa48 - - 1ea4e668bf73 + - 2e8f945f7285 - cf34c344508d - 33d61c89fb8d + - 1ea4e668bf73 + - 83069b38aa85 + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -131,9 +131,9 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - bce29ec10b78 - f768f6183386 - b722161a845a - - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -146,11 +146,11 @@ tools: - name: text_processing 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