From bdff789b0c014eb7404cbe754fa79b8a79ac7f30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Sun, 22 Dec 2024 18:23:38 +0100 Subject: [PATCH] Update workflow tests --- .../metadata/test_workflow_status.tsv | 12 + .../resources/test_curated_workflows.tsv | 12 + .../microgalaxy/resources/test_workflows.json | 434 ++++++++++++++++++ .../microgalaxy/resources/test_workflows.tsv | 24 +- sources/bin/extract_galaxy_workflows.py | 5 +- sources/bin/get_community_workflows.sh | 16 +- 6 files changed, 483 insertions(+), 20 deletions(-) create mode 100644 communities/microgalaxy/metadata/test_workflow_status.tsv create mode 100644 communities/microgalaxy/resources/test_curated_workflows.tsv create mode 100644 communities/microgalaxy/resources/test_workflows.json diff --git a/communities/microgalaxy/metadata/test_workflow_status.tsv b/communities/microgalaxy/metadata/test_workflow_status.tsv new file mode 100644 index 00000000..828a12e5 --- /dev/null +++ b/communities/microgalaxy/metadata/test_workflow_status.tsv @@ -0,0 +1,12 @@ +Link Name Source Projects Creators Creation time Update time To keep Deprecated +https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Halophiles workup of Comparative gene analysis https://usegalaxy.eu Anton Nekrutenko 2024-12-03 2024-12-05 True False +https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 pAllori Blood RNA https://usegalaxy.eu Engy Nasr, Paul Zierep 2023-07-02 2024-11-24 True False +https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Metaproteomics workflow https://usegalaxy.eu Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Feature-Count Table Normalization https://usegalaxy.eu Johannes Effenberger 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 metaQuantome_datacreation_workflow https://usegalaxy.eu Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 metaquantome-function-worklow https://usegalaxy.eu Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu Engy Nasr, Paul Zierep 2023-06-30 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Metatranscriptomics data analysis https://usegalaxy.eu Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False +https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato 2024-11-21 2024-11-21 True False diff --git a/communities/microgalaxy/resources/test_curated_workflows.tsv b/communities/microgalaxy/resources/test_curated_workflows.tsv new file mode 100644 index 00000000..704eea93 --- /dev/null +++ b/communities/microgalaxy/resources/test_curated_workflows.tsv @@ -0,0 +1,12 @@ +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT True False +Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT True False diff --git a/communities/microgalaxy/resources/test_workflows.json b/communities/microgalaxy/resources/test_workflows.json new file mode 100644 index 00000000..4b3cfff6 --- /dev/null +++ b/communities/microgalaxy/resources/test_workflows.json @@ -0,0 +1,434 @@ +[ + { + "create_time": "2024-12-03", + "creators": [ + "Anton Nekrutenko" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "a2c46deea34d9d80", + "keep": true, + "latest_version": 2, + "license": null, + "link": "https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80", + "name": "Halophiles workup of Comparative gene analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "genome-annotation", + "name:microgalaxy" + ], + "tools": [ + "Filter1", + "join1", + "tab2fasta", + "Add_a_column1", + "bg_diamond_view", + "gops_intersect_1", + "collapse_dataset", + "rbc_mafft", + "rapidnj", + "bg_diamond", + "Cut1", + "cat1", + "regexColumn1", + "tp_split_on_column" + ], + "update_time": "2024-12-05", + "versions": 2 + }, + { + "create_time": "2023-07-02", + "creators": [ + "Engy Nasr", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "ca9d3233b0912765", + "keep": true, + "latest_version": 43, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765", + "name": "pAllori Blood RNA", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:pallori", + "name:bloodrna", + "name:umi", + "name:barcode", + "name:transcriptomics" + ], + "tools": [ + "umi_tools_extract", + "__FILTER_FAILED_DATASETS__", + "collection_column_join", + "rna_star", + "featurecounts", + "multiqc", + "fastqc" + ], + "update_time": "2024-11-24", + "versions": 43 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Timothy Griffin", + "Pratik Jagtap", + "James Johnson", + "Clemens Blank", + "Subina Mehta" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "cefc49c13ff73231", + "keep": true, + "latest_version": 40, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231", + "name": "Metaproteomics workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:metaproteomics", + "name:galaxyp", + "name:massspectrometry", + "name:microgalaxy" + ], + "tools": [ + "search_gui", + "peptide_shaker", + "sqlite_to_tabular", + "query_tabular", + "unipept" + ], + "update_time": "2024-11-21", + "versions": 40 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Johannes Effenberger" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "6239178d7cc4ac68", + "keep": true, + "latest_version": 5, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68", + "name": "Feature-Count Table Normalization", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "normalization", + "softmax", + "relative-abundance", + "sigmoid", + "css", + "limma-tmm", + "limma-rle" + ], + "tools": [ + "map_param_value", + "__FILTER_EMPTY_DATASETS__", + "__BUILD_LIST__", + "__EXTRACT_DATASET__", + "Grep1" + ], + "update_time": "2024-11-21", + "versions": 5 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Subina Metha", + "Timothy J. Griffin", + "Pratik Jagtap", + "Emma Leith", + "Marie Crane" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "cd675ab32d3e7833", + "keep": true, + "latest_version": 1, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833", + "name": "metaQuantome_datacreation_workflow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "proteomics", + "name:microgalaxy" + ], + "tools": [ + "Filter1", + "tp_replace_in_column", + "search_gui", + "peptide_shaker", + "tp_replace_in_line", + "flashlfq", + "query_tabular", + "msconvert", + "Remove beginning1", + "Cut1", + "regex1", + "unipept" + ], + "update_time": "2024-11-21", + "versions": 1 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Subina Mehta", + "Timothy J. Griffin", + "Pratik Jagtap", + "Emma Leith", + "Marie Crane", + "Praveen Kumar" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "e5a89ef7b5f1c1d9", + "keep": true, + "latest_version": 3, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9", + "name": "metaquantome-function-worklow", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "proteomics", + "name:microgalaxy" + ], + "tools": [ + "metaquantome_stat", + "metaquantome_db", + "metaquantome_viz", + "metaquantome_sample", + "metaquantome_filter", + "metaquantome_expand" + ], + "update_time": "2024-11-21", + "versions": 3 + }, + { + "create_time": "2023-06-30", + "creators": [ + "Engy Nasr", + "Paul Zierep" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "466bdd8ba7b67264", + "keep": true, + "latest_version": 70, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264", + "name": "pAllori Amplicon 16S Pre-Processing and Taxonomy Classification", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "name:16s", + "name:metagenomics", + "name:pallori" + ], + "tools": [ + "krakentools_kreport2krona", + "unzip", + "trimmomatic", + "ampvis2_load", + "taxonomy_krona_chart", + "ampvis2_heatmap", + "collection_column_join", + "lotus2", + "tp_cut_tool", + "__FLATTEN__", + "kraken2", + "ampvis2_ordinate", + "multiqc", + "fastqc", + "cutadapt" + ], + "update_time": "2024-11-21", + "versions": 70 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr ", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "c09159d7aad0f264", + "keep": true, + "latest_version": 2, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264", + "name": "Cloud Aerosol MT-MG Contamination Filtering", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "filter_tabular", + "fastq_to_tabular", + "kraken2", + "seq_filter_by_id", + "recentrifuge", + "bowtie2" + ], + "update_time": "2024-11-21", + "versions": 2 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Valerie C. Schiml", + "Magnus \u00d8. Arntzen", + "Francesco Delogu", + "Praveen Kumar", + "Benoit Kunath", + "B\u00e9r\u00e9nice Batut", + " Subina Mehta", + "James E. Johnson", + " Bj\u00f6rn Gr\u00fcning", + "Phillip B. Pope", + "Pratik D. Jagtap", + "Timothy J. Griffin" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "fd90652d475ed739", + "keep": true, + "latest_version": 5, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=fd90652d475ed739", + "name": "Metatranscriptomics data analysis", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "name:microgalaxy", + "metatranscriptomics", + "microbiome" + ], + "tools": [ + "__UNZIP_COLLECTION__", + "bg_sortmerna", + "collection_column_join", + "kallisto_quant", + "fastqc", + "trim_galore" + ], + "update_time": "2024-11-21", + "versions": 5 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "63478edcea3f449a", + "keep": true, + "latest_version": 4, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=63478edcea3f449a", + "name": " Cloud-Aerosole MT-MG Functional Profiling", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "multiqc", + "featurecounts", + "bowtie2" + ], + "update_time": "2024-11-21", + "versions": 4 + }, + { + "create_time": "2024-11-21", + "creators": [ + "Engy Nasr", + "B\u00e9r\u00e9nice Batut", + "Rapha\u00eblle P\u00e9guilhan", + "Pierre Amato" + ], + "deprecated": false, + "doi": "", + "edam_operation": [], + "edam_topic": [], + "id": "1ef76b7b86e15792", + "keep": true, + "latest_version": 6, + "license": "MIT", + "link": "https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792", + "name": "Cloud-Aerosole MT-MG Pre-Processing", + "number_of_steps": null, + "projects": [], + "source": "https://usegalaxy.eu", + "tags": [ + "metagenomics", + "metatranscriptomics", + "name:microgalaxy" + ], + "tools": [ + "trimmomatic", + "multiqc", + "fastqc" + ], + "update_time": "2024-11-21", + "versions": 6 + } +] \ No newline at end of file diff --git a/communities/microgalaxy/resources/test_workflows.tsv b/communities/microgalaxy/resources/test_workflows.tsv index 5e61dade..704eea93 100644 --- a/communities/microgalaxy/resources/test_workflows.tsv +++ b/communities/microgalaxy/resources/test_workflows.tsv @@ -1,12 +1,12 @@ -Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI -Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column -pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT -Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT -Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT -metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT -metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT -pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT -Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT -Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT - Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT -Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT +Name Source ID Link Creators Tags Creation time Update time Latest version Versions Number of steps Tools EDAM operations EDAM topics License DOI Projects To keep Deprecated +Halophiles workup of Comparative gene analysis https://usegalaxy.eu a2c46deea34d9d80 https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 Anton Nekrutenko genome-annotation, name:microgalaxy 2024-12-03 2024-12-05 2 2 Filter1, join1, tab2fasta, Add_a_column1, bg_diamond_view, gops_intersect_1, collapse_dataset, rbc_mafft, rapidnj, bg_diamond, Cut1, cat1, regexColumn1, tp_split_on_column True False +pAllori Blood RNA https://usegalaxy.eu ca9d3233b0912765 https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 Engy Nasr, Paul Zierep name:microgalaxy, name:pallori, name:bloodrna, name:umi, name:barcode, name:transcriptomics 2023-07-02 2024-11-24 43 43 umi_tools_extract, __FILTER_FAILED_DATASETS__, collection_column_join, rna_star, featurecounts, multiqc, fastqc MIT True False +Metaproteomics workflow https://usegalaxy.eu cefc49c13ff73231 https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231 Timothy Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta name:metaproteomics, name:galaxyp, name:massspectrometry, name:microgalaxy 2024-11-21 2024-11-21 40 40 search_gui, peptide_shaker, sqlite_to_tabular, query_tabular, unipept MIT True False +Feature-Count Table Normalization https://usegalaxy.eu 6239178d7cc4ac68 https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68 Johannes Effenberger name:microgalaxy, normalization, softmax, relative-abundance, sigmoid, css, limma-tmm, limma-rle 2024-11-21 2024-11-21 5 5 map_param_value, __FILTER_EMPTY_DATASETS__, __BUILD_LIST__, __EXTRACT_DATASET__, Grep1 MIT True False +metaQuantome_datacreation_workflow https://usegalaxy.eu cd675ab32d3e7833 https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833 Subina Metha, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane proteomics, name:microgalaxy 2024-11-21 2024-11-21 1 1 Filter1, tp_replace_in_column, search_gui, peptide_shaker, tp_replace_in_line, flashlfq, query_tabular, msconvert, Remove beginning1, Cut1, regex1, unipept MIT True False +metaquantome-function-worklow https://usegalaxy.eu e5a89ef7b5f1c1d9 https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9 Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, Praveen Kumar proteomics, name:microgalaxy 2024-11-21 2024-11-21 3 3 metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_sample, metaquantome_filter, metaquantome_expand MIT True False +pAllori Amplicon 16S Pre-Processing and Taxonomy Classification https://usegalaxy.eu 466bdd8ba7b67264 https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 Engy Nasr, Paul Zierep name:microgalaxy, name:16s, name:metagenomics, name:pallori 2023-06-30 2024-11-21 70 70 krakentools_kreport2krona, unzip, trimmomatic, ampvis2_load, taxonomy_krona_chart, ampvis2_heatmap, collection_column_join, lotus2, tp_cut_tool, __FLATTEN__, kraken2, ampvis2_ordinate, multiqc, fastqc, cutadapt MIT True False +Cloud Aerosol MT-MG Contamination Filtering https://usegalaxy.eu c09159d7aad0f264 https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 Engy Nasr , Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 2 2 filter_tabular, fastq_to_tabular, kraken2, seq_filter_by_id, recentrifuge, bowtie2 MIT True False +Metatranscriptomics data analysis https://usegalaxy.eu fd90652d475ed739 https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 Valerie C. Schiml, Magnus Ø. Arntzen, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin name:microgalaxy, metatranscriptomics, microbiome 2024-11-21 2024-11-21 5 5 __UNZIP_COLLECTION__, bg_sortmerna, collection_column_join, kallisto_quant, fastqc, trim_galore MIT True False + Cloud-Aerosole MT-MG Functional Profiling https://usegalaxy.eu 63478edcea3f449a https://usegalaxy.eu/published/workflow?id=63478edcea3f449a Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 4 4 multiqc, featurecounts, bowtie2 MIT True False +Cloud-Aerosole MT-MG Pre-Processing https://usegalaxy.eu 1ef76b7b86e15792 https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792 Engy Nasr, Bérénice Batut, Raphaëlle Péguilhan, Pierre Amato metagenomics, metatranscriptomics, name:microgalaxy 2024-11-21 2024-11-21 6 6 trimmomatic, multiqc, fastqc MIT True False diff --git a/sources/bin/extract_galaxy_workflows.py b/sources/bin/extract_galaxy_workflows.py index 9bb85ed9..931eb371 100644 --- a/sources/bin/extract_galaxy_workflows.py +++ b/sources/bin/extract_galaxy_workflows.py @@ -408,7 +408,10 @@ def export_workflows_to_tsv(self, output_fp: str, to_keep_columns: Optional[List tags = shared.load_yaml(args.tags) # get status if file provided if args.status: - status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + try: + status = pd.read_csv(args.status, sep="\t", index_col=0).to_dict("index") + except Exception as ex: + status = {} else: status = {} wfs.filter_workflows_by_tags(tags, status) diff --git a/sources/bin/get_community_workflows.sh b/sources/bin/get_community_workflows.sh index 92b52430..52785cb8 100644 --- a/sources/bin/get_community_workflows.sh +++ b/sources/bin/get_community_workflows.sh @@ -5,14 +5,16 @@ then python sources/bin/extract_galaxy_workflows.py \ filter \ --all "communities/all/resources/test_workflows.json" \ - --filtered "communities/microgalaxy/resources/test_workflows.tsv" \ - --tags "communities/microgalaxy/metadata/workflow_tags" - - python sources/bin/create_interactive_table.py \ - --input "communities/microgalaxy/resources/test_workflows.tsv" \ - --template "sources/data/interactive_table_template.html" \ - --output "communities/microgalaxy/resources/workflows.html" + --filtered "communities/microgalaxy/resources/test_workflows.json" \ + --tsv-filtered "communities/microgalaxy/resources/test_workflows.tsv" \ + --tags "communities/microgalaxy/metadata/workflow_tags" \ + --status "communities/microgalaxy/metadata/test_workflow_status.tsv" + python sources/bin/extract_galaxy_workflows.py \ + curate \ + --filtered "communities/microgalaxy/resources/test_workflows.json" \ + --status "communities/microgalaxy/metadata/test_workflow_status.tsv" \ + --curated "communities/microgalaxy/resources/test_curated_workflows.tsv" else for com_data_fp in communities/* ; do if [[ -d "$com_data_fp" && ! -L "$com_data_fp" ]]; then