From 1e7bfe0c8cf7b15cacee38be1f1fecd25de64457 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 29 Oct 2024 16:52:26 +0100 Subject: [PATCH 1/2] Add tools for IWC workflows --- usegalaxy.org/annotation.yml | 4 ++ usegalaxy.org/annotation.yml.lock | 13 ++++++ usegalaxy.org/assembly.yml.lock | 2 +- usegalaxy.org/bed.yml.lock | 1 + usegalaxy.org/chemicaltoolbox.yml.lock | 4 ++ usegalaxy.org/convert_formats.yml.lock | 2 + usegalaxy.org/datamash.yml.lock | 1 + usegalaxy.org/expression_tools.yml | 14 +++--- usegalaxy.org/expression_tools.yml.lock | 6 +++ usegalaxy.org/fasta_fastq.yml.lock | 1 + usegalaxy.org/graph_display_data.yml.lock | 1 + usegalaxy.org/imaging.yml | 16 +++++++ usegalaxy.org/imaging.yml.lock | 52 +++++++++++++++++++++ usegalaxy.org/metabolomics.yml | 6 +++ usegalaxy.org/metabolomics.yml.lock | 17 +++++++ usegalaxy.org/metagenomic_analysis.yml.lock | 2 +- usegalaxy.org/nanopore.yml | 2 + usegalaxy.org/nanopore.yml.lock | 8 ++++ usegalaxy.org/picard.yml.lock | 1 + usegalaxy.org/sam_bam.yml | 2 + usegalaxy.org/sam_bam.yml.lock | 6 +++ 21 files changed, 153 insertions(+), 8 deletions(-) create mode 100644 usegalaxy.org/imaging.yml create mode 100644 usegalaxy.org/imaging.yml.lock create mode 100644 usegalaxy.org/metabolomics.yml create mode 100644 usegalaxy.org/metabolomics.yml.lock diff --git a/usegalaxy.org/annotation.yml b/usegalaxy.org/annotation.yml index a6e4d33b..a79ff6f7 100644 --- a/usegalaxy.org/annotation.yml +++ b/usegalaxy.org/annotation.yml @@ -136,3 +136,7 @@ tools: owner: iuc - name: agat owner: bgruening +- name: helixer + owner: genouest +- name: omark + owner: iuc diff --git a/usegalaxy.org/annotation.yml.lock b/usegalaxy.org/annotation.yml.lock index ba5c1123..594b02fd 100644 --- a/usegalaxy.org/annotation.yml.lock +++ b/usegalaxy.org/annotation.yml.lock @@ -15,6 +15,7 @@ tools: - name: abricate owner: iuc revisions: + - 3f3e247c053d - 4efdca267d51 - b734db305578 - c2ef298da409 @@ -535,3 +536,15 @@ tools: - e7449b2c14bf tool_panel_section_id: annotation tool_panel_section_label: Annotation +- name: helixer + owner: genouest + revisions: + - c2fc4ac35199 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: omark + owner: iuc + revisions: + - 6f570ba54b41 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation diff --git a/usegalaxy.org/assembly.yml.lock b/usegalaxy.org/assembly.yml.lock index 79119425..6a0d41fd 100644 --- a/usegalaxy.org/assembly.yml.lock +++ b/usegalaxy.org/assembly.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: false +install_repository_dependencies: true install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Assembly diff --git a/usegalaxy.org/bed.yml.lock b/usegalaxy.org/bed.yml.lock index e5234be9..0a1ed762 100644 --- a/usegalaxy.org/bed.yml.lock +++ b/usegalaxy.org/bed.yml.lock @@ -11,6 +11,7 @@ tools: - 64e2edfe7a2c - 7ab85ac5f64b - a1a923cd89e8 + - a68aa6c1204a - b28e0cfa7ba1 - ce3c7f062223 - fe5b4cb8356c diff --git a/usegalaxy.org/chemicaltoolbox.yml.lock b/usegalaxy.org/chemicaltoolbox.yml.lock index 99f72afb..5636770a 100644 --- a/usegalaxy.org/chemicaltoolbox.yml.lock +++ b/usegalaxy.org/chemicaltoolbox.yml.lock @@ -55,12 +55,14 @@ tools: owner: bgruening revisions: - 67ee76f0e497 + - bbbf5fb356dd tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: ctb_rdkit_descriptors owner: bgruening revisions: - 0993ac4f4a23 + - a1c53f0533b0 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: openbabel_compound_convert @@ -81,6 +83,7 @@ tools: owner: chemteam revisions: - 070e3ecc3fda + - 1d4dd4f908d4 - 2c349b027a01 - 4da9ee404eab - a66c193fafdb @@ -148,6 +151,7 @@ tools: - 04abdf96978b - 319a28774da9 - 534ff13ea227 + - 9389cd867cf2 - bc31d02be922 - d1d0efda35c0 tool_panel_section_id: chemicaltoolbox diff --git a/usegalaxy.org/convert_formats.yml.lock b/usegalaxy.org/convert_formats.yml.lock index 9c4ad86d..d53a6a20 100644 --- a/usegalaxy.org/convert_formats.yml.lock +++ b/usegalaxy.org/convert_formats.yml.lock @@ -242,11 +242,13 @@ tools: - 65a69de1e294 - 8d6686664021 - a7387ce2a8ca + - ea93df4b3df2 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: tooldistillator_summarize owner: iuc revisions: + - 24eec94e6dfc - 6ff67d2860e1 - def7a82d23e1 - f3233d395549 diff --git a/usegalaxy.org/datamash.yml.lock b/usegalaxy.org/datamash.yml.lock index c60291af..649a38b2 100644 --- a/usegalaxy.org/datamash.yml.lock +++ b/usegalaxy.org/datamash.yml.lock @@ -8,6 +8,7 @@ tools: revisions: - 2f3c6f2dcf39 - 4c07ddedc198 + - 562f3c677828 - 746e8e4bf929 tool_panel_section_id: datamash tool_panel_section_label: Datamash diff --git a/usegalaxy.org/expression_tools.yml b/usegalaxy.org/expression_tools.yml index 16cb06b8..103292e4 100644 --- a/usegalaxy.org/expression_tools.yml +++ b/usegalaxy.org/expression_tools.yml @@ -1,8 +1,10 @@ tool_panel_section_label: Expression Tools tools: - - name: compose_text_param - owner: iuc - - name: map_param_value - owner: iuc - - name: pick_value - owner: iuc \ No newline at end of file +- name: compose_text_param + owner: iuc +- name: map_param_value + owner: iuc +- name: pick_value + owner: iuc +- name: calculate_numeric_param + owner: iuc diff --git a/usegalaxy.org/expression_tools.yml.lock b/usegalaxy.org/expression_tools.yml.lock index 8b0461eb..e84bc919 100644 --- a/usegalaxy.org/expression_tools.yml.lock +++ b/usegalaxy.org/expression_tools.yml.lock @@ -24,3 +24,9 @@ tools: - b19e21af9c52 tool_panel_section_id: expression_tools tool_panel_section_label: Expression Tools +- name: calculate_numeric_param + owner: iuc + revisions: + - 0e586762f97b + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock index 37ed7f32..61203037 100644 --- a/usegalaxy.org/fasta_fastq.yml.lock +++ b/usegalaxy.org/fasta_fastq.yml.lock @@ -48,6 +48,7 @@ tools: - c59d48774d03 - d60c3f704da0 - dbf9c561ef29 + - dbfc505896e9 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastx_trimmer diff --git a/usegalaxy.org/graph_display_data.yml.lock b/usegalaxy.org/graph_display_data.yml.lock index 20e0ee2c..4e639314 100644 --- a/usegalaxy.org/graph_display_data.yml.lock +++ b/usegalaxy.org/graph_display_data.yml.lock @@ -327,6 +327,7 @@ tools: - 0e592dcaeb7f - 137e08517410 - 2fff478aca4b + - 49f3d3878413 - 4aec47f872b3 - 56f9a6e0fe80 - 74074746ccd8 diff --git a/usegalaxy.org/imaging.yml b/usegalaxy.org/imaging.yml new file mode 100644 index 00000000..7d2511a3 --- /dev/null +++ b/usegalaxy.org/imaging.yml @@ -0,0 +1,16 @@ +tool_panel_section_label: Imaging +tools: +- name: 2d_simple_filter + owner: imgteam +- name: 2d_histogram_equalization + owner: imgteam +- name: 2d_auto_threshold + owner: imgteam +- name: bfconvert + owner: imgteam +- name: binary2labelimage + owner: imgteam +- name: overlay_images + owner: imgteam +- name: count_objects + owner: imgteam diff --git a/usegalaxy.org/imaging.yml.lock b/usegalaxy.org/imaging.yml.lock new file mode 100644 index 00000000..ef9cdcf9 --- /dev/null +++ b/usegalaxy.org/imaging.yml.lock @@ -0,0 +1,52 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Imaging +tools: +- name: 2d_simple_filter + owner: imgteam + revisions: + - d51310ab328a + - f70b215d155c + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: 2d_histogram_equalization + owner: imgteam + revisions: + - 77f7159d775a + - b1c2c210813c + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: 2d_auto_threshold + owner: imgteam + revisions: + - 3df9f0a4bf34 + - 699a5e9146b3 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: bfconvert + owner: imgteam + revisions: + - 85edbb7a436b + - fcadded98e61 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: binary2labelimage + owner: imgteam + revisions: + - 984358e43242 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: overlay_images + owner: imgteam + revisions: + - 37662cbf44b8 + - ca362a9bfa20 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: count_objects + owner: imgteam + revisions: + - b58447a2eed2 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging diff --git a/usegalaxy.org/metabolomics.yml b/usegalaxy.org/metabolomics.yml new file mode 100644 index 00000000..70dd1daf --- /dev/null +++ b/usegalaxy.org/metabolomics.yml @@ -0,0 +1,6 @@ +tool_panel_section_label: Metabolomics +tools: +- name: metams_rungc + owner: yguitton +- name: checkformat + owner: ethevenot diff --git a/usegalaxy.org/metabolomics.yml.lock b/usegalaxy.org/metabolomics.yml.lock new file mode 100644 index 00000000..b920d486 --- /dev/null +++ b/usegalaxy.org/metabolomics.yml.lock @@ -0,0 +1,17 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Metabolomics +tools: +- name: metams_rungc + owner: yguitton + revisions: + - 93508ea69eb5 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: checkformat + owner: ethevenot + revisions: + - e7c5811ec12f + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock index 1e87ad33..2fa04d0b 100644 --- a/usegalaxy.org/metagenomic_analysis.yml.lock +++ b/usegalaxy.org/metagenomic_analysis.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: false +install_repository_dependencies: true install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis diff --git a/usegalaxy.org/nanopore.yml b/usegalaxy.org/nanopore.yml index 3f16f3a3..57f1effd 100644 --- a/usegalaxy.org/nanopore.yml +++ b/usegalaxy.org/nanopore.yml @@ -42,3 +42,5 @@ tools: owner: bgruening - name: pycoqc owner: iuc +- name: clair3 + owner: iuc diff --git a/usegalaxy.org/nanopore.yml.lock b/usegalaxy.org/nanopore.yml.lock index 28de97b5..b1fc9ffa 100644 --- a/usegalaxy.org/nanopore.yml.lock +++ b/usegalaxy.org/nanopore.yml.lock @@ -152,6 +152,7 @@ tools: - 84dcccebad3d - b2aae698b9d3 - d6cddc06aeae + - db25ec99c3ea - eb1f4ba66dc6 - fa11aa8103b2 - fbf007713188 @@ -208,3 +209,10 @@ tools: - fae03f3d4bf7 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore +- name: clair3 + owner: iuc + revisions: + - 3843a30053ee + - 63e02ef6e153 + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore diff --git a/usegalaxy.org/picard.yml.lock b/usegalaxy.org/picard.yml.lock index abafdd03..de2b84ed 100644 --- a/usegalaxy.org/picard.yml.lock +++ b/usegalaxy.org/picard.yml.lock @@ -10,6 +10,7 @@ tools: - 3f254c5ced1d - 585027e65f3b - 7d34178f2812 + - 881d7645d1bf - a1f0b3f4b781 - b502c227b5e6 - f9242e01365a diff --git a/usegalaxy.org/sam_bam.yml b/usegalaxy.org/sam_bam.yml index 4fdab5ee..a3a9c5cd 100644 --- a/usegalaxy.org/sam_bam.yml +++ b/usegalaxy.org/sam_bam.yml @@ -80,3 +80,5 @@ tools: owner: lldelisle - name: mosdepth owner: iuc +- name: samtools_coverage + owner: iuc diff --git a/usegalaxy.org/sam_bam.yml.lock b/usegalaxy.org/sam_bam.yml.lock index d8434320..d7999961 100644 --- a/usegalaxy.org/sam_bam.yml.lock +++ b/usegalaxy.org/sam_bam.yml.lock @@ -340,3 +340,9 @@ tools: - 5854d0da92b4 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM +- name: samtools_coverage + owner: iuc + revisions: + - c4ff13d2aab3 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM From ecb4e3cd1616d3e91827a0ff959af6fe5b95bd29 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 29 Oct 2024 17:18:18 +0100 Subject: [PATCH 2/2] Drop clair3 revision we never want to install --- usegalaxy.org/nanopore.yml.lock | 1 - 1 file changed, 1 deletion(-) diff --git a/usegalaxy.org/nanopore.yml.lock b/usegalaxy.org/nanopore.yml.lock index b1fc9ffa..3e44c8c6 100644 --- a/usegalaxy.org/nanopore.yml.lock +++ b/usegalaxy.org/nanopore.yml.lock @@ -213,6 +213,5 @@ tools: owner: iuc revisions: - 3843a30053ee - - 63e02ef6e153 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore