From 07464616cf0210fd89174c0ede7c045e81f415d8 Mon Sep 17 00:00:00 2001 From: admin Date: Mon, 15 Jan 2024 03:09:48 +0000 Subject: [PATCH] Jenkins install build 1390. --- automated_tool_installation_log.tsv | 1 + requests/pharokka_dm.yml | 7 - staging.gvl.org.au/annotation.yml | 96 +++---- staging.gvl.org.au/assembly.yml | 204 +++++++------- staging.gvl.org.au/bacterial_typing.yml | 10 +- staging.gvl.org.au/bed.yml | 10 +- staging.gvl.org.au/blast.yml | 14 +- staging.gvl.org.au/chemicaltoolbox.yml | 52 ++-- staging.gvl.org.au/chip_seq.yml | 16 +- staging.gvl.org.au/collection_operations.yml | 4 +- staging.gvl.org.au/convert_formats.yml | 42 +-- staging.gvl.org.au/deeptools.yml | 118 ++++----- staging.gvl.org.au/dna_metabarcoding.yml | 6 +- staging.gvl.org.au/emboss.yml | 4 +- staging.gvl.org.au/epigenetics.yml | 6 +- staging.gvl.org.au/fastafastq.yml | 82 +++--- staging.gvl.org.au/fastq_quality_control.yml | 28 +- staging.gvl.org.au/filter_and_sort.yml | 2 +- staging.gvl.org.au/gemini_tools.yml | 22 +- staging.gvl.org.au/genome_editing.yml | 6 +- staging.gvl.org.au/get_data.yml | 36 +-- staging.gvl.org.au/graphdisplay_data.yml | 56 ++-- staging.gvl.org.au/hca_single_cell.yml | 6 +- staging.gvl.org.au/hicexplorer.yml | 16 +- staging.gvl.org.au/imaging.yml | 60 ++--- staging.gvl.org.au/ivar.yml | 60 ++--- .../join_subtract_and_group.yml | 8 +- staging.gvl.org.au/machine_learning.yml | 54 ++-- staging.gvl.org.au/mapping.yml | 44 ++-- staging.gvl.org.au/metagenomic_analysis.yml | 104 ++++---- staging.gvl.org.au/mothur.yml | 4 +- staging.gvl.org.au/multiple_alignments.yml | 42 +-- staging.gvl.org.au/nanopore.yml | 40 +-- staging.gvl.org.au/none.yml | 46 ++-- staging.gvl.org.au/phylogenetics.yml | 92 +++---- staging.gvl.org.au/picard.yml | 8 +- staging.gvl.org.au/proteomic_ai.yml | 10 +- staging.gvl.org.au/proteomics.yml | 154 +++++------ staging.gvl.org.au/rad_seq.yml | 66 ++--- staging.gvl.org.au/rna_seq.yml | 156 +++++------ staging.gvl.org.au/rseqc.yml | 2 +- staging.gvl.org.au/sambam.yml | 66 ++--- staging.gvl.org.au/send_data.yml | 8 +- staging.gvl.org.au/single_cell.yml | 66 ++--- staging.gvl.org.au/statistics.yml | 32 +-- staging.gvl.org.au/text_manipulation.yml | 36 +-- staging.gvl.org.au/variant_calling.yml | 32 +-- staging.gvl.org.au/vcfbcf.yml | 248 +++++++++--------- staging.gvl.org.au/viral_tools.yml | 2 +- usegalaxy.org.au/annotation.yml | 96 +++---- usegalaxy.org.au/assembly.yml | 206 +++++++-------- usegalaxy.org.au/bacterial_typing.yml | 8 +- usegalaxy.org.au/bb_tools.yml | 2 +- usegalaxy.org.au/bed.yml | 16 +- usegalaxy.org.au/blast.yml | 16 +- usegalaxy.org.au/chemicaltoolbox.yml | 56 ++-- usegalaxy.org.au/chip_seq.yml | 14 +- usegalaxy.org.au/collection_operations.yml | 8 +- usegalaxy.org.au/convert_formats.yml | 40 +-- usegalaxy.org.au/deeptools.yml | 116 ++++---- usegalaxy.org.au/dna_metabarcoding.yml | 6 +- usegalaxy.org.au/emboss.yml | 4 +- usegalaxy.org.au/epigenetics.yml | 4 +- usegalaxy.org.au/fastafastq.yml | 76 +++--- usegalaxy.org.au/fastq_quality_control.yml | 28 +- usegalaxy.org.au/filter_and_sort.yml | 2 +- usegalaxy.org.au/gemini_tools.yml | 22 +- usegalaxy.org.au/genome_editing.yml | 4 +- usegalaxy.org.au/get_data.yml | 34 +-- usegalaxy.org.au/graphdisplay_data.yml | 56 ++-- usegalaxy.org.au/hicexplorer.yml | 16 +- usegalaxy.org.au/imaging.yml | 60 ++--- usegalaxy.org.au/ivar.yml | 64 ++--- usegalaxy.org.au/join_subtract_and_group.yml | 6 +- usegalaxy.org.au/machine_learning.yml | 44 ++-- usegalaxy.org.au/mapping.yml | 46 ++-- usegalaxy.org.au/metagenomic_analysis.yml | 104 ++++---- usegalaxy.org.au/mothur.yml | 2 +- usegalaxy.org.au/multiple_alignments.yml | 44 ++-- usegalaxy.org.au/nanopore.yml | 34 +-- usegalaxy.org.au/none.yml | 50 ++-- usegalaxy.org.au/phylogenetics.yml | 86 +++--- usegalaxy.org.au/picard.yml | 10 +- usegalaxy.org.au/proteomic_ai.yml | 8 +- usegalaxy.org.au/proteomics.yml | 134 +++++----- usegalaxy.org.au/rad_seq.yml | 72 ++--- usegalaxy.org.au/rna_seq.yml | 162 ++++++------ usegalaxy.org.au/rseqc.yml | 2 +- usegalaxy.org.au/sambam.yml | 66 ++--- usegalaxy.org.au/send_data.yml | 8 +- usegalaxy.org.au/single_cell.yml | 54 ++-- usegalaxy.org.au/statistics.yml | 28 +- usegalaxy.org.au/text_manipulation.yml | 24 +- usegalaxy.org.au/variant_calling.yml | 32 +-- usegalaxy.org.au/vcfbcf.yml | 226 ++++++++-------- usegalaxy.org.au/viral_tools.yml | 2 +- 96 files changed, 2244 insertions(+), 2238 deletions(-) delete mode 100644 requests/pharokka_dm.yml diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 912815dfd..3b7a827ea 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -6137,3 +6137,4 @@ Update 177 20/12/23 22:47:34 samtools_split False Tests failed devteam bd850490c Update 177 20/12/23 22:48:19 unicycler False Installed iuc 8f9f06995f98 8f9f06995f98 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_177/install_log.txt Install 1386 22/12/23 09:45:06 seq_filter_by_id False Installed peterjc 85ef5f5a0562 85ef5f5a0562 6/6 6/6 Filter and Sort toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1386/install_log.txt Install 1388 15/01/24 11:12:44 pharokka True Tests failed iuc 2f40d2ccb0eb latest Staging Testing 0/2 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1388/install_log.txt +Install 1390 15/01/24 13:09:19 data_manager_pharokka True Shed-tools error iuc 50caca83e7c9 50caca83e7c9 Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1390/install_log.txt diff --git a/requests/pharokka_dm.yml b/requests/pharokka_dm.yml deleted file mode 100644 index a33ba089a..000000000 --- a/requests/pharokka_dm.yml +++ /dev/null @@ -1,7 +0,0 @@ -tools: -- name: data_manager_pharokka - owner: iuc - revisions: - - 50caca83e7c9 - tool_panel_section_label: None - 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 088d12127..9451b140c 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: - - c2ef298da409 - - 3f3e247c053d - - 4efdca267d51 - 78c75f134c16 - 6e9aea89e388 + - 3f3e247c053d + - 4efdca267d51 + - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,30 +36,30 @@ tools: - name: annotatemyids owner: iuc revisions: - - 44018dd6b447 - - fe3ca740a485 - - b5d8e5475247 - - cd2480f35935 - - 133f36c29579 + - 3e1f6f6d557e - 1aae04680c4b - 4f2967b27e67 - - 3e1f6f6d557e + - 133f36c29579 + - fe3ca740a485 + - 44018dd6b447 - f29602ae449e + - b5d8e5475247 + - cd2480f35935 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: - 6519ebe25019 - - 7be22100e5e1 - dc027fa56d55 + - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus @@ -79,8 +79,8 @@ tools: - name: barrnap owner: iuc revisions: - - 8fd427007e93 - fe48aa4ccd5e + - 8fd427007e93 - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -93,8 +93,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat @@ -106,8 +106,8 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 63662ae295d6 - 9d1fbff733cf + - 63662ae295d6 - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,42 +126,42 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - - 14f588312c56 - 582fd74dc2a1 + - 3bbe70fef6df + - 756376aeb1ae - b6b5cd37f2a2 - 9f2455341fac - - 756376aeb1ae + - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 30fb23d4c31c - - 1691af4a0d17 - - 989f7c061f35 - - 73428a792541 - 0ffe5be70caf + - 989f7c061f35 - a230ea445788 + - 73428a792541 + - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - e94187d661df + - 494f0bb4a993 + - 30f08d74024f - b69c46064ec7 - 5a5ae61da69c - 563a19373357 - - 494f0bb4a993 - - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 1bc5a03faf2e - - d6c7106b7b2e - f31125bb85ea + - d6c7106b7b2e + - 1bc5a03faf2e - 2bba2ff070d9 - f77d7b685bb3 - 7abc5f6dd595 @@ -170,12 +170,12 @@ tools: - name: funannotate_sort owner: iuc revisions: - - 520e30695ec3 + - 52af33194019 - b3cf4684e9c7 - 54961e026fe4 - - 52af33194019 - d3af38b9c7e1 - fed64e676186 + - 520e30695ec3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -187,8 +187,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 07d7991bf205 - 79261884facd + - 07d7991bf205 - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,10 +201,10 @@ tools: - name: goseq owner: iuc revisions: - - 43798b4caee0 - 8b3e3657034e - - ef2ad746b589 - 602de62d995b + - 43798b4caee0 + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -222,16 +222,16 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - c55643c3d813 - - 74810db257cc - 98cafcbd2578 + - 74810db257cc + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -256,16 +256,16 @@ tools: - name: maker owner: iuc revisions: + - 3c1a01127868 - 370c210d9541 - d46d803ca6cc - - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -295,11 +295,11 @@ tools: - name: prokka owner: crs4 revisions: + - a17498c603ec - 8a22554cdde2 - d643e3b03500 - - a17498c603ec - - eaee459f3d69 - bf68eb663bc3 + - eaee459f3d69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -311,15 +311,15 @@ 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 @@ -331,22 +331,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5a29ab10dba6 - - cfcf33df7fc0 - - 268d162b9c49 + - 68693743661e - 5c7b70713fb5 - - 8f92c2b26e6d + - 5a29ab10dba6 - 9473cd297a76 - - 68693743661e - 5b80f544c67f + - 8f92c2b26e6d + - 268d162b9c49 + - cfcf33df7fc0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - 5fab4f81391d - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -372,12 +372,12 @@ tools: owner: iuc revisions: - 37213cf56392 - - 45083d070fb8 - - ba6f87115e13 - 809dfc93d593 - - 200c378d85f3 - 037a11682176 - 2c68b0c38785 + - 200c378d85f3 + - ba6f87115e13 + - 45083d070fb8 - ac8250086ac3 - e1a9d6fd258d tool_panel_section_label: Annotation @@ -385,8 +385,8 @@ tools: - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 2c01e2ab7..b365b5356 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,22 +2,22 @@ tools: - name: abyss owner: iuc revisions: - - a929ce596a34 - - 841084c5fc46 - 890b794c997d - - 8f1b150a2487 - - 7547fcab5d19 - 0e93176640ac - fa5259cc561b - 553bfe8bd0b5 + - 8f1b150a2487 + - 841084c5fc46 + - a929ce596a34 + - 7547fcab5d19 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - b2860df42e16 - b9e31c5c01c7 - 067592b6b312 - - b2860df42e16 - ddddce450736 - 94fe43e75ddc - 21e491ad532a @@ -26,18 +26,18 @@ tools: - 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: + - 3371c5bdc17a - faee8629b460 - 22286dab5aa1 - - a7f16f24e9a1 - 5258e18bbe23 - - 3371c5bdc17a + - a7f16f24e9a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,30 +49,30 @@ tools: - name: busco owner: iuc revisions: - - 2a5b8b9936bf + - e824f5d958d0 - 602fb8e63aa7 - - 5ecdeca79a0d - - 41030a6c03b7 + - e4bd1e99bacf - 2dd755c1c6ff - - bb935709506a + - f18f0b887c31 + - 46ae58b1d792 - 94170eee0ad8 + - 5ecdeca79a0d + - 1e62c28ba91d - 0d243f458b53 - cf13a1e03e5b - - e824f5d958d0 - - 46ae58b1d792 - - e4bd1e99bacf - - 1e62c28ba91d - - 1440ae06552f - - f18f0b887c31 - 4048d82f0c88 + - bb935709506a + - 41030a6c03b7 + - 1440ae06552f + - 2a5b8b9936bf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - c5b7390290b1 - 86f150c8019d + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -84,36 +84,36 @@ tools: - name: flye owner: bgruening revisions: + - e27815e82dd4 - 3ee0ef312022 - 276f5d8712d5 - 8d4f03b5fe9d - 1ce9b1d72ec3 - - e27815e82dd4 - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - b2f674562a18 - 3169a38c2656 - 01210c4e9144 - - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - 8b330a577046 - - 06bcf65179fb - 7348b69e5109 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 690c2caa367e - 3fba9c77550a - 3ef480892a9f - - 690c2caa367e - 5127a713de83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,21 +126,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 6505bd37670d - - 3f7be05a1597 - - 9ef6920c3089 - - 5bec28269d95 - 2061fb3b81b4 - - da9d8bf98802 - f3c89da3af16 - - 5f625c63b8bc - - 0ee0c3089254 - 41cea2aa2dce + - da9d8bf98802 - ec9e21e9c71b - - 366a11d316a7 - - 045c7c3d8e59 - 60024a528cbd + - 0ee0c3089254 + - 366a11d316a7 + - 3f7be05a1597 + - 9ef6920c3089 - 71740308d412 + - 045c7c3d8e59 + - 6505bd37670d + - 5bec28269d95 + - 5f625c63b8bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -158,39 +158,39 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - de387b2b2803 - - 7518ee87b53d + - 14ddfc8ffb93 - a96f3ad4e0d8 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 - - f8113c25bc6b - 09c589057ee8 + - f8113c25bc6b - 39edec572bae + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - 51c2360aa807 - 29dabd8db6f2 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - e731ea24e48d - - f338e9942b27 + - 606b09cc9860 - eb7a370f6588 + - 2ecf5a570907 - 3ca2d2a9068c - fd128c111ab0 - - 2ecf5a570907 - - 606b09cc9860 + - f338e9942b27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -202,11 +202,11 @@ tools: - name: miniasm owner: iuc revisions: + - 8b6d0d85252b - a7b889b90140 - - 8dee0218ac7d - 80d1250bd5fd - 73a3846701e1 - - 8b6d0d85252b + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -219,8 +219,8 @@ tools: owner: iuc revisions: - 7c2f5268d01c - - 15200570e926 - 64a1c751d99b + - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -232,75 +232,75 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 - - 02831bf9e95f - - 2b16ba799da9 + - d256a51a656b - 511e5e3cd55e - dfb8a4497339 - - d256a51a656b + - 2b16ba799da9 + - 02831bf9e95f + - bbe19ef04a74 - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - 76d4cbefff85 + - a315c25dc813 - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 7594365c546b - 72472698a2df - 875d0f36d66f + - 59db8ea8c845 - 675488238c96 - ebb0dcdb621a + - 6fcbee531de6 - 3061c8b029e5 - 342a1d1fed7b - - 59db8ea8c845 - - 6fcbee531de6 - - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 78c533842eeb + - a199cd7ac344 - d865b62f501c - cd06929b224b - 39bed8de8017 - aa39b19ca11e - - a199cd7ac344 + - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - 2b2a352488fa - - 33b7d8481a76 - - f11b994b7eb2 - f8564b2d7f63 - 3edba9afc9bc + - f11b994b7eb2 + - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - 1d06c8b38e77 - - ef69617ecb42 - e122f9101584 + - ef69617ecb42 - 378e55aeeb25 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: + - 9a22227bb6d0 - f77f7a7f3b83 - - ab5b7f6b7198 - ba7b0f11e470 - - 9a22227bb6d0 + - ab5b7f6b7198 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -312,21 +312,21 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - f698c7604b3b - - ee17a294d3a3 - - 83ead2be47b2 + - 196a599ec43d + - d9f6a00b6db7 - ad80238462c1 - 865119fcb694 - - 196a599ec43d + - ee17a294d3a3 + - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5a0ddb4dc3a4 - - 5e0825476fb7 - 24e471d13fe9 + - 5e0825476fb7 + - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades @@ -334,29 +334,29 @@ tools: revisions: - 1bb12736175c - 904bf932cf78 - - 7490b213baa9 - - 051fd2db8a27 - 1fc82fe7ebef + - 051fd2db8a27 + - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - 34305b013402 - - 808b3a0a6716 - - ad8b536d1caa - d6e617c4e338 + - ad8b536d1caa + - 808b3a0a6716 - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - e5a3b75a271f - - 6b5a5842531e - b8002c3f7141 - - 21da31ed41a1 - 8d4b90bf9caf + - e5a3b75a271f + - 21da31ed41a1 + - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades @@ -364,59 +364,59 @@ tools: revisions: - f1532cb33c75 - 86f66ab58e14 - - 2a10645aeadd - 9de69775f512 + - 2a10645aeadd - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 1708851f8804 - - 340bc17f49cf - 85fb02c43042 - - 6aad515a5270 - e41dcb0e913b + - 1708851f8804 + - 6aad515a5270 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b3490b036c5a - - d159735a6a9f - d5fb354f745d - - b65a43f70b99 - 249f6a28c751 + - b65a43f70b99 + - b3490b036c5a + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - 9006e5836729 - b7829778729f - 7897763d14ec - - dd7ad84f3943 - d2d1df21dfb9 + - 33368fec3b70 + - dd7ad84f3943 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ced385aa976d - - 8f631679571f - - 6f4c8ad6ea01 - 505a9833ab5d + - 8f631679571f - 189e837009c9 + - ced385aa976d + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e + - 19bdfd1e6fe3 - e59bee4565b3 - 356afed970b4 - - 19bdfd1e6fe3 + - d40ed4eb0c0e - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -424,59 +424,59 @@ tools: owner: iuc revisions: - 6dd935e4984b + - ebd801e712bc + - 80a17897564d - 4688ae3b49b5 - b23249f81bc4 - - 80a17897564d - - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - cb1e3db43020 - 59bd28f6265d - - 937ea677d437 - - b5e35a2ca4f3 - b64696992ee9 + - cb1e3db43020 + - b5e35a2ca4f3 + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b - - 05bd7504fdb2 - - 383bb5ad32e2 - - 6015aa0303f2 - 2628f6790eda + - 6015aa0303f2 + - 383bb5ad32e2 + - 05bd7504fdb2 + - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - - 8f9f06995f98 - 9e3e80cc4ad4 - - e92675014ac9 + - 8f9f06995f98 - 0a3a602cd1e3 + - 6e26c9afd301 + - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 8d09f8be269e - 08256557922f - 5da9a0e2fb2d - 920677cd220f + - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 82398ba86ba7 - 37d88f41c810 - - 0e2b4e3f9ca1 - - 4a53b89fa703 - d81360ea69d8 + - 4a53b89fa703 + - 82398ba86ba7 + - 0e2b4e3f9ca1 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 6f5b4d803..ce34bafa0 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,8 +2,8 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: - - 31812e7a1315 - - 1f5641a52664 - - ded48b36f3b7 - 8e8dc9a1e3e5 + - ded48b36f3b7 + - 1f5641a52664 + - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 5c8ff92e38a9 - 24a7a95867b0 - 17fcac7ddf54 - - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing 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 b8ba27613..8d1fb5ce9 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: - - a68aa6c1204a - - 0a5c785ac6db + - a1a923cd89e8 - 589e7e57fd6d + - a68aa6c1204a + - 87ee588b3d45 - ce3c7f062223 - b28e0cfa7ba1 - - dde39ba9c031 - - 87ee588b3d45 - - a1a923cd89e8 - e19bebe96cd2 - a8eabd2838f6 + - 0a5c785ac6db - 07e8b80f278c + - dde39ba9c031 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 6af0bccc6..74b399262 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 + - f921014aba5a - 54f751e413f4 + - e8ac2b53f262 - 62c9df8382c2 - - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,13 +23,13 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 0e3cf9594bb7 - - d999e774072a - - 5edc472ec434 - - 2889433c7ae1 - - a52d2d93e595 - acf4e47b734c - 6f386c5dc4fb + - a52d2d93e595 + - 5edc472ec434 + - 0e3cf9594bb7 + - 2889433c7ae1 + - d999e774072a - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index 20e412eda..d82da6350 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: + - 27ee142314a9 - da6bd1975a71 - - c8cdde00b105 - - f4230f116196 - - 710301bc46fa - 6ca543ec1bf8 + - 710301bc46fa - 095ad4d096d1 - - 27ee142314a9 + - f4230f116196 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -106,32 +106,32 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 0fac8e2afc13 - - 88076940fa94 - bfb65cb551d8 + - 88076940fa94 - 3b8a9d5ced85 + - 0fac8e2afc13 - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - d532b7e5f64b - - f5d979cb4b54 - eb6564a60136 + - f5d979cb4b54 + - d532b7e5f64b + - b46d4b4d995c - 715cd0e87781 - 55918daa5651 - - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 5579659312e6 - - 97872d87ba80 - fdf2cc80adb5 - - f26afd1b7104 + - 97872d87ba80 - d2f955aea23a + - 5579659312e6 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files @@ -145,52 +145,52 @@ tools: - name: gmx_setup owner: chemteam revisions: - - 2c349b027a01 - - 4da9ee404eab - ed736e6eee39 - - 070e3ecc3fda - cac1886249a2 + - 2c349b027a01 + - 070e3ecc3fda + - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - 73008ef1f487 - - c0c9a5024177 - - f197e34c33a9 - 2e219a2d9327 - - 807aa4c9293d - - 525ca7c8065f - d1f803b5943c + - 525ca7c8065f + - f197e34c33a9 + - c0c9a5024177 - da8753545526 + - 807aa4c9293d tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 - - 1809414a9454 - - 61094e01eff9 - c4fbab8e03c5 - 7568ae18908a - 2c8ed1b52bf7 + - 1809414a9454 + - 61094e01eff9 + - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - ba83f0923369 + - d7ec25187599 - 79e8ab8f1e81 - - 730ef07b90ae - ccfbd956a2d3 - - d7ec25187599 + - 730ef07b90ae 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 @@ -202,8 +202,8 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - 1400d1977e7b - b59c91adeac1 + - 1400d1977e7b - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index 3bc42ef7c..16634e664 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: - - fa56d93f7980 - - c97a786e8fb5 - 163688bb8f73 + - c97a786e8fb5 + - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -22,18 +22,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - f5d67c722d67 - - 86e2413cf3f8 + - 640d3af5d833 - 424aefbd7777 - 495a4173006f - - 640d3af5d833 + - f5d67c722d67 + - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -52,9 +52,9 @@ tools: - name: sicer owner: devteam revisions: - - 4a14714649b4 - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d + - 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 2703a8f7e..5d8c8bb7c 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -26,14 +26,14 @@ tools: owner: bgruening revisions: - baabc30154cd - - 0046692724f9 - 6cbe2f30c2d7 + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 7e6cbb4f7..975497e40 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -8,37 +8,37 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 5e1240a87bcb + - 0b3c3ad92827 - 4a6ee918c13a + - dad9da48a09a + - 6ef0b5664c69 - a3b86937ead6 + - f3a19509108a - 367b1ed91207 - - dad9da48a09a - e3cbd2287f63 - - f3a19509108a - - 0b3c3ad92827 - - 6ef0b5664c69 + - 5e1240a87bcb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 584008e574b2 + - 72ed72122deb + - a4db66553a61 + - e177a8ea0bf1 - 54ccb7e1f49a - - e525f9ffb9ac - 33c99804a32f - - 72ed72122deb + - 584008e574b2 + - 501c21cce614 - bd46669113b9 + - e525f9ffb9ac - 1b5fc03380d4 - - 501c21cce614 - - e177a8ea0bf1 - - a4db66553a61 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 @@ -50,23 +50,23 @@ 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 - - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -78,8 +78,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -92,8 +92,8 @@ tools: owner: devteam revisions: - 4dea02886337 - - 154d00cbbf2d - 3e436657dcd0 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -125,18 +125,18 @@ 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: - - 92ac8e086317 - - 26c6706bfb07 - - 63769c4217a7 - 19e45916daf9 - b9b385097f13 + - 26c6706bfb07 + - 63769c4217a7 + - 92ac8e086317 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 8f536b836..8a5333160 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,46 +2,46 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 29451af70c52 + - 5f6d123679f4 + - de72ba3ed6f2 - 268e91e540ee - a1ca9bccc7f2 - - de72ba3ed6f2 - - 5f6d123679f4 - - e821645ef8fc - c929a006727f + - 29451af70c52 + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e49b109abc2 + - 7a7fd0f5f15d - bb1e4f63e0e6 - - 0e143b4c3987 + - 2d2cf5c1ea8a - 12af64f93288 + - 0e143b4c3987 - 5d11599b8a7d - - 7a7fd0f5f15d - - 0e49b109abc2 - - 2d2cf5c1ea8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - 7c1beb6d6eca - - 81b1e3e1fc6c - - 195e98217334 - - dc059492a995 - c06951d10364 + - dc059492a995 + - 195e98217334 - 1d848bc4585f + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - 07418a30ed01 - 71aa86af6762 - - a67ac707496a - - 3d211717a775 - 93eb012d9eed - - 07418a30ed01 + - 3d211717a775 + - a67ac707496a - 26e7304d6737 - bfff7454b59a tool_panel_section_label: DeepTools @@ -50,157 +50,157 @@ tools: owner: bgruening revisions: - dd0b7398bb96 - - 2bc10a9ca58b + - b8858746dc1f + - 56d5b797ce84 - 26983857c91a - 29fcfd36e90a - - b8858746dc1f + - 2bc10a9ca58b - 5be24eba848d - - 56d5b797ce84 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7ef978dc1b8a - - e6d0bff01239 - - 7e6bcd2e5128 - 72bfafe3330b + - 7e6bcd2e5128 + - c3e012dfe21f - 9384cd033f30 + - e6d0bff01239 + - 7ef978dc1b8a - ee3a1b0f45f1 - - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - 514fa53b5efb - - 9470f29702f8 - b73e213add0c - - a60c359ec43c - - d9a637e83828 - fd1275e01605 - fb9cf9c97ec4 + - 9470f29702f8 - 167788df3b46 + - d9a637e83828 + - a60c359ec43c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - 86febdcc4283 + - ca0616bb2cdf + - c34d11ea4ba6 + - 5bffaa8354a1 - 2c37ce318bc3 - a02cfa31e9cb - e479c7ca5570 - - c34d11ea4ba6 - - 5bffaa8354a1 - - ca0616bb2cdf + - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 - - 69a8621ca2f0 - 004aea905d4d - - 1fcb7adc39b8 - 192ef85c0b0b - - 2d466b530754 + - 1fcb7adc39b8 - 78f405266706 + - 2d466b530754 + - 01fb6a7654e6 + - 69a8621ca2f0 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 - - 137c4beed34b - - d580d6acd1df - - 3c9f0c486cca - - 459cfa861f0b - db940c262830 + - 3c9f0c486cca + - 9ecba5e225a6 - 2f9e4843f480 - d9ce4897dbb2 + - 137c4beed34b + - 459cfa861f0b + - d580d6acd1df tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - bad3ca889618 - - 2c66e43f1c86 - fd408d755394 - - f264afa9fa6f - - 32e451def88c - fbe773640707 + - 2c66e43f1c86 + - f264afa9fa6f + - bad3ca889618 - bd7db9e2f2cb + - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 231994413f89 + - 9368fbc49c8b - 4e12ea27f788 - - 3b9d990a0a0e - 7fda5607e777 + - 3b9d990a0a0e - 7e361d147872 + - 231994413f89 - 56bce3c82278 - - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 94ca68515826 - b1779366c8e9 - c03c3384cd81 - - ce4ce3316f74 - e65d16fb2724 + - 94ca68515826 - 4431f39ede55 + - ce4ce3316f74 - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 2da482e408b8 - d57251071381 - - 23f7c5f1fdaf - 793665fff0f8 + - 23f7c5f1fdaf + - f8fc4e5aff9d - 4ed32329e0ed - b88ebb3672a1 - - 2da482e408b8 - - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 - - a4dfb122e52b - 512155688d98 - e4c7985d4585 - 010e58e9d822 - - ba6efa77fb79 - 25d830337d31 + - ba6efa77fb79 - c60570fa602f + - a7849312d328 + - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 4d678170d29b - - 69264da0ce77 + - 00d869ea03a1 - 443d9a9d6d11 + - 4d678170d29b - 38e3f226248b - c899e0ccff8c - - 00d869ea03a1 + - 69264da0ce77 - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - d806504e96d9 - - 6662b1a8d326 - - 10301d137111 - - aac8444d6681 - c361b12d207a + - aac8444d6681 + - 10301d137111 + - 6662b1a8d326 + - d806504e96d9 - a2d70c4fd406 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index 6bf9a8305..f993881b6 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - f82cefbbcea5 - 3021b9f5809f + - f82cefbbcea5 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -16,15 +16,15 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - 374fd9feb032 + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - fe7ec8a3d35e - e9e49cf06b42 + - fe7ec8a3d35e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 9e65a9209..aaf7a1b11 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 - - 832c20329690 - dba489bfcd62 - 63dd26468588 + - ce385837c160 + - 832c20329690 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index e7f187ab1..3b39a0655 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 - 62f5fab76dfb - - 6da3972210ee - d82648ad25a3 + - 6da3972210ee + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -17,7 +17,7 @@ tools: - name: pileometh owner: bgruening revisions: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 88366bc18..b9b2d056a 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: + - c5e2e5902201 + - de6cebe3c043 + - 8c0175e03cee - 4e5056fefd88 - 5915ea1ec9b1 - - 135b80fb1ac2 - - 093678460093 - - 8c0175e03cee + - 44e2cc14f75b + - e4691e1589d3 - 8665bcc8b847 - - 288f97432497 - c053d4cad713 - - c5e2e5902201 - - c4b82dce8335 - - 49370cb85f0f - 48f587c13075 + - 288f97432497 + - c4b82dce8335 + - 093678460093 - 660cffd8d92a - - e4691e1589d3 - - 44e2cc14f75b - - de6cebe3c043 + - 135b80fb1ac2 + - 49370cb85f0f 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: - - 8889eb864cef - f666895cbebd - 9db07fd39f85 + - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -49,15 +49,15 @@ 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 owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -69,15 +69,15 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - 8cacfcf96a52 - e626b3ff9922 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - 9457a20156db + - 859422bcb689 - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,16 +90,16 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - f81d4362b6c1 - - ec0b5076173a - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -111,10 +111,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - - 0dbb995c7d35 - cd0874854f51 - 9c620a950d3a + - 56022eb50bbd + - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -127,8 +127,8 @@ tools: owner: iuc revisions: - 65b93b623c77 - - dbf9c561ef29 - 1d8fe9bc4cb0 + - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -168,8 +168,8 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -182,8 +182,8 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -197,8 +197,8 @@ tools: owner: devteam revisions: - e39cc71d3ed6 - - 35e38452bb3f - 249c8393f2d4 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -210,9 +210,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 54053ea6c77e - 045f0e1043f7 - 74db4cffab1f - - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -245,9 +245,9 @@ tools: owner: devteam revisions: - 09070cacefd8 - - 529bccd5e4a1 - 567d5b3c52b1 - d5e9e83cd3d8 + - 529bccd5e4a1 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: - - 8abdedf55101 - 4bedca26c133 - 0b7ec11b3c7c + - 8abdedf55101 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: + - bdf1ce174e39 + - cb1e251cac37 - 90858c306551 - 736b8f6ee456 - - cb1e251cac37 - - 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: + - 07497255281e - 7ce1891db6f5 - 421f0af4ee95 - - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -303,9 +303,9 @@ tools: owner: devteam revisions: - f984bb114520 + - b29d37ca9e41 - 3599f5451ee2 - 02f8a17a4ebd - - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -317,9 +317,9 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - e246088b6e34 - - 177f0621c266 - 0c2907307ba4 + - 177f0621c266 + - e246088b6e34 - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -332,10 +332,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: + - 547e8d00f11c - 377ac2829eac - 73194cdd4f57 - 61b4cedc8934 - - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -359,8 +359,8 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -379,8 +379,8 @@ tools: - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -398,8 +398,8 @@ 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 @@ -418,11 +418,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - a535cf1e5da4 + - 24013bf85a6f - b557acca0b56 - 8250ea3a1501 - - 24013bf85a6f - e654095ab143 + - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -441,11 +441,11 @@ tools: owner: iuc revisions: - 828dba98cdb4 - - 9fa7803d1c51 - - 27ac32a22ad2 - 7accf7407811 - - f3759eec3018 + - 27ac32a22ad2 + - 9fa7803d1c51 - 6a675c3aa610 + - 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 f408cdd49..af17dca0c 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c + - e41385662e5e - 7b4468117008 - ce9cd02d5b88 - - e41385662e5e + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,65 +18,65 @@ tools: - name: fastqc owner: devteam revisions: - - 3d0c7bdf12f5 - - 9da02be9c6cc + - f2e8552cf1d0 + - 5ec9f6bceaee - 2b0c9d9fc6ca - ff9530579d1f - - f2e8552cf1d0 + - 9da02be9c6cc - e7b2202befea - - 5ec9f6bceaee + - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 - b6b54ba71bd8 - 18a51655db17 + - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - 59003d0543cd - 7306ec78632a + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - a72af9de6bf5 - 1f296803dfa3 - 8880fb74ef56 - - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - 5e33b465d8d5 - 75c93c70d094 - - 1c2db0054039 - abfd8a6544d7 - bf675f34b056 + - 1c2db0054039 - b2f1f75d49c4 - 9a913cdee30e - - 3d93dd18d9f8 - f7985e0479b9 - - 5e33b465d8d5 + - 3d93dd18d9f8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - 084bbd8ba7b8 - - 949f01671246 - cd7e644cae1d + - 949f01671246 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 9243d596c..e6d5e9548 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -16,7 +16,7 @@ tools: owner: peterjc revisions: - 141612f8c3e3 - - 85ef5f5a0562 - 83a19df00eab + - 85ef5f5a0562 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 78a05789a..54a52d839 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ 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 @@ -16,16 +16,16 @@ tools: - name: gemini_annotate owner: iuc revisions: - - 0c8f7322f8fc - 8f53b238a360 + - 0c8f7322f8fc - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -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 @@ -52,15 +52,15 @@ tools: - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: - - b2c25142267e - cf61daf064fe - 45296e47d565 + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: + - 666f60a9331a - 840fb4850be3 - da74170c55c7 - - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -151,8 +151,8 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index c5b84e945..1445c9d17 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,15 +2,15 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee 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 69d1fca8b..72df04134 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -3,55 +3,55 @@ tools: owner: galaxyp revisions: - c1b437242fee - - 983bf725dfc2 - - e9df53a75f3c - b39347891609 + - e9df53a75f3c + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - - 1c58de56d587 - e063168e0a81 + - 1c58de56d587 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - 6ea73833cf67 - - f5ea3ce9b9b0 - - 69ebb7f46e45 - - 6591f049cf7e - - 4df8de2d0e48 - - 653e89d73fc4 + - 7068f48d0ef9 - 5e6237d58b0c - - 83c7d564b128 - aad3885b3216 + - 4df8de2d0e48 + - e08a7ad4378b + - 653e89d73fc4 - 1790dcf3c32d - - 7068f48d0ef9 - - 4317d3cb6cba - - c441583adae5 + - 9a776b080193 + - 69ebb7f46e45 + - f5ea3ce9b9b0 - 734abc7ac21d + - 83c7d564b128 + - 4317d3cb6cba - e407b9da183a - - 9a776b080193 - - e08a7ad4378b + - c441583adae5 + - 6591f049cf7e tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 34758ab8aaa4 + - 7863f1abcdda - 9aaa46d45472 + - 34758ab8aaa4 - 75b3b3d0adbf - - 7863f1abcdda tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a - af5eccf83605 + - bfdc6a7ffd3a - 054483e27a35 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 9df186d2f..eb0b080c7 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,14 +2,14 @@ tools: - name: circos owner: iuc revisions: - - 7f13dc906cb9 - - ae9994cf526f - - df7356989ac1 - 290a11559985 + - ae9994cf526f - a64dc31ab7f2 + - 4b519282a05b + - 7f13dc906cb9 - fd59d783248a - c4bde687c846 - - 4b519282a05b + - df7356989ac1 - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: + - f95284aa2946 - 867ab348287d - 7cf5b1d072b5 - - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,31 +48,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - '566197475670' - 3b37b1b1c3a7 - ca7cb0eaad62 + - 53460afd5115 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 391a4cc45fea + - d3a9e32672ec - da4c086cff5b - 10515715c940 - - 391a4cc45fea - 3d059e9c2fba - - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - e3a675da7fd0 - - 3b12bf9b4b87 - - 1acf88921176 - d0fc8b746d57 + - 1acf88921176 + - 5fe1dc76176e - 299307abd804 + - 3b12bf9b4b87 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -84,8 +84,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - cf1df6b2220a + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -105,17 +105,17 @@ tools: - name: jbrowse owner: iuc revisions: - - a6e57ff585c0 - - 1cfc579079a6 - - fd5dbf0f732e + - 2bb2e07a7a21 - 667e17248bfe - - ca2def38369c + - 836d1aa3e89a - 112eb40ba6cf + - fd5dbf0f732e - 4542035c1075 - 17359b808b01 + - 1cfc579079a6 - 6cd09d7b5f37 - - 836d1aa3e89a - - 2bb2e07a7a21 + - a6e57ff585c0 + - ca2def38369c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -134,8 +134,8 @@ tools: owner: iuc revisions: - 03c13085aecc - - f1691de443a7 - fe154a7af404 + - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -147,15 +147,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -167,8 +167,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 - 0a10fddd97d2 + - 44c66e8d21e6 - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,22 +181,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 326a3db8d9d1 + - a1abfa420d9d - 2824d77cd8f8 + - 4ac4e7083b7e - 59fd173ac850 - - 7dd841a32245 - - a1abfa420d9d - 14e7c35f3d00 - - 4ac4e7083b7e + - 7dd841a32245 + - 326a3db8d9d1 - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 44608d0193ed - 83c573f2e73c - 73b8cb5bddcd - - 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 48e3e9ec5..62c263775 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -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 diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 4a584124c..a6f878dd0 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,45 +2,45 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 921a2da49a0c - - ed2cca6b5de4 - 29f66c353bcb - 9edf8894a22d + - 921a2da49a0c + - ed2cca6b5de4 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - d404277cc87a - ec4b948dc6f0 - 5746d61f0a91 - 78fb5e286609 - - d404277cc87a tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 977dc15add20 + - 9e357a8b2ec3 - 03dd3c16ae4e - 4d511437b1e5 - - 9e357a8b2ec3 - - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 77919cc3618e - 0ba4f56a3613 - 3b5b54ed6392 - 41dbf4d162a2 + - 77919cc3618e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 5308ca68ef3d - - 7babd8a46fe0 - - 9939786dd9c9 - b63363075c2e + - 9939786dd9c9 + - 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 398b937d9..3f2844e11 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,16 +2,16 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 81f0cbca04a7 - 3df9f0a4bf34 + - 81f0cbca04a7 - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - 0a53256b48c6 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features @@ -38,9 +38,9 @@ tools: - name: bfconvert owner: imgteam revisions: - - 85edbb7a436b - - f3360fbeda64 - 10eed33aa9b2 + - f3360fbeda64 + - 85edbb7a436b - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -55,55 +55,55 @@ tools: owner: imgteam revisions: - 664232d2a3f7 - - 5bf8eb50b280 - b58447a2eed2 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 - e917a2424690 + - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - 670975e92458 - - 6070780813d9 - e7273daa5ae2 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - - cdf8e3c57dae - df3ad3ba5c6f + - cdf8e3c57dae + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 6a7da2e5f696 - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet @@ -125,81 +125,81 @@ tools: - name: cp_identify_primary_objects owner: bgruening revisions: - - 87d4d92d7487 - 993faa34333b - b6eec6087271 + - 87d4d92d7487 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - - ff1a86a87364 - c09dcda1143f + - ff1a86a87364 + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: + - 667a513e67e4 - b178453ea8d1 - 3a05117669cf - - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - ac5bea85a391 - a1a961c46d4b + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - 20dbb1f7ec7b - - a32c3f810ade - 91e03287f285 + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: + - b64af54c5c09 - 5499dc6f8ac1 - 8536b1ae0254 - - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - e52c75a28c4b - 407925835dd9 - 980aed9e8fd5 - - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - - acf3aa487283 - d85f11570109 + - acf3aa487283 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 80b200ae516b - - b76841ee5560 - 035a58c7f54a + - b76841ee5560 + - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -211,17 +211,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 8083a87d2fdf - 3a3033222f61 + - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 4ecf93628f97 - 27edbb90ab2b - 33f4fa1413fb - - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -247,7 +247,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 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 e4691cbcf..98178cc20 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: - - 3e4f434a69c6 - - a38934e303b9 - - 78bbd17d0703 - d6e72da3ec35 - - e319b5b65879 + - e4ee04da1c19 + - 78bbd17d0703 - 17f911830a8c - f362150bef41 - - e4ee04da1c19 + - e319b5b65879 - 1069f6db0a0e + - 3e4f434a69c6 + - a38934e303b9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 2b95d5c04908 - f91cfb73d369 + - 1ef5b6e3e09d - c88553ec696e + - 2b95d5c04908 - 72ddd32392cd - - 7fe36019c073 - 8f8df367470d - 9537184d421f - - 1ef5b6e3e09d + - 7fe36019c073 - 0135f1d487a0 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: + - 2cf4a1cafc16 - ad0dc9f4c9e2 - d7e79eb3bcb3 - - 2cf4a1cafc16 - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee29337f905c - - 43aac8d29685 - - 6a1515bb0687 - - 28a6f1908fcc + - 8d36959b000d + - 9eaadf03e0df + - 8c05afb547fa - 69797fa273c3 + - 6a1515bb0687 + - bd2a7d1316b9 + - 3d18f8c3c0f6 - ee2beb764a7b - 94df24c6bc00 - - 3d18f8c3c0f6 - - 8c05afb547fa + - 43aac8d29685 + - ee29337f905c - 7f1cfa4c0e32 - - 9eaadf03e0df - - bd2a7d1316b9 - - 8d36959b000d + - 28a6f1908fcc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - bcaa0d571ce2 + - 9f978da6528a - db536ad45f28 - e3bb03cf207a + - 5d6ed46cc101 + - 8858fa037a15 + - d37ede8589b2 - 0893a1dbb807 - 364f4ffec275 - - d37ede8589b2 - - 8858fa037a15 - - 5671e1d3d5ee - - 9f978da6528a - - c092052ed673 - cb903c9dc33d - - 5d6ed46cc101 - - bcaa0d571ce2 + - c092052ed673 + - 5671e1d3d5ee tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - ed28dd32141c - - 045d6d00f606 - - 230b05597996 - - 49236b03e4fd - - c5c9f02b6167 - 12d66d0d05ac + - c5c9f02b6167 + - 230b05597996 + - ed28dd32141c - 584beffa972b - f95f403841ad - 3b6a16d82c1b - e1a015876aa9 + - 045d6d00f606 - 38b91a3190cd + - 49236b03e4fd 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 6b29f0d02..8e0f740c8 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -4,17 +4,17 @@ tools: revisions: - b8a457820315 - f198773344e4 - - 17e3b698dd52 - 0f1724dd59d2 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - a513e3fbb4c5 - - ac092723240d + - ba0c40780ecf - 374cb875d38a + - ac092723240d - 22c2a1ac7ae3 - - ba0c40780ecf + - a513e3fbb4c5 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index 3fb3aa762..52a622129 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,99 +2,99 @@ tools: - name: keras_model_builder owner: bgruening revisions: + - 772e0e89fc68 - 522137aaa9c4 - 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 - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - b6ef6d0cb6b7 - - f1b9a42d6809 + - 2af1346e68c9 - e1317b5502fa - 818f9b69d8a0 - - 2af1346e68c9 + - f1b9a42d6809 + - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - - 8334dc98c48e + - 947c2eacccb8 - 1588f9076e32 + - 8334dc98c48e + - c80db5d6fd8c - 05143043ca13 - - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 25b46af53232 - - 9991c4ddde14 - - 29e4122c90de - - 83228baae3c5 - 1552b8cb4a94 + - 83228baae3c5 + - 29e4122c90de + - 9991c4ddde14 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 - 841a6cc5fc58 + - a07ab242b0b5 - f3dfa4bdf87e + - 060ca94ac049 - 1a53edc4b438 - 53616c8b0865 - - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 - - d4808d5b83da - 40f4447733b2 - 2fc89dcd41c8 - - 927586a18553 + - d4808d5b83da - 91c4e3331208 + - dc4b5fd604a6 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 7626ea9c2e1b + - 36e8d6d5d01b - 301e07345c93 - - e5a5ad882f1f - - 25ab6b4e376e + - 7626ea9c2e1b - c6ae57f774c6 - - 36e8d6d5d01b + - 25ab6b4e376e + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 02d2be90dedb - - f9639b488779 - - 4ed102b922cb - 80852884053f - - b7c3e9a3b954 + - 4ed102b922cb + - 02d2be90dedb - 0630258dcf35 + - b7c3e9a3b954 + - f9639b488779 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - - ec69cbe34b73 - 14180f9c831e + - ec69cbe34b73 - 61634a87efc7 + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index 076d039d8..7ac9ce1f5 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: - - 3ba8d4563129 + - 17062a0decb7 - a6d65b0c67af + - 03e9b2fbc005 - cd659e8cc5fa - 017aba02828d + - 3ba8d4563129 - 937aa69e715f - - f6877ad76b00 - - 03e9b2fbc005 - 749c918495f7 - - 17062a0decb7 + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -29,11 +29,11 @@ tools: - name: bwa owner: devteam revisions: - - e188dc7a68e6 - - 64f11cf59c6e - - 3fe632431b68 - 53646aaaafef - dfd8b7f78c37 + - 3fe632431b68 + - 64f11cf59c6e + - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -46,42 +46,42 @@ tools: owner: devteam revisions: - 2ff111fac1d7 - - 60afcc2c1d05 - - 3e1ea2facca6 - 37b497aa133f + - 3e1ea2facca6 - e7f19d6a9af8 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - c0c2d0941de8 + - 09b53c1d4ab1 + - 77b2770508f6 - be1d967337e4 + - 53c0b7a1a0c3 - 11a0d50a54e6 - - 6b1e195506a3 - - f54f5baedfdd + - b3eab4b67562 - 037c6e54df11 - - 09b53c1d4ab1 - 3f4d6399997b - - 77b2770508f6 - - b3eab4b67562 - - c0c2d0941de8 + - 6b1e195506a3 + - f54f5baedfdd - 8c6cd2650d1f - - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 1cd2511a396e - - b8f5f6e87f5c - - 79b885ce78d7 - - 9ee34ba73ebf + - 13022c3d3076 - ec9cbd6b9a49 + - 9ee34ba73ebf - 00fbfac99d39 - - 5ef7ec16b04f - 178bdbdb6d24 + - 1cd2511a396e + - 79b885ce78d7 + - b8f5f6e87f5c + - 5ef7ec16b04f - e403d27e8f24 - - 13022c3d3076 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 85d8ce24a..b3f7fa326 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -15,8 +15,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - 388e6678fa98 - 7f1aaa1932d8 + - 388e6678fa98 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: collector_curve @@ -34,98 +34,98 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 7c2100246a2f - 63f86089423e - 5b5a7af9fbb4 - 76d3d2b10738 + - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 1c35dadbe76f - - 84fd33a60b35 - - 18a502a9d287 - 96336c6a2bb7 + - 18a502a9d287 + - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - a9f4a217dcd6 - - f732237754fc - addaf9d22850 - 34e55239e68b + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 0776d824d896 - - 04c15826a0b8 - 75403243703a + - 04c15826a0b8 + - 0776d824d896 - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - 8470de786d47 - 1c9b3bcd4261 - e96bbb9e24ea + - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 84743da21318 - 1d75bd0595e2 - 306a40d4bb8f - - 84743da21318 - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - 78faebd0879c - ac72310b038a + - 8daf4564ccda - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - 7b8cb2b02978 - d60df8727f59 - - f947b4bb5107 - a58e4a43f49c - - 7b8cb2b02978 + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - 7136e9ab70db - - 1bc3657cd694 - 7f3b59dee073 + - 04144473e59e + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - 19299bb1c6af - - 9058d8943303 - d943081510da + - 9058d8943303 + - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf @@ -168,16 +168,16 @@ tools: - name: humann2_renorm_table owner: iuc revisions: + - d77397f09da1 - c6676a890f50 - b084117133af - - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - cad93abecac9 + - 9704f1a3b32d - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -190,19 +190,19 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 79706f10d680 - - e88b731dad59 - 31c6d107e7a5 + - e88b731dad59 - c409a495841f + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 - - 714d5a28cc5c - - 71ea608ddfa3 - 094ad9c068af + - 71ea608ddfa3 + - 714d5a28cc5c + - 172920f67a84 - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -210,40 +210,40 @@ tools: owner: iuc revisions: - d7e9a3c41657 - - 12fb63b5f63f - - 4137b492233e - - a293a742194f - a4d7148ccee4 + - a293a742194f + - 4137b492233e + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: + - e2c71b852aba + - cf87759761eb - 97f7bb0851e7 - - 64bc7acc22a9 - 75bedfb2078b - - cf87759761eb - - e2c71b852aba - 6fcb8ac37a3e + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - c82508e76ad1 - 080ea153677c - - 5e5a999ffaa9 - 4033827c76b8 + - c82508e76ad1 - 2d35528d2141 + - 5e5a999ffaa9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - 95bf7479d53c - - 2cd76b089570 - - 6b7622dda516 - fc6c328c292f + - 6b7622dda516 + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -317,8 +317,8 @@ tools: - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -330,15 +330,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -388,19 +388,19 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 2cff76cf35c6 + - 27250f92a01a - 0270541aaf46 - - e073891b2afc - 4fd3b5d8706b - - 27250f92a01a - - 2cff76cf35c6 + - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb - eb50e7eca3dc + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -466,20 +466,20 @@ 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: + - ff8f55893e7d + - 2131d7dca455 - a92a632c4d9b + - b89b0765695d - a16313517e55 - - 6dee4abadccb - - 2131d7dca455 - - ff8f55893e7d - 1a6cdf55390f - - b89b0765695d + - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -551,8 +551,8 @@ 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 @@ -601,13 +601,13 @@ tools: - name: staramr owner: nml revisions: + - 141afacabcfa + - aeaa20b96ef2 + - 4b9a8031ab74 - 4d83eccf5f81 + - be818ae858e4 - 2fd4d4c9c5c2 - 3b22de20bd4b - - 141afacabcfa - - be818ae858e4 - - 4b9a8031ab74 - - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 46e11a4be..429d251d3 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 4e9136c2c4c3 - ab12df91b47f + - 4e9136c2c4c3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 6c7b9cad1..123c6c5c0 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: - - 2263989660f5 - - a74dbfee5a86 - 9eeb13a92d79 - - 80f03df2e2ce - - 8b67dd48fec1 + - 2263989660f5 - 94b8c6013083 - - 6ae5a7b5a0a2 + - cd07731e4434 - 9422c5a87ee2 + - a74dbfee5a86 - bdfbaf0c10aa + - 80f03df2e2ce + - 6ae5a7b5a0a2 + - 8b67dd48fec1 - 9baa871cb1d1 - 48c13389050d - - cd07731e4434 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - bc3831dd65c1 - - f14193ec1f50 - - aaa0d6a8b808 - - 2e093badc689 - - f0af8936ed41 - - d7ce0ec78e51 - - fc2e49f91e52 - 4a60927aaca5 - - 5abf2c2249aa - - d390fe1567dc + - be78f13134e2 - c18157c68134 - 3ff17bad4006 - - be78f13134e2 + - d7ce0ec78e51 - '764845535798' + - f0af8936ed41 + - f14193ec1f50 + - fc2e49f91e52 + - 5abf2c2249aa + - d390fe1567dc + - aaa0d6a8b808 + - 2e093badc689 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -64,19 +64,19 @@ tools: - name: mafft owner: rnateam revisions: + - c5908940967d - f1a5908ea2cb - a65296ffb4a0 - - 15974dd17515 - - c5908940967d - 6f28e90db932 - f0d493f8f84f + - 15974dd17515 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -89,15 +89,15 @@ tools: - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - bcd65de9725b + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer @@ -110,7 +110,7 @@ tools: - 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/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index f8599c399..16d4d87f5 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,35 +8,35 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 72b5e9dda577 - - 0e9e7fcdd543 - - fc8804320156 + - 79e9a869f40e - cb34f00cc10f + - fc8804320156 + - 72b5e9dda577 - a7228a7ea146 - - 79e9a869f40e + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - d6cddc06aeae + - 18505fe2bdb1 - db25ec99c3ea - fa11aa8103b2 - - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 43815fa60f3a - 2bf63b38ee9b + - edf6d4003fad - eb746fa6f514 - - cc36773a3681 - 0f5f4a208660 - - edf6d4003fad + - 222669c4afb6 - 19f3b583a9b3 + - 43815fa60f3a - ec699520444c - - 222669c4afb6 + - cc36773a3681 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -55,57 +55,57 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - a3c4fe6f49ab - - edbb6c5028f5 - 0f1c34698076 + - 645159bcee2d + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - 85a394edc247 - - 3b6f94fc7e1d - d219b6d8158a + - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - be95355fef8d - a8d4be409446 + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - d376944466bf - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - a3afc5f0a96c + - bec636361cfd - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - - 543cbeef3949 - 93d623d9979c + - 543cbeef3949 + - 5f76b20953e5 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 @@ -150,8 +150,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -181,8 +181,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - ca22d8497db5 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 921e41712..b1f5ea951 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -53,16 +53,16 @@ tools: owner: iuc revisions: - 3e73c97f025d - - d74850cf4e42 - adfd6bf710bd + - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 9dd107db92c2 - 83da94c0e4a6 - 1586b111d2a3 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -75,16 +75,16 @@ tools: owner: iuc revisions: - e4b4837f06f5 - - edacc4bcd3cb - 2f27f3b86827 - ed1518ce2237 + - edacc4bcd3cb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -103,16 +103,16 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - 48a42ca61006 - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder 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 @@ -125,15 +125,15 @@ tools: - 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 owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -152,10 +152,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 172815da3d41 - - 5bcf0e24f42c - 27a6a256cd23 + - 172815da3d41 - b4b2b284230a + - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -180,9 +180,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - - 87febc68b45b - 19bbd19b74b3 + - 87febc68b45b + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -213,10 +213,10 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 - 0cb27ea69dc1 - - 5fe20c915fa6 - 4ba60cb14cb0 + - 9c43baa60906 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -228,18 +228,24 @@ 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: + - 29c738066906 - ed7a967cb11b - - 6e24e79d3d69 - df30a2f1db55 - - 29c738066906 + - 6e24e79d3d69 + tool_panel_section_label: None + tool_shed_url: toolshed.g2.bx.psu.edu +- name: data_manager_pharokka + owner: iuc + revisions: + - 50caca83e7c9 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder @@ -266,16 +272,16 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - d63c1442407f - 64deddb6a8ec - c520a52b5174 - - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 9946bc39c834 + - 94a50db37d1a - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1034,8 +1040,8 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - e4b7d1507a75 - a22969b08177 + - e4b7d1507a75 - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index b2c75e22f..cf467a9af 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -33,115 +33,115 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 26de3a7b1cb9 + - a6619171428e - f04a1264e2a2 - - 5a7c56a5cc08 - - 3b8b5bde0bd9 - - cce7b18495e4 - - '841557158611' - 6a457678efcb - - 8834daeb9892 - - 107d3ba7024a - - d033ffc1c161 + - 81e66674859e - c78f3d7dd1db - - d7c7ef3353fe - - f73435dc282b - - a6619171428e - 3f59ebfbfe3d - - 81e66674859e + - cce7b18495e4 + - 107d3ba7024a + - 5a7c56a5cc08 - b89cac5156ec + - 8834daeb9892 + - 26de3a7b1cb9 + - d7c7ef3353fe + - d033ffc1c161 + - f73435dc282b + - '841557158611' + - 3b8b5bde0bd9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6a726db04d4b - 88c4aa435ded - - e75442c7f4da - - 5b777002c2de + - 02b8758214b0 + - df47d4845b62 + - 6283babe736e - 659517798cc4 - - 3b96e92e8ec3 - - a185b079b095 + - b0af57c1a968 - 4755f52427c4 - - 6223845127ea + - 3b96e92e8ec3 + - 6a726db04d4b - aa8cc71438cf - - 6283babe736e - - b0af57c1a968 - - 5fcd1ece3a6e + - 6223845127ea + - 5b777002c2de - 7a2092844346 - - 02b8758214b0 - - df47d4845b62 + - 5fcd1ece3a6e + - a185b079b095 + - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 524d31add34a - b8476e82ac20 + - 524d31add34a - 9b892d7f82cc - - f97743d52b87 - d1c340a5664b + - f97743d52b87 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 9e10ba792be2 - feb40665d7cd - - daddf188c13f + - 9e10ba792be2 - 128ba8da994f + - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - b7e297c2ede6 + - 2f1019071464 + - 2fa9d4f1b48f + - 437e28791761 - 81804a978fc0 - - a2099fb98cdb - - 36912871ccdc - - ca0d8cf80567 + - 14ae456b8cc5 - 83a69484cb87 - - 2fa9d4f1b48f - - abf6dbe8c9d7 - b6abccb1f25b - - ca337cce3888 + - 3a43c3982401 + - 36912871ccdc - 5f8727ff21e7 + - 7bb8726be37c + - ca337cce3888 + - a2099fb98cdb - 42a174224817 - - 14ae456b8cc5 - - 3a43c3982401 - - 03ed9524dcd1 - 9d61d3fa046c - - 437e28791761 - - 2f1019071464 - - 7bb8726be37c + - ca0d8cf80567 + - 03ed9524dcd1 + - b7e297c2ede6 + - abf6dbe8c9d7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: raxml owner: iuc revisions: + - ea30d3089354 - 73a469f7dc96 - - a4b71be30c3c + - 29ff6a849eac - ba29b5e2a4be - - ea30d3089354 + - a4b71be30c3c - b1e68bbe4cef - - 29ff6a849eac tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 15ac71df11a0 - - e88a7de55d6e - 809e42326fc2 - - f1ccc8a6eb05 - 91887494eb97 + - e88a7de55d6e - dbe2b2204555 + - f1ccc8a6eb05 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index e5b9ae428..246cc75c4 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -3,12 +3,12 @@ tools: owner: devteam revisions: - f6ced08779c4 - - 1aac2a13842a - - fc288950c3b7 - - 881d7645d1bf - a1f0b3f4b781 - - b502c227b5e6 + - fc288950c3b7 - f9242e01365a + - 1aac2a13842a - 7d34178f2812 + - 881d7645d1bf + - b502c227b5e6 tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 5e927b386..cd139a586 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - 3bd420ec162d + - 7fbec959cf2b - ca90d17ff51b - - d00e15139065 - - c0e71cb2bd1b - e4a053d67e24 - - eb085b3dbaf8 + - c0e71cb2bd1b - 5b85006245f3 - - 7fbec959cf2b + - d00e15139065 + - eb085b3dbaf8 - a58f7eb0df2c - - 3bd420ec162d 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 2c84eaccb..9e7010f0e 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,48 +2,48 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 0a18ac48ac53 - - 277dc652246e - b18329a8ac14 - - ece627528a78 - - f28ad96b76dc - b574b84afc4d + - f28ad96b76dc + - ece627528a78 + - 0a18ac48ac53 + - 277dc652246e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - - b41107d8fe89 - - bf06d196e23d - 525f201b86c1 - e215f71d7983 + - bf06d196e23d + - b41107d8fe89 + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - 8da3511c9467 - - bb6397b94018 - 4fbffddde8cd + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - a8157342d9a3 + - 528fb09022be - f23d67e28cc8 - b8c79e70516d - - 528fb09022be - - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 80600735685d - 25b83cbd596a - - a69865da6f80 - 59e85306eae5 + - 80600735685d + - a69865da6f80 - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,36 +51,36 @@ tools: owner: galaxyp revisions: - 611d80c0e29d - - ed9ed1e6cca2 - f1897eb07081 - 798da6bdff3d + - ed9ed1e6cca2 - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - 74b61bf5bc4b - 5a35e3a8d013 + - 74b61bf5bc4b + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff - - df2187f9013b - 82f6c2f4332d + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 - c5aa9fca18c6 + - 043f9c91f686 + - 1693b2126f30 - 10566783d718 - d2483487e077 - - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -99,8 +99,8 @@ tools: owner: galaxyp revisions: - bf0728e000cd - - 9fa3dbf06f17 - ae4dc0c041f9 + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -120,8 +120,8 @@ tools: owner: galaxyp revisions: - 4081e4faa4ab - - 0fa397f4f40b - 1c5cbf8f79ce + - 0fa397f4f40b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -147,16 +147,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - 160538a890a6 + - d286ff4600dd - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -169,60 +169,60 @@ tools: - name: maxquant owner: galaxyp revisions: - - 1f39c833f65f - - 2133b0be850a - 7f432d87c82c + - e42225f8a659 - 8934bc76bb52 - - 837224ad1694 - - 4d17fcdeb8ff + - 2133b0be850a - 97a7f34fcb6a - - e42225f8a659 + - 837224ad1694 + - 1f39c833f65f - f522c08e900c - 37d669de2828 + - 4d17fcdeb8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - - '860429737408' - a72ac2c7cc5b + - '860429737408' - 85b8866f06d7 + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 4187b6df1a40 - 1974224d63c2 - - 990b4560ead7 - 352b37c66d97 - - 4187b6df1a40 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - - 99450519d727 - a1daafbf5233 + - 4f359549383c - deaf035bbe9f + - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: + - c1343e3389ca - c7745841de24 - e79958768a2c - 40ca115438d2 - - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - d46d64e7964d - da986f83631b - d2eac53666f0 - - d46d64e7964d - b648e45fd3cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -230,9 +230,9 @@ tools: owner: galaxyp revisions: - 9bf325045235 - - 944b43462104 - eb811f3018ea - 1199751329b0 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -250,10 +250,10 @@ tools: - name: msstats owner: galaxyp revisions: + - 8212e342e482 - 28434abe6c5c - - b7034eff0db1 - 593839e1f2c3 - - 8212e342e482 + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -266,8 +266,8 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - 8960fb791701 + - 01dbaf6a57e0 - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -281,116 +281,116 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: + - c9eff69a7c62 - 518b1730cf2a - 9cdf15d3cfc8 - - c9eff69a7c62 - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - ca88bd28f116 - 5e948629bc73 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 658494a2cb00 - - 41859bbdc16e - 890025d6e426 + - 41859bbdc16e + - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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 - - 05d5e1ddc985 - 0bb5056cb775 + - 05d5e1ddc985 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - febd569ad26f - 52ba9695e752 - 5ad830edc021 + - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 39e8fde08881 - 27cba4c5fc42 - 92352a475eed + - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - d413dc49d650 + - 0efbc235f314 - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 3720e349ba2a - c28f13cab67a - 8a04ed1c1d1b + - 3720e349ba2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - - 382cde407f81 - ca799a7246e7 + - 382cde407f81 - c427a8628cbe + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 39caaa778d2e - b5d0905419da + - 39caaa778d2e - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - f817513840a9 - 1c5f31b8d632 - 8d4db262964c - 18f93351f8b6 - - f817513840a9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - c69f69d7867a + - 5d9f175dff81 - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - - 476b5e296979 - 0e52c85f3b15 + - 476b5e296979 + - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -411,15 +411,15 @@ tools: - 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: - - ee860980edc6 - bf32e0bcf554 + - ee860980edc6 - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -433,22 +433,22 @@ tools: - 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 owner: galaxyp revisions: - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -475,32 +475,32 @@ 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 owner: galaxyp revisions: - - bc63b4d12779 - 2aebe58de46e + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 3d8d4ada5405 - 5ae104d0da6e + - 3d8d4ada5405 + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - dd173849c3d8 - - 539a3a4dcc9e + - e039cc5c7aed - 5182338d5e7c + - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -519,8 +519,8 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - 9020199dba0a - d063e2fe4ba4 + - 9020199dba0a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -547,21 +547,21 @@ 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: - - 3634c90301af - - 3ec27b4cee7c - - 1beff3ddce58 - - 7fdd9119cc4f + - 943a34df6047 - 07ff622ec007 + - 3ec27b4cee7c - a72c48001f7c + - 3634c90301af - da885ca16cb2 - - 943a34df6047 + - 7fdd9119cc4f + - 1beff3ddce58 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -616,9 +616,9 @@ tools: owner: galaxyp revisions: - 1a5690a5eedc - - a371252a2cf6 - 265c35540faa - 12692567c7f9 + - a371252a2cf6 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 0b008acf8..57b29930d 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 42201b90e3f4 - 2f1d464ebfd2 - - 289b7d6b69a4 - - e345aadf914f - 110a346daf36 - cd5f98911089 + - 42201b90e3f4 + - 289b7d6b69a4 + - e345aadf914f 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: - - 0345dbaaa79b - 8501601a118d - - c207119ba5f6 - 42d9087b4789 - 0cd2df8af811 + - 0345dbaaa79b - fcce77c09289 + - c207119ba5f6 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 - - 89eb29319bf4 - - 33486216eec0 + - 421c33b8bf17 - 405a212b32ab - 04db7fd6b238 - - 421c33b8bf17 + - ad5ab22ffe24 + - 33486216eec0 + - 89eb29319bf4 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 - - 1d839ead7ad3 - fa51dc5e8386 + - 1d839ead7ad3 - 7370bb65bad4 - 7b72fde3d27e - f6e91108b7b1 + - eb784fa07f80 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: - - a3e86cd9cac7 - - 8a55d29c8fcf - - 1544278c272e - - d30e36c48c93 - 3d70c2996730 - c9b77ced9a78 + - 8a55d29c8fcf + - a3e86cd9cac7 + - d30e36c48c93 + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - e2db212d64ad - a5969aa9347e - - 7b881f5f5ad5 + - e2db212d64ad - 887cf585cafc - - b242deb58952 - 564c33e5c3e3 + - 7b881f5f5ad5 + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,10 +104,10 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - 8cff84759bf6 - - 9a171f9a450b - b4bab607eb05 + - 8cff84759bf6 - e897c74a48bb + - 9a171f9a450b - bd5ff77e2036 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: + - 4f65e343ecdf + - adc7a7610d4f - 6dafad990086 - 887e0991eb24 - - adc7a7610d4f - 33f0793edf93 - 5e10f396979e - - 4f65e343ecdf 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: - - 97575d01f06b + - 4e280b27a831 - c287418eb288 + - 17d39bf0a63a - 43e3eeb2e0ec - - 4e280b27a831 - c5d7050e4ad7 - - 17d39bf0a63a + - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,11 +154,11 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - d9bf483266a1 - - a819ec3b362d - - 0b8c84a7fdb5 - cd034465d4a4 - 9586f08634c0 + - 0b8c84a7fdb5 + - d9bf483266a1 + - a819ec3b362d - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - a4b4bd84f69e + - a9c34a289493 - 69842dd5aa48 - 95351dd0fd3f - 2645575d1bf2 - bf0e43ab0416 - - a9c34a289493 + - a4b4bd84f69e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,11 +188,11 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - - d1fda11e602f - bb0475c884ff - 912f904a6e1e + - d1fda11e602f - cfb504394ae1 + - d033e1ccb386 - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 4a470095c..a4a61aa0f 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,9 +2,9 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - cf01dd6c6b1f - 31f8063eedea - 2d4e3aff9dc7 - - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -56,8 +56,8 @@ 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 @@ -70,9 +70,9 @@ tools: - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - - 86285ddd4512 - cf747d1bd79a + - 86285ddd4512 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -109,10 +109,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 8f0181aacb7a - - 3b36efd62b3e - 0693ccd171c4 + - 8f0181aacb7a - e3b16fd7dd08 + - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -124,13 +124,13 @@ tools: - name: deseq2 owner: iuc revisions: - - d027d1f4984e + - cd9874cb9019 + - 24a09ca67621 + - 0696db066a5b - 8fe98f7094de - - 6a3a025714d3 + - d027d1f4984e - 9a882d108833 - - 0696db066a5b - - 24a09ca67621 - - cd9874cb9019 + - 6a3a025714d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -142,10 +142,10 @@ tools: - name: dexseq owner: iuc revisions: - - df929f257179 - 62adf13b86ea - - b47c006d90c5 - 2872c633f07e + - b47c006d90c5 + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -157,17 +157,17 @@ tools: - name: edger owner: iuc revisions: - - 3d89af8a44f0 - - 555659de7321 - - 6e53e565fc6a + - 070900306913 - 334ce9b1bac5 + - df0c8d0a5992 - f2843df56434 - 9bdff28ae1b1 - 5bf899c13979 - - 0cb907a2a810 - - df0c8d0a5992 - - 070900306913 + - 6e53e565fc6a - a8305cf0c951 + - 3d89af8a44f0 + - 0cb907a2a810 + - 555659de7321 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -179,8 +179,8 @@ tools: - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -198,17 +198,17 @@ tools: - name: featurecounts owner: iuc revisions: + - f9d49f5cb597 - 6f66ae7c5f7a - - ea04b737afa0 - - e6a2a912677a - - a56fbe2d6ba7 - - 38b6d12edc68 - 90d16db017d7 - - f9d49f5cb597 - f3a5f075498f - - a37612abf7f9 + - ea04b737afa0 + - e6a2a912677a - 7db9d3ea71c9 + - 38b6d12edc68 - af814359d244 + - a37612abf7f9 + - a56fbe2d6ba7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -232,9 +232,9 @@ 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 @@ -252,13 +252,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6ab42baa56e9 - - 26371a1df031 - - 3fb01a8c902d - - f4af63aaf57a - 6c19daec423d - d4b55e2beb12 + - f4af63aaf57a + - 3fb01a8c902d - a86e80d3c09c + - 26371a1df031 + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -297,9 +297,9 @@ tools: revisions: - 5ae5c312d718 - ce5d418183c5 - - 1c75aa5de15e - - 01247aaf0a10 - 87c11c05d238 + - 01247aaf0a10 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -312,9 +312,9 @@ tools: owner: iuc revisions: - 40985510cd98 + - c971db6f0fe5 - 10c98fab6c5a - 4f9c4e6566e5 - - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -326,13 +326,13 @@ tools: - name: limma_voom owner: iuc revisions: + - 58c35179ebf0 - 97e06a4c7c75 - - 32511f586472 - - d6f5fa4ee473 + - 708348a17fa1 - 0921444c832d - e827f9aae031 - - 58c35179ebf0 - - 708348a17fa1 + - d6f5fa4ee473 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -393,19 +393,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4074fc1940e2 - - 4df95e2d7f61 - - 0a563fd2f22e - - c7c55b694974 - - e132e7d02a3e - - 7ed2edc1337f - - 980d2a2e1180 - - 3ea5a2a63fa2 - 79de45b5069b - - b9e04854e2bb - - 99b17b74a8cd - c772497b2c32 + - c7c55b694974 - 5ec75f5dae3c + - b9e04854e2bb + - 980d2a2e1180 + - 7ed2edc1337f + - e132e7d02a3e + - 99b17b74a8cd + - 4074fc1940e2 + - 3ea5a2a63fa2 + - 4df95e2d7f61 + - 0a563fd2f22e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -429,13 +429,13 @@ tools: - name: salmon owner: bgruening revisions: - - 53e9709776a0 - - e3d32471da11 - 49121db48873 + - e3d32471da11 - 2c0ca397d302 - - ebab418107f5 - 15cd64d7c58b + - ebab418107f5 - cc05793bb896 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -447,20 +447,20 @@ tools: - name: seurat owner: iuc revisions: - - fab6ff46e019 - - 8c28affc7c48 - c0fd285eb553 - 56242ff81c84 + - fab6ff46e019 + - 8c28affc7c48 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 1ebd14235b92 - 258d696dbd7e - cef79931dda5 - - 76d290331481 + - 1ebd14235b92 - ae618321f34a + - 76d290331481 - 914cfcba0ec8 - dd4df992d93d tool_panel_section_label: RNA-seq @@ -498,10 +498,10 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - d0d4cef4f967 - - ffd1300599a1 + - 0db979fead3a - c6334cb383ff + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -513,10 +513,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - d6a479fd4281 - 74217fbfba4d - - bcc5f03f1900 - ba3720d7e68b - - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -543,8 +543,8 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - 9ff3765e7172 - 3f4094b6a565 + - 9ff3765e7172 - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -557,9 +557,9 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - 34a018cbee9c - 870ac06dff8e + - 4687ecf0eb2d - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -572,11 +572,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 05ab8d5e04a2 - - c5fbddcac63a - 33406f5a445c - 65e7dea767ea - 5192f657f305 + - 05ab8d5e04a2 + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -588,10 +588,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - a35cba31d904 - - 1fdb25a8384d - e406ac71165d + - a35cba31d904 - 6f0fb35b799c + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -603,10 +603,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - c2c039e421af - 964b7efe2639 - - 7c7fbf13aadd - 37a1129c89d2 + - 7c7fbf13aadd + - c2c039e421af tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -618,10 +618,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - eafea3083352 + - 1d689e4e1caf - 047c22569787 + - eafea3083352 - 24e94d84adc9 - - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -633,10 +633,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 3a4ac03d1266 - 04bb8bb7c198 - 9871104ea630 + - 1812dbc5bb7b + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -648,15 +648,15 @@ tools: - name: trinity owner: iuc revisions: + - cee61b3fcf78 + - db1f362cca3e + - d84caa5a98ad - 32b86cd8eb50 - d2bc35f3d1c5 - - cee61b3fcf78 - 9fa24d5aac68 + - 8f1c3df4dd49 - 48636f857c4b - - db1f362cca3e - c9cfec002f71 - - d84caa5a98ad - - 8f1c3df4dd49 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -668,10 +668,10 @@ tools: - name: trinotate owner: iuc revisions: - - 2b093007fab9 - 6fd16fad465d - - 4383070d29ed - 9e61bc67866f + - 4383070d29ed + - 2b093007fab9 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 ad071beec..b41c54fe8 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: - - 473382134e56 - 080fd5739bb4 - 1a052c827e88 + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 98e3f3909..e4ae861db 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 88eedb4abea0 - a53efedba9e7 + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -17,8 +17,8 @@ tools: owner: devteam revisions: - cb20f99fd45b - - 108db6635177 - 1dfd95ee241e + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -36,8 +36,8 @@ 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 @@ -55,8 +55,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - 5f8e69cc4c6e + - e7fd6754d093 - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -69,8 +69,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 8c737b8ddc45 - 75557c0908a9 + - 8c737b8ddc45 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -108,18 +108,18 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - dc6ff68ea5e8 - 56c31114ad4a + - dc6ff68ea5e8 - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 6856f8a01905 - - 9149ad20699a - 12749212f61b - 46c6639921f1 + - 6856f8a01905 + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -131,9 +131,9 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - 33208952b99d - 92ec40abcdcf + - 06dc50b7b711 - c89806670ab9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -147,8 +147,8 @@ tools: owner: iuc revisions: - b3d99709fe1a - - a8d69aee190e - 66e23b11feae + - a8d69aee190e - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -161,11 +161,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - cc61ade70eb8 - fe34990e5ce7 - - 22970df7a40e - fefd89ab563c - db17d5321bad + - 22970df7a40e + - cc61ade70eb8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -177,11 +177,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: + - 7a6034296ae9 - 88b8c2916784 - 811fc2d75ad4 - - fa5d3e61e429 - 7def34e6cf4d - - 7a6034296ae9 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -193,8 +193,8 @@ tools: - name: samtools_merge owner: iuc revisions: - - 65a38e8c8e2a - 36677f429310 + - 65a38e8c8e2a - 740ce0a18f0d - b40e2d865d52 tool_panel_section_label: SAM/BAM @@ -202,11 +202,11 @@ tools: - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - - fa7ad9b89f4a - 9da0311ab1dd - - b61f5d6a7f25 + - fa7ad9b89f4a + - 329deb17a9f7 - 583abf29fc8e + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -218,8 +218,8 @@ 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 @@ -231,10 +231,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 - - bb8cfc6f6e0c - d7b4851d1971 - db000c6007a0 + - bb8cfc6f6e0c + - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -252,9 +252,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - b5c88b7b153e - 344fc91e1bfd - a4a10c7924d1 + - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -281,10 +281,10 @@ tools: - name: samtools_split owner: devteam revisions: - - 5d9ae78f34d3 + - bcedabb53ddf - b7f7826ef1cd - 135c85f4cfaf - - bcedabb53ddf + - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -296,12 +296,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 1cc79f49b8d5 - - 5a08c09b9311 - - fed4aa48ba09 - - 145f6d74ff5e - 3a0efe14891f - 24c5d43cb545 + - fed4aa48ba09 + - 5a08c09b9311 + - 145f6d74ff5e + - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -313,14 +313,14 @@ tools: - name: samtools_view owner: iuc revisions: - - b01db2684fa5 - c370440f901e - - 350bbc5c2ffd - - b72793637686 + - b01db2684fa5 + - bf328cec6a42 + - 5826298f6a73 - 6be888be75f9 + - 350bbc5c2ffd - 0dbf49c414ae - - 5826298f6a73 - - bf328cec6a42 + - b72793637686 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 a21d149bc..de62478bc 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d - - 480d9e9d156b - - 4aab5ae907b6 - - 59bb6d34fca6 - 6f6537780379 + - 4aab5ae907b6 - d147d6455873 + - 59bb6d34fca6 + - a62c4a11a67d + - 480d9e9d156b 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 e70cc5117..89f77b57a 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -3,11 +3,11 @@ tools: owner: iuc revisions: - cfc3f5a57dc6 - - 55e35e9203cf - - 32e547223c9e - - 93dd15e13e6a - 00712416fdaa - fb9e030ffae4 + - 93dd15e13e6a + - 32e547223c9e + - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -19,12 +19,12 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 688357ad5e61 - - 6f0d0c784f09 - 038e32885fec - 39e945f0b2c1 + - 688357ad5e61 - b9fac48532eb - ee98d611afc6 + - 6f0d0c784f09 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -36,11 +36,11 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 3d748954434b - - b85871dd69f9 - 43cb7b5a6fe7 - - ed4996a16f7f - d4af736e7b83 + - ed4996a16f7f + - b85871dd69f9 + - 3d748954434b - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,9 +54,9 @@ tools: owner: iuc revisions: - a9caad671439 - - 2c1200fba922 - - cdf4443d5625 - 8855361fcfc5 + - cdf4443d5625 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -81,8 +81,8 @@ 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 @@ -101,9 +101,9 @@ tools: - name: raceid_clustering owner: iuc revisions: + - 0bff0ee0683a - 7e014059a88d - f911a64454fb - - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -121,8 +121,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - f3eb2291da05 - 37a47c4fd84d + - f3eb2291da05 - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -135,9 +135,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - a6821f856a1e - 69018f285aa3 + - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -149,9 +149,9 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - - 44b935f2271b - 2af7c5086a96 + - 44b935f2271b + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -163,10 +163,10 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - 77b91b9bdf52 - - aaa5da8e73a9 - 6acb08931836 + - b2df381a6004 + - aaa5da8e73a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -178,10 +178,10 @@ tools: - name: scanpy_filter owner: iuc revisions: - - b409c2486353 - - 3c86f71498bc - a03ff8633507 - a97abb8cd15b + - 3c86f71498bc + - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -194,10 +194,10 @@ tools: owner: iuc revisions: - cc0deb593fc8 - - 3081ff5c84a3 - - 6c145a6868cc - - c5d3684f7c4c - 5e9171dc8244 + - c5d3684f7c4c + - 6c145a6868cc + - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -209,10 +209,10 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 3bcd5445cd7a - ab55fe8030b6 - - a407e7f8bdc1 - 94c19fb1281c + - a407e7f8bdc1 + - 3bcd5445cd7a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -224,9 +224,9 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 6adf98e782f3 - - dbbe1ea8ecb1 - aa0c474463c2 + - dbbe1ea8ecb1 + - 6adf98e782f3 - 9b0cdb8cf6be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,11 +239,11 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - 458e8f43a775 - - 73ab2ac53d06 - - 215733a383f2 - f2f6c703da06 + - 73ab2ac53d06 - bf2017df9837 + - 215733a383f2 + - 458e8f43a775 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -255,8 +255,8 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - b834074a9aff + - 8f333f90d8d6 - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -269,9 +269,9 @@ 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 @@ -297,8 +297,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - c99ba278dfa9 + - 9e5c0bb18d08 - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index c80041072..64404e27b 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: - - 419027d822d6 - - 562f3c677828 + - 2f3c6f2dcf39 - 746e8e4bf929 + - 562f3c677828 + - 419027d822d6 - 4c07ddedc198 - - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,8 +56,8 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e - - aef56d0e7a61 - - 4c4ec859c31a - 840f29aad145 - - 9c3e1d3235c8 + - 4c4ec859c31a + - aef56d0e7a61 - b1eda492f063 + - 7442b94d6a1e + - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 375bbd555f4a - - 30d21a6041f6 + - d0352e8b4c10 - 9fda0b82f419 + - 30d21a6041f6 - 07843f917990 - - d0352e8b4c10 + - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d - - 4cc980df6265 + - 8b1b2b91f8d0 - 2c58b83c9bad - cd02bf168d23 - - 8b1b2b91f8d0 + - 7ae443e6217d + - 4cc980df6265 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 4bbaf77573ef - ad7e0b4291ee - 1dd433d2c92c - bb9fc9d46ea4 - e10e776f2109 - 7dd3fb35904f + - 4bbaf77573ef 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 55b131cfc..0e6dcb5d8 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -28,14 +28,14 @@ tools: - name: column_maker owner: devteam revisions: - - 6595517c2dd8 - - 464b9305180e - - 626658afe4cb + - 02026300aa45 - 6e8d94597139 - 9cd341095afd - - 13b6f0007d9e - - 02026300aa45 - be25c075ed54 + - 13b6f0007d9e + - 464b9305180e + - 626658afe4cb + - 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: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -72,10 +72,10 @@ tools: - name: filter_tabular owner: iuc revisions: + - 557ec8d7087d - 34d29339abab - - 37cde8134c6a - 9cc411a62277 - - 557ec8d7087d + - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -100,28 +100,28 @@ tools: owner: devteam revisions: - f2aac0c5c60d - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 3a6b78c39dca - - 33d61c89fb8d - 623f3eb7aa48 - - 2e8f945f7285 - - 83069b38aa85 - cf34c344508d - 1ea4e668bf73 + - 3a6b78c39dca + - 83069b38aa85 + - 33d61c89fb8d + - 2e8f945f7285 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - 399da6b5ec21 - 503bcd6ebe4b + - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -141,19 +141,19 @@ tools: - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - 9ff72e942410 - - f46f0e4f75c4 - d698c222f354 + - f46f0e4f75c4 - a6f147a050a2 + - 0a8c6b61f0f4 - ddf54b12c295 + - 9ff72e942410 - 74a8bef53a00 - - 0a8c6b61f0f4 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 80b80064c..b6fe8aeca 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - 82fb5e3bb93e - - 85c57cc9b558 - 0d18a3ba2d1c + - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,40 +16,40 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 - - 57def2d7c093 - - 156b60c1530f - ef2c525bd8cd - a5937157062f + - 156b60c1530f + - 04fa42777df9 + - 57def2d7c093 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 435b157bed6d - - 09d6e4693887 - e61c9ac190ad + - 09d6e4693887 - 791f73caa0c8 + - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 03627f24605f - 65432c3abf6c + - e1461b5c52a0 + - 03627f24605f + - dfadc322b065 - 074d44697036 - 3b4b2121842f - - e1461b5c52a0 - 4805fe3d8fda - - dfadc322b065 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 9cb929f21cfa - 701d134358ad - 7dfca164d2e3 - - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual @@ -64,9 +64,9 @@ tools: - name: lofreq_viterbi owner: iuc revisions: + - aa35ee7f3ab2 - dbd9f2db9ed8 - cdaab621d454 - - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -85,10 +85,10 @@ tools: owner: iuc revisions: - 5bbf9eada9c2 - - 9bccc8404a3c - - c9a8ef2aa380 - d220115f882b + - 9bccc8404a3c - fa016f1eea1a + - 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 - e7aff4a85df5 - 40f0591deda0 - 32f14a2723ec + - 3b1e7c170b10 - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 02d81b994ef5 - - 4934c0ac6197 - adc0645b945c + - 4934c0ac6197 + - 02d81b994ef5 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 46ec908de..20120d5da 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,12 +2,12 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - 8a2e296c07ef - 6a88248893c4 - - b7ea370b8f5d - 265fe0f9ea64 - - ebe5fc018e72 + - b7ea370b8f5d + - 8a2e296c07ef - e075b1be5abb + - ebe5fc018e72 - 3f62d4939d54 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -21,12 +21,12 @@ tools: owner: iuc revisions: - b03984136ce4 - - 22637b1a55bf + - 0fba2c15b40d + - f0d44631365f - 21687e35f066 + - 22637b1a55bf - c37b684e7f4e - 544cb432072b - - f0d44631365f - - 0fba2c15b40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 8627b2b383b4 - - bf1f4994f104 - 0238f68ad641 - - 6d35a3780bfd - - 01d6b7d6365e - - 8ca3647c90fd + - 8627b2b383b4 - 8408bffd5616 + - 8ca3647c90fd + - 01d6b7d6365e - 3a7084316a6e + - 6d35a3780bfd + - bf1f4994f104 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -57,14 +57,14 @@ tools: - name: bcftools_concat owner: iuc revisions: - - 6b6c992d3a14 + - 9b5abbf50d23 - 81426b3cf18b - - f430a1ec7ee4 - - 08296952d12f - - d144af39073a - 62ca6da715bf + - 08296952d12f + - f430a1ec7ee4 + - 6b6c992d3a14 - 03e0645395d2 - - 9b5abbf50d23 + - d144af39073a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -76,13 +76,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - d37e313a41be - 95c6f3f4c77f - - e522022137f6 + - d37e313a41be - 147de996e34f + - 2363ef414c9b - 1829900b5dcd + - e522022137f6 - d3081540d175 - - 2363ef414c9b 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: + - 9b29129fb491 + - 09f37afb3621 + - 1137ce8efc1e - b14ff40958cb - 92c0aff8b53e - - 348cd212dbad - - 9b29129fb491 - cacc9970727a - - 1137ce8efc1e - - 09f37afb3621 + - 348cd212dbad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -112,12 +112,12 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 55c0e906c14c + - 4935320a59a8 - de68c11034f6 + - 367ba501b6eb + - 55c0e906c14c - ecc9192912b8 - - 4935320a59a8 - 1f2183a23823 - - 367ba501b6eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 039ea3f1dea9 - - 7cbf3c66d4ad - 6c790a091c7c - ae68ceb4cca3 - - f01b2c9506b9 + - 039ea3f1dea9 - 64a8f7dae3ad + - 7cbf3c66d4ad + - f01b2c9506b9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -146,13 +146,13 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 963a3635b2e1 - - 277719af4dd7 - - 6ea7170a016d + - e7452697afd9 - 33bd9301568c + - 963a3635b2e1 - cdb7b4927742 - - e7452697afd9 + - 6ea7170a016d - 656a916779fe + - 277719af4dd7 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: - - 3eac729e66c9 - - 26d97cdd5410 - - a1213a0b7b66 - - 5a321fab1fe4 - 501bfb078342 - - b7f0f59baa7e + - 5a321fab1fe4 + - a1213a0b7b66 + - 3eac729e66c9 - a29a2f40b665 + - b7f0f59baa7e + - 26d97cdd5410 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -182,14 +182,14 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 5f27e814a119 - - 97d19c008d15 - - 709dd8291b83 - c803c34361e0 + - 709dd8291b83 - 63aabc920911 - 81e4014fa809 + - 5f27e814a119 - d7d1663559e9 - 768d04526638 + - 97d19c008d15 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: + - 85ee7e6c4204 + - b1eba148b35b + - 2215287d5cc9 - af163c712539 - - 86296490704e - 7ba36babba2d - - b1eba148b35b - - 85ee7e6c4204 - b931e65638b8 - - 2215287d5cc9 + - 86296490704e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 4e1d23e5c691 - - 37757ffb4c5f - 03191140c66a - - 31ea13dfe5e6 - - ce9396ddcb2b - cf06b44624c7 - 5660b21a0dbd - - 9c711df3258d - f506df85c652 + - ce9396ddcb2b + - 31ea13dfe5e6 + - 4e1d23e5c691 + - 9c711df3258d + - 37757ffb4c5f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -240,11 +240,11 @@ tools: owner: iuc revisions: - ebb2e12a6de1 - - a404f786a94c - 021693fdadaa + - 48291658fdf6 - 19905c025d2a + - a404f786a94c - 6deb4d549bc9 - - 48291658fdf6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 71c78e0eea52 - 5ad5d4243987 - - c450406f722b - f7879f1e77f9 - - 97e8145d7e30 - - 69d8b7567281 + - c450406f722b - be6b217710af + - 71c78e0eea52 + - 69d8b7567281 + - 97e8145d7e30 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: + - cc7f9a4e186b - 2514e684f8a3 + - 89720ec3d58e - 52f9e4a660e3 - - cc7f9a4e186b + - d31a2e310a52 - 0fe007201caf - 79f7a1acc2cd - - d31a2e310a52 - - 89720ec3d58e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -293,10 +293,10 @@ tools: owner: iuc revisions: - 0a62420cb9cd - - 230e424bde67 - 1411bef27a75 - - 026a989b7cee - 75ddd081f608 + - 026a989b7cee + - 230e424bde67 - 80e6e399ccd0 - 99f4a81a47be tool_panel_section_label: VCF/BCF @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - c01be0ab9806 + - e493702b19eb + - 444e6a756c35 - 5acfca5a76af - - 5808f77b2bb6 + - c01be0ab9806 - ba20340426fe - - 444e6a756c35 - bca7ce81688f - - e493702b19eb + - 5808f77b2bb6 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: - - d52b8947b269 - - 12152af85697 - - 68fec03a63b7 - 157ffcdd3fa7 - - 7fe09ad6a939 + - d52b8947b269 - f2482aa4862e - 4d236c696844 + - 7fe09ad6a939 + - 12152af85697 + - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -346,13 +346,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: + - 0e5d11004815 + - 6f8e223f78f3 + - 8dbce095986c - cbe39e530cbf + - 27e2611639a9 - 8f2fc0ab30fb - 29ba253e2e05 - - 6f8e223f78f3 - - 0e5d11004815 - - 27e2611639a9 - - 8dbce095986c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 9708e3086f32 - - a367a15c6de5 - - a8630d4fbaf8 - - af36eb5418fe - e0a856def0b0 - 88bb477f45f7 + - a367a15c6de5 - 3ff5654b4e7d + - a8630d4fbaf8 + - 9708e3086f32 + - af36eb5418fe tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -382,13 +382,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 5c9729d54721 - - 96d0145c041a - 4ed46189d6c6 - - 03e30f06f15f + - 5c9729d54721 - 6ce175385dd9 + - 96d0145c041a - 2f4eef1f0d22 - 31c096c6b156 + - 03e30f06f15f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 2c4941386820 - - 09f5e45a8212 - - 46eb13bc2c73 - - a1aad8b559c6 - 262bba5b90ef - - 40daf124be88 + - 46eb13bc2c73 + - 2c4941386820 - 11af7fce71cf + - 40daf124be88 + - a1aad8b559c6 + - 09f5e45a8212 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -418,14 +418,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 743cd1472aeb - - 0594ea1417c8 - - 4b796b58938b - - 6cbb9c47795c - 882b2e649602 - - 8cb121b6a1d2 - f272b8ba0983 - 12038f59c0f4 + - 0594ea1417c8 + - 6cbb9c47795c + - 8cb121b6a1d2 + - 4b796b58938b + - 743cd1472aeb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -438,11 +438,11 @@ tools: owner: iuc revisions: - cced6715f926 - - 238f78e38a8b - 8c3ff4ef1190 - - dba06328556a + - 238f78e38a8b - eccb508bb678 - adee7e8b746f + - dba06328556a - 18cf9de1cf73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -455,13 +455,13 @@ tools: - name: bcftools_query owner: iuc revisions: - - e53501abf992 - - 3ce32adc55b2 - - 9f36041495a3 - - f64e7ca2efd2 - - e0ad88dec40d - c9935c9e8a24 + - 3ce32adc55b2 - a850902cac64 + - e0ad88dec40d + - f64e7ca2efd2 + - e53501abf992 + - 9f36041495a3 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: - - 79489d5685dd - - b7be725976b6 - - 8057cf55fa41 - - d43eb39b989e - d68c43202172 - fd3539749127 + - 79489d5685dd + - d43eb39b989e + - b7be725976b6 - 4db0695a6fc7 + - 8057cf55fa41 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -491,13 +491,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 1ccf0e7fb4f6 - - 6a636d58dfc2 - 5296d26b0373 - - 58091e1be01b - b0d39ef600a7 - - 78cd8b69da4c - bdc67eeb0bc9 + - 6a636d58dfc2 + - 1ccf0e7fb4f6 + - 78cd8b69da4c + - 58091e1be01b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -510,12 +510,12 @@ tools: owner: iuc revisions: - e8af591435d1 + - b17394940c7a + - '388983871932' - baa8823f8073 - a2f8dc22d7c0 - 4d3ce9dc1525 - b641062a2587 - - b17394940c7a - - '388983871932' tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,13 +527,13 @@ tools: - name: bcftools_view owner: iuc revisions: - - e6b5cbbf449b - - 3a233c8eb814 - - 3ca3de4e5291 - - 38d75661c235 - 59fa8742285e - d1f8f55f564d - abc3ced31cd1 + - e6b5cbbf449b + - 38d75661c235 + - 3a233c8eb814 + - 3ca3de4e5291 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -552,15 +552,15 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives owner: devteam revisions: - - a8a4f94aa321 - 57a16b310fe8 + - a8a4f94aa321 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate @@ -573,8 +573,8 @@ tools: - name: vcfannotategenotypes owner: devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -622,23 +622,23 @@ tools: - name: vcffilter owner: devteam revisions: - - fa24bf0598f4 - - eae7c08ebb6f - 6b935ab36d7b + - eae7c08ebb6f + - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten owner: devteam revisions: - - f285aa6bdcfb - b24e368ae7b1 + - f285aa6bdcfb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo @@ -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 @@ -679,22 +679,22 @@ tools: - name: vcfrandomsample owner: devteam revisions: - - 6257ee3b50d3 - 12b570dd0bc5 + - 6257ee3b50d3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - dd44c3f416c3 - 5b7120c66efc + - dd44c3f416c3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -724,7 +724,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 24baabc5f..259949bc9 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,10 +2,10 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - 78c75f134c16 - - 6e9aea89e388 + - 3f3e247c053d - c2ef298da409 + - 6e9aea89e388 - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: + - 133f36c29579 - fe3ca740a485 - b5d8e5475247 - - f29602ae449e + - cd2480f35935 + - 4f2967b27e67 - 44018dd6b447 - - 133f36c29579 - 1aae04680c4b - - 4f2967b27e67 + - f29602ae449e - 3e1f6f6d557e - - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -79,9 +79,9 @@ tools: - name: barrnap owner: iuc revisions: + - 7355bbf5e05f - 8fd427007e93 - fe48aa4ccd5e - - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -93,8 +93,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat @@ -106,8 +106,8 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 63662ae295d6 - d9c3016f7283 + - 63662ae295d6 - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -126,56 +126,56 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - 14f588312c56 - - b6b5cd37f2a2 - - 756376aeb1ae - 582fd74dc2a1 - 9f2455341fac + - 756376aeb1ae + - 3bbe70fef6df + - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 1691af4a0d17 + - 0ffe5be70caf - 73428a792541 - a230ea445788 - - 30fb23d4c31c + - 1691af4a0d17 - 989f7c061f35 - - 0ffe5be70caf + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - b69c46064ec7 - - 494f0bb4a993 - 5a5ae61da69c + - 494f0bb4a993 + - e94187d661df + - b69c46064ec7 - 30f08d74024f - 563a19373357 - - e94187d661df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - d6c7106b7b2e + - f77d7b685bb3 - 7abc5f6dd595 - - 1bc5a03faf2e - - f31125bb85ea - 2bba2ff070d9 - - f77d7b685bb3 + - f31125bb85ea + - 1bc5a03faf2e + - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d3af38b9c7e1 + - 52af33194019 - 520e30695ec3 + - fed64e676186 - 54961e026fe4 + - d3af38b9c7e1 - b3cf4684e9c7 - - 52af33194019 - - fed64e676186 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -187,8 +187,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 79261884facd - 07d7991bf205 + - 79261884facd - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,10 +201,10 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b + - ef2ad746b589 - 8b3e3657034e + - 602de62d995b - 43798b4caee0 - - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -229,9 +229,9 @@ tools: - name: interproscan owner: bgruening revisions: - - 98cafcbd2578 - - 74810db257cc - c55643c3d813 + - 74810db257cc + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -256,16 +256,16 @@ tools: - name: maker owner: iuc revisions: + - 3c1a01127868 - 370c210d9541 - d46d803ca6cc - - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 033755194fe9 - 624606f7c996 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -289,10 +289,10 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - - bf68eb663bc3 - d643e3b03500 - a17498c603ec + - bf68eb663bc3 + - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -311,8 +311,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training @@ -324,22 +324,22 @@ tools: - name: snpeff owner: iuc revisions: - - 8f92c2b26e6d + - 5b80f544c67f + - 68693743661e + - 5c7b70713fb5 - cfcf33df7fc0 + - 268d162b9c49 + - 8f92c2b26e6d - 9473cd297a76 - - 68693743661e - 5a29ab10dba6 - - 268d162b9c49 - - 5b80f544c67f - - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - - 2b3e65a4252f - 09d6806c609e + - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna @@ -358,22 +358,22 @@ tools: - name: tbprofiler owner: iuc revisions: - - e1a9d6fd258d + - 200c378d85f3 - ac8250086ac3 - - 809dfc93d593 - - ba6f87115e13 - - 037a11682176 - 45083d070fb8 + - 037a11682176 + - ba6f87115e13 - 37213cf56392 - - 200c378d85f3 + - 809dfc93d593 - 2c68b0c38785 + - e1a9d6fd258d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 265a9cdc6..849f1d65b 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,25 +2,25 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - 890b794c997d - 841084c5fc46 + - 8f1b150a2487 - 0e93176640ac - - a929ce596a34 - - fa5259cc561b - 553bfe8bd0b5 - - 8f1b150a2487 + - fa5259cc561b + - a929ce596a34 + - 890b794c997d + - 7547fcab5d19 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - ddddce450736 + - 067592b6b312 - 21e491ad532a - - b2860df42e16 - - 94fe43e75ddc - b9e31c5c01c7 - - 067592b6b312 + - ddddce450736 + - 94fe43e75ddc + - b2860df42e16 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -33,11 +33,11 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 3371c5bdc17a - - 5258e18bbe23 - faee8629b460 + - 3371c5bdc17a - a7f16f24e9a1 - 22286dab5aa1 + - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,29 +49,29 @@ tools: - name: busco owner: iuc revisions: - - bb935709506a - - 1e62c28ba91d - - 46ae58b1d792 - - 0d243f458b53 + - e824f5d958d0 - cf13a1e03e5b - - 2a5b8b9936bf - - 602fb8e63aa7 + - 41030a6c03b7 + - 1e62c28ba91d - 4048d82f0c88 - 5ecdeca79a0d - - 94170eee0ad8 - - e4bd1e99bacf - - 41030a6c03b7 - - e824f5d958d0 - 2dd755c1c6ff + - 0d243f458b53 + - 94170eee0ad8 - 1440ae06552f + - 602fb8e63aa7 + - 46ae58b1d792 + - 2a5b8b9936bf + - e4bd1e99bacf + - bb935709506a 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 @@ -83,36 +83,36 @@ tools: - name: flye owner: bgruening revisions: + - 3ee0ef312022 - 1ce9b1d72ec3 - cb8dfd28c16f - - 3ee0ef312022 + - 276f5d8712d5 - e27815e82dd4 - 8d4f03b5fe9d - - 276f5d8712d5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - 01210c4e9144 + - 3169a38c2656 - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - 8b330a577046 + - 06bcf65179fb - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - - 3ef480892a9f - 3fba9c77550a + - 3ef480892a9f + - 690c2caa367e - 5127a713de83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -125,21 +125,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 045c7c3d8e59 + - 6505bd37670d - 5f625c63b8bc - f3c89da3af16 - 60024a528cbd + - da9d8bf98802 - 366a11d316a7 - - 6505bd37670d - 2061fb3b81b4 - ec9e21e9c71b + - 5bec28269d95 + - 3f7be05a1597 - 0ee0c3089254 - - da9d8bf98802 - 41cea2aa2dce - - 3f7be05a1597 - - 9ef6920c3089 - - 5bec28269d95 - 71740308d412 + - 9ef6920c3089 + - 045c7c3d8e59 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -157,39 +157,39 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - - 7518ee87b53d - de387b2b2803 - 14ddfc8ffb93 + - a96f3ad4e0d8 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - 39edec572bae - - f8113c25bc6b - 9d79beb19ac3 + - f8113c25bc6b - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - eadfd71dde37 + - 29dabd8db6f2 - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f338e9942b27 - - 3ca2d2a9068c - - e731ea24e48d - 606b09cc9860 - - eb7a370f6588 - fd128c111ab0 + - eb7a370f6588 - 2ecf5a570907 + - f338e9942b27 + - 3ca2d2a9068c + - e731ea24e48d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -201,11 +201,11 @@ tools: - name: miniasm owner: iuc revisions: + - a7b889b90140 - 80d1250bd5fd - 8dee0218ac7d - - a7b889b90140 - - 8b6d0d85252b - 73a3846701e1 + - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -231,53 +231,53 @@ tools: - name: pretext_map owner: iuc revisions: - - 02831bf9e95f + - 511e5e3cd55e - dfb8a4497339 - - 2b16ba799da9 - d256a51a656b - - 511e5e3cd55e - - 8fef980d48b5 - bbe19ef04a74 + - 8fef980d48b5 + - 2b16ba799da9 + - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - - a315c25dc813 - 76d4cbefff85 + - a315c25dc813 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 875d0f36d66f - - 342a1d1fed7b - ebb0dcdb621a - - 675488238c96 - - 3061c8b029e5 - - 6fcbee531de6 - - 7594365c546b - 59db8ea8c845 + - 3061c8b029e5 + - 675488238c96 - 72472698a2df + - 7594365c546b + - 875d0f36d66f + - 342a1d1fed7b + - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e - - cd06929b224b - a199cd7ac344 - 39bed8de8017 - - d865b62f501c - 78c533842eeb + - aa39b19ca11e + - d865b62f501c + - cd06929b224b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 2b2a352488fa - 33b7d8481a76 + - 2b2a352488fa - f11b994b7eb2 - f8564b2d7f63 - 3edba9afc9bc @@ -286,19 +286,19 @@ tools: - name: rnaspades owner: iuc revisions: - - 53c2bc8c2ae3 - e122f9101584 + - 378e55aeeb25 - ef69617ecb42 + - 53c2bc8c2ae3 - 1d06c8b38e77 - - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - 9a22227bb6d0 - - ab5b7f6b7198 - ba7b0f11e470 + - ab5b7f6b7198 + - 9a22227bb6d0 - f77f7a7f3b83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -311,101 +311,101 @@ tools: - name: shovill owner: iuc revisions: - - f698c7604b3b - 196a599ec43d + - f698c7604b3b + - d9f6a00b6db7 - 83ead2be47b2 - - 865119fcb694 - ad80238462c1 - ee17a294d3a3 - - d9f6a00b6db7 + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - - 5e0825476fb7 - 5a0ddb4dc3a4 + - 5e0825476fb7 + - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 904bf932cf78 + - 051fd2db8a27 - 1fc82fe7ebef - 1bb12736175c - - 051fd2db8a27 + - 904bf932cf78 - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 808b3a0a6716 - - ad8b536d1caa + - d6e617c4e338 - 34305b013402 - fee85957cebe - - d6e617c4e338 + - 808b3a0a6716 + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - e5a3b75a271f - 21da31ed41a1 - - b8002c3f7141 - 8d4b90bf9caf + - b8002c3f7141 - 6b5a5842531e + - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 328aa71f0f3c - - 2a10645aeadd - 9de69775f512 - 86f66ab58e14 + - 2a10645aeadd + - 328aa71f0f3c - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 1708851f8804 - - 85fb02c43042 - - e41dcb0e913b - 6aad515a5270 + - e41dcb0e913b + - 85fb02c43042 - 340bc17f49cf + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d5fb354f745d - b65a43f70b99 - - b3490b036c5a - 249f6a28c751 + - b3490b036c5a - d159735a6a9f + - d5fb354f745d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - d2d1df21dfb9 - - 9006e5836729 + - 7897763d14ec - dd7ad84f3943 - - b7829778729f - 33368fec3b70 - - 7897763d14ec + - b7829778729f + - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - 505a9833ab5d - - 6f4c8ad6ea01 - - 8f631679571f - 189e837009c9 + - 8f631679571f + - 6f4c8ad6ea01 - ced385aa976d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -413,73 +413,73 @@ tools: owner: iuc revisions: - 19bdfd1e6fe3 - - d40ed4eb0c0e - 9ded6109434a - - 356afed970b4 + - d40ed4eb0c0e - e59bee4565b3 + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b + - b23249f81bc4 - 80a17897564d + - 6dd935e4984b - ebd801e712bc - 4688ae3b49b5 - - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 937ea677d437 - - cb1e3db43020 + - 59bd28f6265d - b5e35a2ca4f3 + - cb1e3db43020 + - 937ea677d437 - b64696992ee9 - - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b - 05bd7504fdb2 - - 383bb5ad32e2 - 6015aa0303f2 - 2628f6790eda + - 383bb5ad32e2 + - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - 8f9f06995f98 - - e92675014ac9 - 6e26c9afd301 - - 0a3a602cd1e3 - 9e3e80cc4ad4 + - 0a3a602cd1e3 + - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 920677cd220f - 08256557922f - - 5da9a0e2fb2d + - 920677cd220f - 8d09f8be269e + - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 82398ba86ba7 - - 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 9ba37af21..68c5dd813 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,24 +2,24 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - ded48b36f3b7 - - 1f5641a52664 - 31812e7a1315 + - ded48b36f3b7 - 8e8dc9a1e3e5 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 24a7a95867b0 - - 17fcac7ddf54 - 5c8ff92e38a9 + - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 70adf3e9d..05eb64807 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 204a131e47db - 159b04e36791 + - 204a131e47db - a9c9d768b751 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 6a51bdf32..7b2c91778 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - b28e0cfa7ba1 - - a1a923cd89e8 - - 589e7e57fd6d - - a8eabd2838f6 - - ce3c7f062223 - - a68aa6c1204a - - 87ee588b3d45 - e19bebe96cd2 - dde39ba9c031 - - 0a5c785ac6db + - ce3c7f062223 + - a68aa6c1204a + - 589e7e57fd6d + - a1a923cd89e8 - 07e8b80f278c + - 0a5c785ac6db + - a8eabd2838f6 + - 87ee588b3d45 + - b28e0cfa7ba1 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index 2f8127629..0ce3add98 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,29 +8,29 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - - 54f751e413f4 - f921014aba5a - 62c9df8382c2 + - 54f751e413f4 + - e8ac2b53f262 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - 6f386c5dc4fb - - acf4e47b734c - 2889433c7ae1 - - 0e3cf9594bb7 + - 5edc472ec434 + - a52d2d93e595 - d999e774072a + - 6f386c5dc4fb + - 0e3cf9594bb7 + - acf4e47b734c - e25d3acf6e68 - - a52d2d93e595 - - 5edc472ec434 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 7754df683..f794e203f 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 095ad4d096d1 - - 6ca543ec1bf8 - - c8cdde00b105 - - da6bd1975a71 - 27ee142314a9 + - da6bd1975a71 - f4230f116196 + - 6ca543ec1bf8 + - c8cdde00b105 - 710301bc46fa + - 095ad4d096d1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -80,8 +80,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: enumerate_charges @@ -106,31 +106,31 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 - - bfb65cb551d8 - - 0fac8e2afc13 - 88076940fa94 + - 3b8a9d5ced85 - 79cfd9ead848 + - 0fac8e2afc13 + - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - d532b7e5f64b + - b46d4b4d995c - 55918daa5651 - - f5d979cb4b54 - 715cd0e87781 - - b46d4b4d995c - eb6564a60136 + - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - - 5579659312e6 - fdf2cc80adb5 + - 5579659312e6 - f26afd1b7104 + - d2f955aea23a - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -138,52 +138,52 @@ tools: owner: chemteam revisions: - bc31d02be922 - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - 4da9ee404eab - - 070e3ecc3fda + - cac1886249a2 - ed736e6eee39 - 2c349b027a01 - - cac1886249a2 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - 73008ef1f487 - - 525ca7c8065f - - d1f803b5943c - c0c9a5024177 - - 2e219a2d9327 - - da8753545526 + - 525ca7c8065f - f197e34c33a9 + - da8753545526 - 807aa4c9293d + - d1f803b5943c + - 2e219a2d9327 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 - - 2c8ed1b52bf7 - - 27ea4e1a3f95 - - 61094e01eff9 - 1809414a9454 + - 27ea4e1a3f95 - 7568ae18908a + - c4fbab8e03c5 + - 61094e01eff9 + - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - d7ec25187599 - - 730ef07b90ae + - ba83f0923369 - 79e8ab8f1e81 - ccfbd956a2d3 - - ba83f0923369 + - d7ec25187599 + - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -234,10 +234,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 - bf99565cec1f - - 9b48456a96fe - d4c67ced6abc - - 85fad59f8168 + - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index a9358ee21..e5cfe2e4c 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - fa56d93f7980 - c97a786e8fb5 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,31 +16,31 @@ 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 + - 424aefbd7777 - 640d3af5d833 - - 495a4173006f - 86e2413cf3f8 - - 424aefbd7777 - - f5d67c722d67 + - 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 owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index a97c186cd..d19293e84 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - 830961c48e42 + - 33151a38533a - 25136a2b0cfe - 90981f86000f - - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -25,15 +25,15 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - 0046692724f9 - baabc30154cd + - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 0d8580879..7d42a6743 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,30 +8,30 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - dad9da48a09a - - e3cbd2287f63 - - f3a19509108a - 6ef0b5664c69 - - 5e1240a87bcb - 0b3c3ad92827 - - 367b1ed91207 + - f3a19509108a - 4a6ee918c13a - a3b86937ead6 + - 5e1240a87bcb + - dad9da48a09a + - e3cbd2287f63 + - 367b1ed91207 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - bd46669113b9 - 33c99804a32f - - 1b5fc03380d4 - - 72ed72122deb - - a4db66553a61 + - 54ccb7e1f49a + - e177a8ea0bf1 + - bd46669113b9 - e525f9ffb9ac - 584008e574b2 + - 1b5fc03380d4 - 501c21cce614 - - 54ccb7e1f49a - - e177a8ea0bf1 + - 72ed72122deb + - a4db66553a61 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -49,30 +49,30 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 77b41c89d856 - - 8979c288aefb - 186b8d913e6c + - 8979c288aefb + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -85,8 +85,8 @@ tools: owner: devteam revisions: - 154d00cbbf2d - - 3e436657dcd0 - 4dea02886337 + - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -117,18 +117,18 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - 26c6706bfb07 + - b9b385097f13 - 63769c4217a7 - 92ac8e086317 - - b9b385097f13 + - 19e45916daf9 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 2f5720491..a877d883c 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -3,204 +3,204 @@ tools: owner: bgruening revisions: - c929a006727f - - 5f6d123679f4 - - 268e91e540ee - e821645ef8fc + - a1ca9bccc7f2 - de72ba3ed6f2 - 29451af70c52 - - a1ca9bccc7f2 + - 268e91e540ee + - 5f6d123679f4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e143b4c3987 + - 7a7fd0f5f15d - 2d2cf5c1ea8a - 0e49b109abc2 + - bb1e4f63e0e6 - 5d11599b8a7d - 12af64f93288 - - bb1e4f63e0e6 - - 7a7fd0f5f15d + - 0e143b4c3987 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - c06951d10364 - - 7c1beb6d6eca - 1d848bc4585f + - 7c1beb6d6eca - 81b1e3e1fc6c - - 195e98217334 - dc059492a995 + - 195e98217334 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 71aa86af6762 - a67ac707496a - - 93eb012d9eed - - 3d211717a775 - bfff7454b59a - - 07418a30ed01 - 26e7304d6737 + - 71aa86af6762 + - 93eb012d9eed + - 07418a30ed01 + - 3d211717a775 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - dd0b7398bb96 - - 2bc10a9ca58b - - 26983857c91a + - 56d5b797ce84 - 5be24eba848d + - 2bc10a9ca58b - 29fcfd36e90a - - 56d5b797ce84 + - 26983857c91a - b8858746dc1f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - ee3a1b0f45f1 - 7ef978dc1b8a - - 9384cd033f30 - - 7e6bcd2e5128 - - 72bfafe3330b - c3e012dfe21f + - 9384cd033f30 - e6d0bff01239 + - ee3a1b0f45f1 + - 72bfafe3330b + - 7e6bcd2e5128 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fb9cf9c97ec4 - - b73e213add0c - d9a637e83828 - - 514fa53b5efb - - 9470f29702f8 - 167788df3b46 + - 514fa53b5efb - a60c359ec43c - fd1275e01605 + - b73e213add0c + - 9470f29702f8 + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - c34d11ea4ba6 + - 86febdcc4283 - ca0616bb2cdf - - a02cfa31e9cb + - c34d11ea4ba6 - 2c37ce318bc3 + - a02cfa31e9cb - e479c7ca5570 - 5bffaa8354a1 - - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 004aea905d4d - - 192ef85c0b0b - 78f405266706 + - 2d466b530754 - 01fb6a7654e6 + - 192ef85c0b0b - 1fcb7adc39b8 - 69a8621ca2f0 - - 2d466b530754 + - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 - - d580d6acd1df - db940c262830 - - 459cfa861f0b - 3c9f0c486cca - 137c4beed34b - - 9ecba5e225a6 + - d580d6acd1df - 2f9e4843f480 + - 9ecba5e225a6 + - 459cfa861f0b + - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fbe773640707 + - 32e451def88c - bd7db9e2f2cb + - fbe773640707 - fd408d755394 - 2c66e43f1c86 - - 32e451def88c - - f264afa9fa6f - bad3ca889618 + - f264afa9fa6f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 3b9d990a0a0e - - 7fda5607e777 - 56bce3c82278 - - 7e361d147872 - 4e12ea27f788 - - 9368fbc49c8b - 231994413f89 + - 7fda5607e777 + - 3b9d990a0a0e + - 7e361d147872 + - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - ce4ce3316f74 + - c03c3384cd81 + - b1779366c8e9 - 94ca68515826 + - ce4ce3316f74 + - d9114ef1c8a5 - 4431f39ede55 - - b1779366c8e9 - - c03c3384cd81 - e65d16fb2724 - - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - f8fc4e5aff9d + - 4ed32329e0ed - b88ebb3672a1 - 23f7c5f1fdaf - 793665fff0f8 - d57251071381 - 2da482e408b8 - - f8fc4e5aff9d - - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - e4c7985d4585 - 25d830337d31 - - ba6efa77fb79 - - c60570fa602f - - a4dfb122e52b - - 010e58e9d822 - a7849312d328 + - a4dfb122e52b - 512155688d98 + - c60570fa602f + - ba6efa77fb79 + - 010e58e9d822 + - e4c7985d4585 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - 4d678170d29b - - 00d869ea03a1 - - 69264da0ce77 - - c899e0ccff8c - - aa200e4f3939 - 38e3f226248b + - aa200e4f3939 + - 69264da0ce77 + - 00d869ea03a1 - 443d9a9d6d11 + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 10301d137111 - a2d70c4fd406 - - d806504e96d9 - - 6662b1a8d326 + - 10301d137111 - aac8444d6681 + - 6662b1a8d326 + - d806504e96d9 - c361b12d207a 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 d3712dc89..e76f8140e 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: - - 7d16de45c021 - 12baadec7809 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,15 +23,15 @@ 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 diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 90da8fd01..df5ff4121 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 - 63dd26468588 - - dba489bfcd62 - 832c20329690 + - ce385837c160 + - dba489bfcd62 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 9e5b4b27f..85a3f9836 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - - 29bdbc353f20 - d82648ad25a3 - 62f5fab76dfb + - 29bdbc353f20 + - 6da3972210ee 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 1fbdeb1cf..e0eff1f22 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,37 +8,37 @@ tools: - name: cutadapt owner: lparsons revisions: - - c4b82dce8335 - - 093678460093 - - 44e2cc14f75b + - 135b80fb1ac2 + - 5915ea1ec9b1 - 8c0175e03cee + - 49370cb85f0f - 660cffd8d92a - - 8665bcc8b847 - - 4e5056fefd88 - - e4691e1589d3 + - 44e2cc14f75b - de6cebe3c043 - - c5e2e5902201 + - 4e5056fefd88 - 288f97432497 - - 135b80fb1ac2 + - 093678460093 + - c5e2e5902201 + - e4691e1589d3 - c053d4cad713 - - 49370cb85f0f - - 5915ea1ec9b1 + - 8665bcc8b847 + - c4b82dce8335 - 48f587c13075 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - f666895cbebd - 8889eb864cef - 9db07fd39f85 + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - - 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 - 859422bcb689 - 516b97a23d7e + - 9457a20156db tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -71,9 +71,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - - ec0b5076173a - f81d4362b6c1 + - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -81,8 +81,8 @@ tools: revisions: - cd0874854f51 - 0dbb995c7d35 - - 9c620a950d3a - 56022eb50bbd + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -96,8 +96,8 @@ tools: - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - b05e39b9c170 + - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -124,15 +124,15 @@ tools: - 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 @@ -153,16 +153,16 @@ tools: owner: devteam revisions: - 249c8393f2d4 - - 35e38452bb3f - e39cc71d3ed6 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - 74db4cffab1f - - 045f0e1043f7 - 54053ea6c77e + - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -189,61 +189,61 @@ tools: owner: devteam revisions: - d5e9e83cd3d8 - - 567d5b3c52b1 - 529bccd5e4a1 - 09070cacefd8 + - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 0b7ec11b3c7c - 4bedca26c133 + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - 90858c306551 - - cb1e251cac37 - 736b8f6ee456 + - cb1e251cac37 - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - - 421f0af4ee95 - 07497255281e + - 421f0af4ee95 + - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd - b29d37ca9e41 - - f984bb114520 - 3599f5451ee2 + - 02f8a17a4ebd + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - 0c2907307ba4 - - e246088b6e34 - 177f0621c266 - 6027ef51ef91 + - e246088b6e34 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 377ac2829eac - 73194cdd4f57 - 547e8d00f11c - 61b4cedc8934 + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -262,22 +262,22 @@ 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 owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -290,11 +290,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - e654095ab143 - 8250ea3a1501 + - 24013bf85a6f - a535cf1e5da4 - b557acca0b56 + - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -307,10 +307,10 @@ tools: owner: iuc revisions: - 9fa7803d1c51 - - 7accf7407811 - - 828dba98cdb4 - - 6a675c3aa610 - f3759eec3018 + - 828dba98cdb4 - 27ac32a22ad2 + - 7accf7407811 + - 6a675c3aa610 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 1f9ecd1e4..e2cb93c60 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: - - e41385662e5e - - 64e9a6afdd0c - ce9cd02d5b88 - 7b4468117008 + - 64e9a6afdd0c + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,13 +18,13 @@ tools: - name: fastqc owner: devteam revisions: + - e7b2202befea - 5ec9f6bceaee + - 3d0c7bdf12f5 + - f2e8552cf1d0 - ff9530579d1f - - e7b2202befea - 2b0c9d9fc6ca - - 3d0c7bdf12f5 - 9da02be9c6cc - - f2e8552cf1d0 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -37,39 +37,39 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - ad116ae3f4d9 - b6b54ba71bd8 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - 7306ec78632a - - 59003d0543cd - cc0fd298cc17 + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 1f296803dfa3 - - 8880fb74ef56 - a72af9de6bf5 + - 8880fb74ef56 + - 1f296803dfa3 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - abfd8a6544d7 - - 75c93c70d094 - 3d93dd18d9f8 - - c1a4b5f3b432 + - bf675f34b056 + - 9a913cdee30e - 5e33b465d8d5 - b2f1f75d49c4 - 1c2db0054039 - - bf675f34b056 - - 9a913cdee30e + - c1a4b5f3b432 + - abfd8a6544d7 + - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index d934ded82..5cce5f4a7 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -16,7 +16,7 @@ tools: owner: peterjc revisions: - 85ef5f5a0562 - - 141612f8c3e3 - 83a19df00eab + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 15ffefd3d..086947d83 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,30 +16,30 @@ tools: - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - 0c8f7322f8fc - 8f53b238a360 + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -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 @@ -79,23 +79,23 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - cf61daf064fe - 45296e47d565 + - cf61daf064fe - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -108,8 +108,8 @@ tools: - 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 @@ -122,16 +122,16 @@ tools: - name: gemini_query owner: iuc revisions: - - da74170c55c7 - 840fb4850be3 - 666f60a9331a + - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 095be2eba..2a6e45eeb 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 094a7a615..a95a5c639 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -3,55 +3,55 @@ tools: owner: galaxyp revisions: - b39347891609 - - 983bf725dfc2 - c1b437242fee + - 983bf725dfc2 - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - - 1c58de56d587 - 28587613264f + - 1c58de56d587 + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 4317d3cb6cba - - e08a7ad4378b - - 7068f48d0ef9 - - 6ea73833cf67 - - 4df8de2d0e48 - - e407b9da183a - - 83c7d564b128 - c441583adae5 - - f5ea3ce9b9b0 - - 734abc7ac21d - - 5e6237d58b0c + - e407b9da183a + - 6ea73833cf67 - 653e89d73fc4 + - 69ebb7f46e45 + - 734abc7ac21d - aad3885b3216 + - 5e6237d58b0c + - 4317d3cb6cba - 6591f049cf7e + - 83c7d564b128 + - 4df8de2d0e48 - 9a776b080193 + - e08a7ad4378b + - 7068f48d0ef9 + - f5ea3ce9b9b0 - 1790dcf3c32d - - 69ebb7f46e45 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - 7863f1abcdda - - 9aaa46d45472 - 34758ab8aaa4 + - 9aaa46d45472 + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - 054483e27a35 - - bfdc6a7ffd3a - 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 3eb22f9c6..47c7db458 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - c4bde687c846 + - a64dc31ab7f2 - 740057a5126d - - fd59d783248a + - ae9994cf526f + - c4bde687c846 - 290a11559985 - - 7f13dc906cb9 + - fd59d783248a - 4b519282a05b + - 7f13dc906cb9 - df7356989ac1 - - ae9994cf526f - - a64dc31ab7f2 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: + - f95284aa2946 - 867ab348287d - 7cf5b1d072b5 - - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,31 +42,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 3b37b1b1c3a7 - '566197475670' - - ca7cb0eaad62 + - 3b37b1b1c3a7 - 53460afd5115 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 391a4cc45fea - da4c086cff5b - 3d059e9c2fba - - 10515715c940 + - 391a4cc45fea - d3a9e32672ec + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - 5fe1dc76176e - 3b12bf9b4b87 - e3a675da7fd0 - - 299307abd804 - d0fc8b746d57 + - 5fe1dc76176e + - 1acf88921176 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -78,8 +78,8 @@ 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 @@ -99,16 +99,16 @@ tools: owner: iuc revisions: - 6cd09d7b5f37 - - 667e17248bfe - - 4542035c1075 + - 1cfc579079a6 + - a6e57ff585c0 - fd5dbf0f732e - 2bb2e07a7a21 - - a6e57ff585c0 - - 112eb40ba6cf - - 836d1aa3e89a - - 1cfc579079a6 - - 17359b808b01 + - 667e17248bfe - ca2def38369c + - 4542035c1075 + - 17359b808b01 + - 836d1aa3e89a + - 112eb40ba6cf tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -126,9 +126,9 @@ tools: - name: pathview owner: iuc revisions: + - f1691de443a7 - fe154a7af404 - 03c13085aecc - - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -140,15 +140,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - 62e3a4e8c54c + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -160,9 +160,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: + - 7c9417381ad5 - 44c66e8d21e6 - 0a10fddd97d2 - - 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: - - 14e7c35f3d00 - - 360df4999907 - a1abfa420d9d - 2824d77cd8f8 - 7dd841a32245 - 326a3db8d9d1 - 59fd173ac850 + - 14e7c35f3d00 - 4ac4e7083b7e + - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - 73b8cb5bddcd - - 83c573f2e73c - 44608d0193ed + - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 315f3ddde..96df62355 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,10 +2,10 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - ed2cca6b5de4 - 29f66c353bcb - - 921a2da49a0c - 9edf8894a22d - - ed2cca6b5de4 + - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads @@ -13,34 +13,34 @@ tools: revisions: - ec4b948dc6f0 - d404277cc87a - - 5746d61f0a91 - 78fb5e286609 + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - 977dc15add20 + - 9e357a8b2ec3 - 4d511437b1e5 - 03dd3c16ae4e - - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 77919cc3618e + - 41dbf4d162a2 - 0ba4f56a3613 + - 77919cc3618e - 3b5b54ed6392 - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - - 7babd8a46fe0 - 5308ca68ef3d + - 7babd8a46fe0 - b63363075c2e + - 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 f5f3a1eb3..6a1197a44 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -3,8 +3,8 @@ tools: owner: imgteam revisions: - 3df9f0a4bf34 - - 0c777d708acc - 81f0cbca04a7 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -31,15 +31,15 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - f70b215d155c + - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - 85edbb7a436b - f3360fbeda64 + - 85edbb7a436b - b07f4839ca77 - 10eed33aa9b2 tool_panel_section_label: Imaging @@ -47,15 +47,15 @@ tools: - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - b58447a2eed2 - 5bf8eb50b280 + - b58447a2eed2 - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -70,8 +70,8 @@ tools: - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common @@ -85,136 +85,136 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - - df3ad3ba5c6f - ef4aed1d34c4 + - df3ad3ba5c6f + - cdf8e3c57dae tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 2484086dee41 + - 6a7da2e5f696 - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: + - f24c370e5ea4 - f8fa0f6718a3 - d0178bdcd00e - - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 3245681b2f6d - - ad271f78a87a - 31d195bedf6d + - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - - c09dcda1143f - ff1a86a87364 + - c09dcda1143f + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - 667a513e67e4 - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - - ac5bea85a391 - a1a961c46d4b + - ac5bea85a391 + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - 91e03287f285 - - a32c3f810ade - 20dbb1f7ec7b + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - 6f4715b8540a - d3890df07463 + - e972e07c7845 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - 980aed9e8fd5 - 407925835dd9 - e52c75a28c4b - - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - - d85f11570109 - acf3aa487283 + - d85f11570109 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 035a58c7f54a - 80b200ae516b - b76841ee5560 - - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - 91560258e972 - b44b081bcf37 + - 91560258e972 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: + - 48102a685037 - 3a3033222f61 - 8083a87d2fdf - - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images @@ -234,14 +234,14 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 440504fea..e9ce965e5 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 - - e4ee04da1c19 - - 1069f6db0a0e + - 78bbd17d0703 + - 3e4f434a69c6 - a38934e303b9 - - d6e72da3ec35 - f362150bef41 - - 3e4f434a69c6 - 17f911830a8c - - 78bbd17d0703 + - e319b5b65879 + - d6e72da3ec35 + - 1069f6db0a0e + - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 8f8df367470d - 9537184d421f - - 0135f1d487a0 - - 72ddd32392cd + - 8f8df367470d - 2b95d5c04908 - 7fe36019c073 - - f91cfb73d369 - 1ef5b6e3e09d + - 72ddd32392cd + - f91cfb73d369 - c88553ec696e + - 0135f1d487a0 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - fafb3d685fa9 - - ad0dc9f4c9e2 - d7e79eb3bcb3 + - ad0dc9f4c9e2 - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee29337f905c - - 3d18f8c3c0f6 + - ee2beb764a7b + - 69797fa273c3 + - 28a6f1908fcc + - 7f1cfa4c0e32 - 8d36959b000d - - 9eaadf03e0df + - 8c05afb547fa + - 6a1515bb0687 - 94df24c6bc00 - bd2a7d1316b9 - - 28a6f1908fcc - - 69797fa273c3 - - 8c05afb547fa - - ee2beb764a7b + - 9eaadf03e0df + - ee29337f905c + - 3d18f8c3c0f6 - 43aac8d29685 - - 6a1515bb0687 - - 7f1cfa4c0e32 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 0893a1dbb807 - e3bb03cf207a - - db536ad45f28 - - bcaa0d571ce2 - - c092052ed673 + - 9f978da6528a - cb903c9dc33d - - 5671e1d3d5ee + - 8858fa037a15 + - db536ad45f28 - 5d6ed46cc101 - - 9f978da6528a - 364f4ffec275 - - 8858fa037a15 + - 5671e1d3d5ee - d37ede8589b2 + - c092052ed673 + - bcaa0d571ce2 + - 0893a1dbb807 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - ed28dd32141c + - 38b91a3190cd - f95f403841ad - - 49236b03e4fd - - e1a015876aa9 - 230b05597996 + - 12d66d0d05ac + - e1a015876aa9 - 045d6d00f606 - - 38b91a3190cd - - 3b6a16d82c1b - c5c9f02b6167 + - 49236b03e4fd + - 3b6a16d82c1b - 584beffa972b - - 12d66d0d05ac 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 ec3febcd7..b047cac4e 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,10 +2,10 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 - - f198773344e4 - 0f1724dd59d2 - b8a457820315 + - f198773344e4 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose @@ -13,8 +13,8 @@ tools: revisions: - ac092723240d - 22c2a1ac7ae3 - - 374cb875d38a - a513e3fbb4c5 - ba0c40780ecf + - 374cb875d38a 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 aa72129b0..9cf4ed542 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -3,16 +3,16 @@ tools: owner: bgruening revisions: - 66d7efc06000 - - 772e0e89fc68 - 522137aaa9c4 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: + - f22a9297440f - 4d81e3e2fb63 - 8a794e6d3388 - - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval @@ -20,81 +20,81 @@ tools: revisions: - 818f9b69d8a0 - e1317b5502fa - - f1b9a42d6809 - b6ef6d0cb6b7 - 2af1346e68c9 + - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - 1588f9076e32 - - 05143043ca13 - 947c2eacccb8 - - 8334dc98c48e - c80db5d6fd8c + - 05143043ca13 + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 83228baae3c5 - - 1552b8cb4a94 - - 25b46af53232 - 9991c4ddde14 + - 25b46af53232 + - 1552b8cb4a94 + - 83228baae3c5 - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - - a07ab242b0b5 + - f3dfa4bdf87e - 060ca94ac049 - 1a53edc4b438 - - f3dfa4bdf87e + - 53616c8b0865 - 841a6cc5fc58 + - a07ab242b0b5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 927586a18553 - - 91c4e3331208 - - d4808d5b83da - - dc4b5fd604a6 - 40f4447733b2 - 2fc89dcd41c8 + - d4808d5b83da + - dc4b5fd604a6 + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - 25ab6b4e376e - - 7626ea9c2e1b - - c6ae57f774c6 - - e5a5ad882f1f - 301e07345c93 + - e5a5ad882f1f + - c6ae57f774c6 - 36e8d6d5d01b + - 7626ea9c2e1b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 80852884053f - - 4ed102b922cb - f9639b488779 - 0630258dcf35 - - b7c3e9a3b954 - 02d2be90dedb + - 80852884053f + - b7c3e9a3b954 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - - 61634a87efc7 - ec69cbe34b73 + - 14180f9c831e - caeb57858702 + - 61634a87efc7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 73976cb4d..ddffe9407 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: + - f6877ad76b00 + - 17062a0decb7 - 937aa69e715f - cd659e8cc5fa - - f6877ad76b00 + - a6d65b0c67af + - 017aba02828d - 3ba8d4563129 - 749c918495f7 - 03e9b2fbc005 - - 017aba02828d - - a6d65b0c67af - - 17062a0decb7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -22,18 +22,18 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: + - dfd8b7f78c37 - 3fe632431b68 - - 64f11cf59c6e - - 53646aaaafef - e188dc7a68e6 - - dfd8b7f78c37 + - 53646aaaafef + - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -46,42 +46,42 @@ tools: owner: devteam revisions: - e7f19d6a9af8 - - 37b497aa133f - - 60afcc2c1d05 - 2ff111fac1d7 - 3e1ea2facca6 + - 37b497aa133f + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - be1d967337e4 - 77b2770508f6 - - 037c6e54df11 + - b3eab4b67562 + - 53c0b7a1a0c3 + - f54f5baedfdd + - 6b1e195506a3 - 09b53c1d4ab1 + - 037c6e54df11 + - 3f4d6399997b - 11a0d50a54e6 - - 53c0b7a1a0c3 - 8c6cd2650d1f + - be1d967337e4 - c0c2d0941de8 - - f54f5baedfdd - - 3f4d6399997b - - 6b1e195506a3 - - b3eab4b67562 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 13022c3d3076 - - 00fbfac99d39 - - ec9cbd6b9a49 - - b8f5f6e87f5c - 5ef7ec16b04f + - e403d27e8f24 + - 00fbfac99d39 - 1cd2511a396e + - 9ee34ba73ebf + - 13022c3d3076 - 79b885ce78d7 + - b8f5f6e87f5c - 178bdbdb6d24 - - 9ee34ba73ebf - - e403d27e8f24 + - ec9cbd6b9a49 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 cb3635494..26deb9968 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -23,9 +23,9 @@ tools: owner: iuc revisions: - 63f86089423e - - 76d3d2b10738 - - 5b5a7af9fbb4 - 7c2100246a2f + - 5b5a7af9fbb4 + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada @@ -33,70 +33,70 @@ tools: revisions: - 96336c6a2bb7 - 84fd33a60b35 - - 1c35dadbe76f - 18a502a9d287 + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - f732237754fc + - a9f4a217dcd6 - addaf9d22850 - 34e55239e68b - - a9f4a217dcd6 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 8c202e741d68 - - 75403243703a - 04c15826a0b8 - 0776d824d896 + - 75403243703a + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - e96bbb9e24ea + - 8470de786d47 - 1c9b3bcd4261 - 43c99742158b - - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - 5c865a382933 - - 306a40d4bb8f - 84743da21318 + - 306a40d4bb8f + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 555ccac8a4c5 - - ac72310b038a - - 8daf4564ccda - 78faebd0879c + - 8daf4564ccda + - ac72310b038a + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - f947b4bb5107 - d60df8727f59 - a58e4a43f49c - 7b8cb2b02978 - - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7136e9ab70db - 1bc3657cd694 - 7f3b59dee073 + - 7136e9ab70db - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,38 +105,38 @@ tools: revisions: - d943081510da - 0a1224c4b781 - - 19299bb1c6af - 9058d8943303 + - 19299bb1c6af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: + - c4db8c4de66f - 6501b5b33988 - dbf1798c0dcc - - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - fa35f1106d3e - 15dbb444df71 + - fa35f1106d3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 6c84982ee6f7 - 6d364c65c946 - 654548ae1357 - - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -148,17 +148,17 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - bd7a9c6efb10 - 6aad8ca3918b - e66ab198ec15 - - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - b084117133af - c6676a890f50 - d77397f09da1 + - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -178,40 +178,40 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - c409a495841f - 31c6d107e7a5 - - 79706f10d680 - e88b731dad59 + - c409a495841f + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 - - 714d5a28cc5c - - 172920f67a84 - 094ad9c068af + - 714d5a28cc5c - d24841f5c3d2 + - 172920f67a84 + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - a293a742194f - - a4d7148ccee4 - 12fb63b5f63f - 4137b492233e + - a4d7148ccee4 + - d7e9a3c41657 + - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - 6fcb8ac37a3e - - cf87759761eb - 97f7bb0851e7 - - 64bc7acc22a9 - e2c71b852aba + - 64bc7acc22a9 + - cf87759761eb - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -219,18 +219,18 @@ tools: owner: iuc revisions: - 4033827c76b8 - - 5e5a999ffaa9 + - 2d35528d2141 - 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 + - 6b7622dda516 + - 2cd76b089570 - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -291,16 +291,16 @@ tools: - name: kraken2 owner: iuc revisions: - - e674066930b2 - - 4a9da2b6c2e3 - 328c607150ff + - 4a9da2b6c2e3 + - e674066930b2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - f03c7ba8d8bc - 50bd98b3ae5a + - f03c7ba8d8bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -312,15 +312,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1902d3de4a4f + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -370,19 +370,19 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 0270541aaf46 - 4fd3b5d8706b - e073891b2afc - 27250f92a01a - - 0270541aaf46 - 2cff76cf35c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - eb50e7eca3dc - 76bc4efa1aeb - 708abf08a626 - - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -455,13 +455,13 @@ tools: - name: metaphlan owner: iuc revisions: - - 6dee4abadccb + - a92a632c4d9b - ff8f55893e7d - - 2131d7dca455 - - a16313517e55 - b89b0765695d + - 6dee4abadccb + - a16313517e55 + - 2131d7dca455 - 1a6cdf55390f - - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -552,8 +552,8 @@ 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 @@ -571,20 +571,20 @@ tools: - name: staramr owner: nml revisions: - - 3b22de20bd4b - aeaa20b96ef2 - - 4d83eccf5f81 - - be818ae858e4 - 4b9a8031ab74 - 2fd4d4c9c5c2 - 141afacabcfa + - 3b22de20bd4b + - be818ae858e4 + - 4d83eccf5f81 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - 9495df9dd6ef + - 576963db5f1b - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 63a07202b..2274dc82a 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 4e9136c2c4c3 - ab12df91b47f + - 4e9136c2c4c3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 9f6f631b7..d03c60778 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: - - 2263989660f5 - - 48c13389050d + - 94b8c6013083 + - 80f03df2e2ce - bdfbaf0c10aa - cd07731e4434 - - 6ae5a7b5a0a2 + - 8b67dd48fec1 - 9eeb13a92d79 + - 6ae5a7b5a0a2 + - 2263989660f5 + - 48c13389050d - 9422c5a87ee2 - - 9baa871cb1d1 - a74dbfee5a86 - - 94b8c6013083 - - 80f03df2e2ce - - 8b67dd48fec1 + - 9baa871cb1d1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 5abf2c2249aa - - '764845535798' - - f14193ec1f50 - fc2e49f91e52 + - f0af8936ed41 - aaa0d6a8b808 - - 2e093badc689 + - '764845535798' - c18157c68134 - - bc3831dd65c1 + - d390fe1567dc + - f14193ec1f50 - 4a60927aaca5 + - bc3831dd65c1 + - 3ff17bad4006 + - 2e093badc689 - be78f13134e2 - d7ce0ec78e51 - - f0af8936ed41 - - 3ff17bad4006 - - d390fe1567dc + - 5abf2c2249aa 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: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -64,12 +64,12 @@ tools: - name: mafft owner: rnateam revisions: + - f0d493f8f84f - 15974dd17515 - - f1a5908ea2cb - - a65296ffb4a0 - 6f28e90db932 - - f0d493f8f84f + - a65296ffb4a0 - c5908940967d + - f1a5908ea2cb tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -82,8 +82,8 @@ tools: - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - 60698466facd + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -103,14 +103,14 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 636b049e6141 + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords 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 cb65aa2fb..22dba8204 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,11 +2,11 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 79e9a869f40e - 0e9e7fcdd543 - cb34f00cc10f - fc8804320156 - a7228a7ea146 - - 79e9a869f40e - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -14,8 +14,8 @@ tools: owner: iuc revisions: - fa11aa8103b2 - - 18505fe2bdb1 - db25ec99c3ea + - 18505fe2bdb1 - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,14 +23,14 @@ tools: owner: iuc revisions: - 222669c4afb6 - - ec699520444c - - 0f5f4a208660 - - 2bf63b38ee9b - - edf6d4003fad - - 19f3b583a9b3 - eb746fa6f514 + - 19f3b583a9b3 + - edf6d4003fad + - 2bf63b38ee9b - cc36773a3681 + - ec699520444c - 43815fa60f3a + - 0f5f4a208660 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -49,50 +49,50 @@ tools: - name: nanoplot owner: iuc revisions: - - edbb6c5028f5 - - 645159bcee2d - a3c4fe6f49ab - 0f1c34698076 + - 645159bcee2d + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 3b6f94fc7e1d - d219b6d8158a + - 3b6f94fc7e1d - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: + - a8d4be409446 - be95355fef8d - 90a922f32523 - - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - d376944466bf - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - bec636361cfd - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: + - 543cbeef3949 - 5f76b20953e5 - 93d623d9979c - - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -111,8 +111,8 @@ 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 @@ -124,8 +124,8 @@ 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 @@ -175,8 +175,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - ca22d8497db5 + - 64a83664b814 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 16117c449..9f8f0dd6b 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -20,8 +20,8 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - d74850cf4e42 - adfd6bf710bd + - d74850cf4e42 - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -43,16 +43,16 @@ tools: owner: iuc revisions: - 2f27f3b86827 - - 19b6a2f0dbe2 - ed1518ce2237 - e4b4837f06f5 + - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 9e993022c762 - 46066df8813d + - 9e993022c762 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -64,16 +64,16 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - 48a42ca61006 - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -86,22 +86,22 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a 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 @@ -120,9 +120,9 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - - b4b2b284230a - 172815da3d41 + - b4b2b284230a + - 27a6a256cd23 - 52b6a4d98009 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -135,8 +135,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -148,9 +148,9 @@ 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 @@ -181,9 +181,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 - - 0cb27ea69dc1 - 5fe20c915fa6 + - 0cb27ea69dc1 + - 9c43baa60906 - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -196,25 +196,31 @@ 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: - - 6e24e79d3d69 - - ed7a967cb11b - 29c738066906 - df30a2f1db55 + - 6e24e79d3d69 + - ed7a967cb11b + tool_panel_section_label: None + tool_shed_url: toolshed.g2.bx.psu.edu +- name: data_manager_pharokka + owner: iuc + revisions: + - 50caca83e7c9 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 1865e693d8b2 + - ad90c2da4f38 - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -234,17 +240,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - d63c1442407f + - 64deddb6a8ec - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 9946bc39c834 - 94a50db37d1a - 625fd9476402 - - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -292,8 +298,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -737,8 +743,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index ce12103ff..f52d50278 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,87 +33,87 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 3f59ebfbfe3d + - 81e66674859e + - d7c7ef3353fe + - '841557158611' + - 26de3a7b1cb9 + - f73435dc282b + - cce7b18495e4 + - b89cac5156ec + - c78f3d7dd1db + - f04a1264e2a2 - d033ffc1c161 - 3b8b5bde0bd9 - - c78f3d7dd1db - 6a457678efcb - - '841557158611' - - 81e66674859e + - 8834daeb9892 - 107d3ba7024a - - f73435dc282b - - b89cac5156ec - - cce7b18495e4 - - 26de3a7b1cb9 - 5a7c56a5cc08 - - d7c7ef3353fe - a6619171428e - - 8834daeb9892 - - f04a1264e2a2 + - 3f59ebfbfe3d tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 7a2092844346 - - 6283babe736e - - 88c4aa435ded + - 3b96e92e8ec3 + - 659517798cc4 + - 4755f52427c4 + - b0af57c1a968 + - df47d4845b62 - 5b777002c2de + - a185b079b095 + - 6223845127ea - 02b8758214b0 - 5fcd1ece3a6e - - a185b079b095 - - 3b96e92e8ec3 + - 88c4aa435ded + - 7a2092844346 + - 6283babe736e - aa8cc71438cf - - df47d4845b62 - - b0af57c1a968 - - e75442c7f4da - - 659517798cc4 - - 4755f52427c4 - 6a726db04d4b - - 6223845127ea + - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - f97743d52b87 + - c1d53e95327f - d1c340a5664b - b8476e82ac20 + - f97743d52b87 - 9b892d7f82cc - - c1d53e95327f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - 128ba8da994f - - 9e10ba792be2 - daddf188c13f - feb40665d7cd + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: + - 42a174224817 - a2099fb98cdb - - 2fa9d4f1b48f - - 7bb8726be37c - 83a69484cb87 + - ca0d8cf80567 + - 2f1019071464 + - abf6dbe8c9d7 - b6abccb1f25b - - 42a174224817 - - 9d61d3fa046c - - 36912871ccdc - - ca337cce3888 - - 03ed9524dcd1 + - 14ae456b8cc5 - b7e297c2ede6 - - 2f1019071464 + - ca337cce3888 - 437e28791761 - - 81804a978fc0 - - ca0d8cf80567 - - 14ae456b8cc5 + - 03ed9524dcd1 + - 7bb8726be37c + - 2fa9d4f1b48f - 3a43c3982401 + - 81804a978fc0 - 5f8727ff21e7 - - abf6dbe8c9d7 + - 9d61d3fa046c + - 36912871ccdc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -126,22 +126,22 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac - ba29b5e2a4be - a4b71be30c3c + - b1e68bbe4cef + - 29ff6a849eac - ea30d3089354 - 73a469f7dc96 - - b1e68bbe4cef tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - e88a7de55d6e - - f1ccc8a6eb05 - - 809e42326fc2 - - 15ac71df11a0 - 91887494eb97 + - 809e42326fc2 - dbe2b2204555 + - 15ac71df11a0 + - f1ccc8a6eb05 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 4060af1cc..c4ae287d6 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - fc288950c3b7 + - a1f0b3f4b781 + - f9242e01365a + - f6ced08779c4 + - 7d34178f2812 - 881d7645d1bf + - fc288950c3b7 - 1aac2a13842a - b502c227b5e6 - - a1f0b3f4b781 - - 7d34178f2812 - - f6ced08779c4 - - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 9459551d1..6d45831e3 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - a58f7eb0df2c + - 7fbec959cf2b + - 3bd420ec162d - 5b85006245f3 - ca90d17ff51b - - a58f7eb0df2c - c0e71cb2bd1b - - e4a053d67e24 - eb085b3dbaf8 - - 7fbec959cf2b - - 3bd420ec162d - d00e15139065 + - e4a053d67e24 tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index e2cf8dabb..6b6aded82 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,22 +2,22 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b574b84afc4d - - f28ad96b76dc - - 0a18ac48ac53 - 277dc652246e - ece627528a78 + - f28ad96b76dc + - b574b84afc4d - b18329a8ac14 + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 + - b41107d8fe89 + - bf06d196e23d - e215f71d7983 + - 525f201b86c1 - e988563cc6e5 - - bf06d196e23d - - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter @@ -31,10 +31,10 @@ tools: - name: cardinal_filtering owner: galaxyp revisions: - - b8c79e70516d - a8157342d9a3 - - f23d67e28cc8 - 528fb09022be + - b8c79e70516d + - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images @@ -50,37 +50,37 @@ tools: - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - - e0669b1854b1 - ed9ed1e6cca2 + - 611d80c0e29d - 798da6bdff3d + - e0669b1854b1 - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - 5a35e3a8d013 - 74b61bf5bc4b + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - df2187f9013b - 82f6c2f4332d - cc430977c8ff - - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - d2483487e077 - - 1693b2126f30 - 10566783d718 + - d2483487e077 - 043f9c91f686 - c5aa9fca18c6 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,9 +98,9 @@ tools: - name: diann owner: galaxyp revisions: - - 9fa3dbf06f17 - - ae4dc0c041f9 - bf0728e000cd + - ae4dc0c041f9 + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -119,23 +119,23 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 4081e4faa4ab - 0fa397f4f40b + - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - fb192dd6658a - 36880dfd9fa7 + - fb192dd6658a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -147,16 +147,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - - e66f552a3c47 - d286ff4600dd + - e66f552a3c47 + - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -169,34 +169,34 @@ tools: - name: maxquant owner: galaxyp revisions: - - e42225f8a659 - - 8934bc76bb52 + - 7f432d87c82c + - 37d669de2828 - 97a7f34fcb6a - - 2133b0be850a - 4d17fcdeb8ff - - 7f432d87c82c - - 837224ad1694 - f522c08e900c + - 2133b0be850a + - 8934bc76bb52 - 1f39c833f65f - - 37d669de2828 + - 837224ad1694 + - e42225f8a659 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - 85b8866f06d7 - 0ed07016d668 + - a72ac2c7cc5b - '860429737408' tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 352b37c66d97 - - 990b4560ead7 - 4187b6df1a40 + - 990b4560ead7 - 1974224d63c2 + - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter @@ -211,17 +211,17 @@ tools: - name: metaquantome_sample owner: galaxyp revisions: - - 40ca115438d2 - c7745841de24 - c1343e3389ca + - 40ca115438d2 - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b648e45fd3cf - da986f83631b + - b648e45fd3cf - d46d64e7964d - d2eac53666f0 tool_panel_section_label: Proteomics @@ -229,10 +229,10 @@ tools: - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - - eb811f3018ea - 1199751329b0 - 9bf325045235 + - 944b43462104 + - eb811f3018ea tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -251,9 +251,9 @@ tools: owner: galaxyp revisions: - 28434abe6c5c - - 8212e342e482 - 593839e1f2c3 - b7034eff0db1 + - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -266,48 +266,48 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - 01dbaf6a57e0 + - 4e77b8f12cd3 - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 25529df60a81 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - f7fef900f5b2 - - 9cdf15d3cfc8 - c9eff69a7c62 + - 9cdf15d3cfc8 + - f7fef900f5b2 - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - 5e948629bc73 + - dff6c756eee5 - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: + - 658494a2cb00 - 890025d6e426 - 41859bbdc16e - - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 6634cad7d797 + - 5ad0b5bf1deb - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -322,24 +322,24 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: + - 5ad830edc021 - 52ba9695e752 - febd569ad26f - - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 92352a475eed - 39e8fde08881 + - 92352a475eed - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - d413dc49d650 + - 0efbc235f314 - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -347,42 +347,42 @@ tools: owner: galaxyp revisions: - c28f13cab67a - - 3720e349ba2a - 8a04ed1c1d1b + - 3720e349ba2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe - - ca799a7246e7 - 382cde407f81 + - c427a8628cbe - c55dddc5844a + - ca799a7246e7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: + - 8ddb7bab1138 - b5d0905419da - 39caaa778d2e - - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - 8d4db262964c - 1c5f31b8d632 - f817513840a9 - - 8d4db262964c - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - c69f69d7867a - 5d9f175dff81 - 111c3a00136d - - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher @@ -403,16 +403,16 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - c18d8efa4474 - 2b2a7551a857 - a407b6790342 + - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -433,8 +433,8 @@ tools: - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -447,15 +447,15 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - f861ec9fbe59 - 9f505cd4428f + - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter @@ -482,15 +482,15 @@ tools: - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e - 3d8d4ada5405 + - 5ae104d0da6e - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -519,8 +519,8 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - 9020199dba0a - d063e2fe4ba4 + - 9020199dba0a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -533,15 +533,15 @@ tools: owner: galaxyp revisions: - 7f6a1f27553e - - c8b225c69a7f - fb52e95a370c + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -554,14 +554,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: + - 7fdd9119cc4f - 3634c90301af - - a72c48001f7c - 3ec27b4cee7c - - da885ca16cb2 + - a72c48001f7c - 1beff3ddce58 - 943a34df6047 - 07ff622ec007 - - 7fdd9119cc4f + - da885ca16cb2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -615,10 +615,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: + - 265c35540faa - 1a5690a5eedc - - a371252a2cf6 - 12692567c7f9 - - 265c35540faa + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 0c7912043..501733f7f 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -4,130 +4,130 @@ tools: revisions: - 42201b90e3f4 - cd5f98911089 - - 2f1d464ebfd2 + - 289b7d6b69a4 - e345aadf914f + - 2f1d464ebfd2 - 110a346daf36 - - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b + - 0cd2df8af811 + - c207119ba5f6 - 8501601a118d - fcce77c09289 - - c207119ba5f6 - - 0cd2df8af811 - 42d9087b4789 + - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 89eb29319bf4 - - 04db7fd6b238 - - ad5ab22ffe24 - 421c33b8bf17 - - 405a212b32ab - 33486216eec0 + - 405a212b32ab + - 04db7fd6b238 + - 89eb29319bf4 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: + - 1d839ead7ad3 - 7370bb65bad4 - - fa51dc5e8386 - 7b72fde3d27e - - 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6dafad990086 - adc7a7610d4f + - 887e0991eb24 - 4f65e343ecdf - 5e10f396979e - - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 - - 4e280b27a831 + - 17d39bf0a63a - 43e3eeb2e0ec - 97575d01f06b - - 17d39bf0a63a + - 4e280b27a831 - c5d7050e4ad7 + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - 0b8c84a7fdb5 - - cd034465d4a4 - - 09b8edb56d80 - a819ec3b362d + - 9586f08634c0 + - cd034465d4a4 - d9bf483266a1 + - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - a4b4bd84f69e - - 2645575d1bf2 - - bf0e43ab0416 - a9c34a289493 - 69842dd5aa48 + - bf0e43ab0416 - 95351dd0fd3f + - a4b4bd84f69e + - 2645575d1bf2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: + - d1fda11e602f + - 8a35a3bc6752 - 912f904a6e1e - - bb0475c884ff - cfb504394ae1 - d033e1ccb386 - - d1fda11e602f - - 8a35a3bc6752 + - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,8 +163,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - d1fad35bdb4a + - d504d945a655 - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 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 a734ed27e..a573b0a55 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,9 +2,9 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - - 31f8063eedea - 2d4e3aff9dc7 + - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -18,8 +18,8 @@ tools: - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: circexplorer @@ -50,15 +50,15 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - e66b9b5b8580 + - f648e5180e40 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -72,8 +72,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -98,8 +98,8 @@ tools: owner: iuc revisions: - 0693ccd171c4 - - e3b16fd7dd08 - 3b36efd62b3e + - e3b16fd7dd08 - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -107,37 +107,37 @@ tools: owner: iuc revisions: - 9a882d108833 - - 8fe98f7094de - - 0696db066a5b - cd9874cb9019 - - 24a09ca67621 - - 6a3a025714d3 - d027d1f4984e + - 6a3a025714d3 + - 0696db066a5b + - 8fe98f7094de + - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - df929f257179 - 62adf13b86ea - 2872c633f07e + - df929f257179 - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 6e53e565fc6a - a8305cf0c951 - - 3d89af8a44f0 - - df0c8d0a5992 - - 555659de7321 + - 5bf899c13979 + - f2843df56434 - 070900306913 + - 9bdff28ae1b1 - 334ce9b1bac5 - - f2843df56434 + - df0c8d0a5992 + - 6e53e565fc6a + - 555659de7321 - 0cb907a2a810 - - 9bdff28ae1b1 - - 5bf899c13979 + - 3d89af8a44f0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -156,17 +156,17 @@ tools: - name: featurecounts owner: iuc revisions: - - ea04b737afa0 - - e6a2a912677a - - 7db9d3ea71c9 - - 38b6d12edc68 + - 90d16db017d7 - 6f66ae7c5f7a - - af814359d244 - - a56fbe2d6ba7 - - f9d49f5cb597 - a37612abf7f9 - - 90d16db017d7 + - a56fbe2d6ba7 + - af814359d244 + - 7db9d3ea71c9 - f3a5f075498f + - e6a2a912677a + - ea04b737afa0 + - 38b6d12edc68 + - f9d49f5cb597 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -184,9 +184,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 0f710191a66d - 3c97c841a443 - f99dd58de04f - - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -198,20 +198,20 @@ tools: - name: hisat2 owner: iuc revisions: - - d4b55e2beb12 - a86e80d3c09c + - f4af63aaf57a - 6ab42baa56e9 + - 26371a1df031 - 3fb01a8c902d - - f4af63aaf57a + - d4b55e2beb12 - 6c19daec423d - - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -223,20 +223,20 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - - ce5d418183c5 + - 5ae5c312d718 - 1c75aa5de15e + - 87c11c05d238 - 01247aaf0a10 - - 5ae5c312d718 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 + - 40985510cd98 - 10c98fab6c5a - c971db6f0fe5 - - 40985510cd98 + - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -244,11 +244,11 @@ tools: revisions: - 58c35179ebf0 - e827f9aae031 - - 97e06a4c7c75 - - 32511f586472 - d6f5fa4ee473 - 708348a17fa1 + - 32511f586472 - 0921444c832d + - 97e06a4c7c75 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -260,8 +260,8 @@ 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 @@ -298,18 +298,18 @@ tools: owner: iuc revisions: - 5ec75f5dae3c - - 79de45b5069b - - 4074fc1940e2 + - 0a563fd2f22e - e132e7d02a3e - - 7ed2edc1337f - - 3ea5a2a63fa2 + - 79de45b5069b - c7c55b694974 - - 0a563fd2f22e - c772497b2c32 - - 99b17b74a8cd - - b9e04854e2bb + - 4074fc1940e2 + - 7ed2edc1337f - 980d2a2e1180 + - 3ea5a2a63fa2 - 4df95e2d7f61 + - b9e04854e2bb + - 99b17b74a8cd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -321,34 +321,34 @@ tools: - name: salmon owner: bgruening revisions: - - ebab418107f5 - - 49121db48873 - - 2c0ca397d302 - - 15cd64d7c58b - cc05793bb896 - - e3d32471da11 - 53e9709776a0 + - 15cd64d7c58b + - e3d32471da11 + - 2c0ca397d302 + - 49121db48873 + - ebab418107f5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - c0fd285eb553 - - 56242ff81c84 - fab6ff46e019 - 8c28affc7c48 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - ae618321f34a + - 76d290331481 - 914cfcba0ec8 - - 258d696dbd7e - 1ebd14235b92 + - 258d696dbd7e - cef79931dda5 - dd4df992d93d - - ae618321f34a - - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -379,27 +379,27 @@ tools: owner: iuc revisions: - ffd1300599a1 - - 0db979fead3a - - c6334cb383ff - d0d4cef4f967 + - c6334cb383ff + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - ba3720d7e68b - d6a479fd4281 - - bcc5f03f1900 - 74217fbfba4d - - 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 - 2fb4ee002432 - - c2b82a94493e - 56162e446004 + - 478f36effca1 + - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -414,17 +414,17 @@ tools: owner: iuc revisions: - 870ac06dff8e - - 4687ecf0eb2d - - 34a018cbee9c - be3f26533209 + - 34a018cbee9c + - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 33406f5a445c - 05ab8d5e04a2 - 5192f657f305 - - 33406f5a445c - 65e7dea767ea - c5fbddcac63a tool_panel_section_label: RNA-seq @@ -432,51 +432,51 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - 6f0fb35b799c + - a35cba31d904 - e406ac71165d - 1fdb25a8384d - - a35cba31d904 - - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 7c7fbf13aadd - - c2c039e421af - - 964b7efe2639 - 37a1129c89d2 + - 964b7efe2639 + - c2c039e421af + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: + - 047c22569787 + - 24e94d84adc9 - 1d689e4e1caf - eafea3083352 - - 24e94d84adc9 - - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - - 9871104ea630 - - 3a4ac03d1266 - 1812dbc5bb7b + - 3a4ac03d1266 + - 9871104ea630 + - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - 32b86cd8eb50 - - 8f1c3df4dd49 - - 48636f857c4b - - cee61b3fcf78 - d84caa5a98ad - - 9fa24d5aac68 - db1f362cca3e - c9cfec002f71 + - 32b86cd8eb50 + - 48636f857c4b + - cee61b3fcf78 - d2bc35f3d1c5 + - 8f1c3df4dd49 + - 9fa24d5aac68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index dfa03fca7..ba833d62f 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 080fd5739bb4 - 473382134e56 - 1a052c827e88 + - 080fd5739bb4 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index f2b33beb6..5289e377c 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,17 +2,17 @@ tools: - name: bam_to_sam owner: devteam revisions: - - a53efedba9e7 - 88eedb4abea0 + - a53efedba9e7 - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 108db6635177 - - cb20f99fd45b - 1dfd95ee241e + - cb20f99fd45b + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -43,8 +43,8 @@ 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 @@ -68,15 +68,15 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - 9bd1568619cd - cf1ffd88f895 + - 9bd1568619cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -95,48 +95,48 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b + - 6856f8a01905 - 46c6639921f1 - 9149ad20699a - - 6856f8a01905 + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - c89806670ab9 - - 33208952b99d - 06dc50b7b711 + - c89806670ab9 - 92ec40abcdcf + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - - 720217c23995 - b3d99709fe1a + - 720217c23995 - 66e23b11feae + - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: + - db17d5321bad + - fefd89ab563c - fe34990e5ce7 - 22970df7a40e - - db17d5321bad - cc61ade70eb8 - - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7def34e6cf4d + - fa5d3e61e429 - 88b8c2916784 + - 7def34e6cf4d - 7a6034296ae9 - 811fc2d75ad4 - - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge @@ -152,10 +152,10 @@ tools: owner: devteam revisions: - 583abf29fc8e - - 329deb17a9f7 - 9da0311ab1dd - 8da515fbc1bf - b61f5d6a7f25 + - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -168,10 +168,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - - d7b4851d1971 - 30388d878f81 - bb8cfc6f6e0c + - db000c6007a0 + - d7b4851d1971 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -183,50 +183,50 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - b5c88b7b153e + - a4a10c7924d1 - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - cab3f8d35989 - - 6c2c1836728b + - e613c1ad4c4c - a577ea614bed + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd + - 135c85f4cfaf - bcedabb53ddf + - b7f7826ef1cd - 5d9ae78f34d3 - - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f - - 1cc79f49b8d5 - 24c5d43cb545 + - 1cc79f49b8d5 + - 3a0efe14891f - 5a08c09b9311 - - 145f6d74ff5e - fed4aa48ba09 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - b01db2684fa5 - - b72793637686 - - 0dbf49c414ae - - 5826298f6a73 - - bf328cec6a42 - 6be888be75f9 - - c370440f901e - 350bbc5c2ffd + - 5826298f6a73 + - 0dbf49c414ae + - b72793637686 + - c370440f901e + - b01db2684fa5 + - bf328cec6a42 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 ba938068c..a9e974c9a 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d - - 4aab5ae907b6 - - 6f6537780379 - 480d9e9d156b - - d147d6455873 - 59bb6d34fca6 + - d147d6455873 + - 6f6537780379 + - 4aab5ae907b6 + - a62c4a11a67d 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 ae786f729..52c0bfcf4 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -2,43 +2,43 @@ tools: - name: anndata_import owner: iuc revisions: - - 32e547223c9e + - 00712416fdaa - 55e35e9203cf + - 32e547223c9e - cfc3f5a57dc6 - - 00712416fdaa - - fb9e030ffae4 - 93dd15e13e6a + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - ee98d611afc6 - - 038e32885fec - 6f0d0c784f09 + - ee98d611afc6 - b9fac48532eb - - 688357ad5e61 + - 038e32885fec - 39e945f0b2c1 + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - ed4996a16f7f - 3d748954434b - - 43cb7b5a6fe7 - - d4af736e7b83 - b85871dd69f9 - - ed4996a16f7f + - d4af736e7b83 - 9bd945a03d7b + - 43cb7b5a6fe7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: - 2c1200fba922 + - cdf4443d5625 - 8855361fcfc5 - a9caad671439 - - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -50,8 +50,8 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 282819d09a4f - 7ffaa0968da3 + - 282819d09a4f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -77,8 +77,8 @@ 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 @@ -106,35 +106,35 @@ tools: owner: iuc revisions: - b2df381a6004 + - 77b91b9bdf52 - 6acb08931836 - aaa5da8e73a9 - - 77b91b9bdf52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - a03ff8633507 - b409c2486353 - - 3c86f71498bc - a97abb8cd15b + - 3c86f71498bc + - a03ff8633507 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - c5d3684f7c4c - - 5e9171dc8244 - 6bd82ed14acd - 3081ff5c84a3 + - 5e9171dc8244 + - c5d3684f7c4c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - 3bcd5445cd7a - - ab55fe8030b6 - a407e7f8bdc1 + - ab55fe8030b6 - 94c19fb1281c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,35 +142,35 @@ tools: owner: iuc revisions: - aa0c474463c2 - - 6adf98e782f3 - - 9b0cdb8cf6be - dbbe1ea8ecb1 + - 9b0cdb8cf6be + - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 215733a383f2 - 73ab2ac53d06 + - bf2017df9837 + - 215733a383f2 - f2f6c703da06 - 458e8f43a775 - - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - b834074a9aff + - 8f333f90d8d6 - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - 652923ce664f - - 7a365ec81b52 - b7ea9f09c02f + - 7a365ec81b52 + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -184,8 +184,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - - c99ba278dfa9 - 9e5c0bb18d08 + - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index f502a65a1..2a473b361 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 - 419027d822d6 - 4c07ddedc198 - 746e8e4bf929 + - 562f3c677828 - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,22 +56,22 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - cb1c59d69557 + - 6c29c7e347e8 - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,31 +114,31 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - b1eda492f063 - 7442b94d6a1e + - 4c4ec859c31a - 840f29aad145 + - b1eda492f063 - aef56d0e7a61 - - 4c4ec859c31a - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - 9fda0b82f419 + - d0352e8b4c10 - 30d21a6041f6 - - 375bbd555f4a - 07843f917990 + - 375bbd555f4a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 4cc980df6265 - cd02bf168d23 - - 7ae443e6217d + - 4cc980df6265 - 8b1b2b91f8d0 + - 7ae443e6217d - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -146,10 +146,10 @@ tools: owner: bgruening revisions: - ad7e0b4291ee - - 4bbaf77573ef - - e10e776f2109 - - bb9fc9d46ea4 - 7dd3fb35904f + - bb9fc9d46ea4 + - e10e776f2109 + - 4bbaf77573ef - 1dd433d2c92c tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index c4a88d98d..0d108bdee 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: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 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: - - 464b9305180e - 6595517c2dd8 - 13b6f0007d9e - 6e8d94597139 + - 464b9305180e - be25c075ed54 - - 9cd341095afd - 02026300aa45 + - 9cd341095afd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -72,8 +72,8 @@ tools: owner: iuc revisions: - 557ec8d7087d - - 37cde8134c6a - 9cc411a62277 + - 37cde8134c6a - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,20 +105,20 @@ tools: - name: query_tabular owner: iuc revisions: - - 33d61c89fb8d - 1ea4e668bf73 - - 623f3eb7aa48 + - 33d61c89fb8d - 83069b38aa85 + - 623f3eb7aa48 - cf34c344508d - - 3a6b78c39dca - 2e8f945f7285 + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - 399da6b5ec21 + - ae8c4b2488e7 - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -131,9 +131,9 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - f768f6183386 - bce29ec10b78 - b722161a845a - - f768f6183386 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 owner: bgruening revisions: - - 74a8bef53a00 - - ddf54b12c295 + - f46f0e4f75c4 - d698c222f354 - 9ff72e942410 - - f46f0e4f75c4 + - ddf54b12c295 + - 74a8bef53a00 - a6f147a050a2 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index f521d56df..cee098df4 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -2,8 +2,8 @@ tools: - name: breseq owner: iuc revisions: - - 85c57cc9b558 - 82fb5e3bb93e + - 85c57cc9b558 - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -16,57 +16,57 @@ tools: - name: freebayes owner: devteam revisions: - - 04fa42777df9 - ef2c525bd8cd + - a5937157062f - 156b60c1530f + - 04fa42777df9 - 57def2d7c093 - - a5937157062f tool_panel_section_label: Variant 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VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate @@ -412,8 +412,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -440,9 +440,9 @@ tools: - name: vcffilter owner: devteam revisions: + - fa24bf0598f4 - eae7c08ebb6f - 6b935ab36d7b - - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -462,15 +462,15 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -483,8 +483,8 @@ tools: - name: vcfleftalign owner: devteam revisions: - - d2406f98a782 - 29f9b782727e + - 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