From 7b5d0a8cbb60508b5d693dacfdc22c3c7c2bffa8 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Fri, 28 Jun 2024 09:34:43 +0000 Subject: [PATCH 1/2] Updating workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation from 0.1 to 0.2 --- .../CHANGELOG.md | 5 ++++ ...R-Samples-Aggregation-and-Visualisation.ga | 30 +++++++++---------- 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md index be92d9f01..a71bd36fa 100644 --- a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md +++ b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2] 2024-06-28 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0` + ## [0.1] 2024-04-24 First release. diff --git a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga index 02fa90d5a..0387866c6 100644 --- a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga +++ b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga @@ -191,7 +191,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "Bérénice Batut", + "name": "B\u00e9r\u00e9nice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { @@ -202,7 +202,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation", "report": { "markdown": "# Pathogen Detection - PathoGFAIR Samples Aggregation and Visualisation Workflow Report\nBelow are the results for the PathoGFAIR Samples Aggregation and Visualisation Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nTabular files and a FASTA file from the Gene-based Pathogen Identification workflow, four other tabular files from Nanopore Preprocessing and Nanopore - Allele-based Pathogen Identification workflow, and an optional Metadata tabular file with more sample information:\n\nFrom Gene-based Pathogenic Identification workflow: \n- contigs, FASTA file\n- VFs, Tabular file\n- vfs_of_genes_identified_by_vfdb, Tabular file\n- AMRs, Tabular file\n- amr_identified_by_ncbi, Tabular file\n\nFrom Nanopore - Allele bases Pathogen Identification workflow: \n- number_of_variants_per_sample, Tabular file\n- mapping_mean_depth_per_sample, Tabular file\n- mapping_coverage_percentage_per_sample, Tabular file\n\nFrom Nanopore Preprocessing: \n- removed_hosts_percentage_tabular, Tabular file\n\n## Some of the Workflow Outputs\n\n1- All Samples VFs Heatmap\n\n```galaxy\nhistory_dataset_as_image(output=\"heatmap_png\")\n```\n\n2- All samples phylogenetic tree VFs based\n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_vfs\")\n```\n\n3- All samples Phylogenetic tree AMR based \n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_amrs\")\n```\n\n4- Bar-plot for the Number of reads before host sequences removal and Number of found host reads per sample, performed in the Nanopore - Preprocessing workflow\n\n\n5- Barplot for the total number of removed host sequences per sample\n\n \n6- Barplot for the Mapping mean depth of coverage per sample\n\n\n6- Barplot for the Mapping breadth of coverage percentage per sample\n\n\n7- Barplot for the total number of complex variants and SNPs identified per sample\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" @@ -1474,7 +1474,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "errors": null, "id": 36, "input_connections": { @@ -1506,15 +1506,15 @@ "top": 1132.9745890557185 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a1a923cd89e8", + "changeset_revision": "64e2edfe7a2c", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": false, \"nameOnly\": false, \"split\": false, \"strand\": false, \"tab\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.30.0+galaxy1", + "tool_version": "2.31.1+galaxy0", "type": "tool", "uuid": "8018f07e-551c-4fef-b7ef-42589ff5b59e", "when": null, @@ -1576,7 +1576,7 @@ }, "38": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "errors": null, "id": 38, "input_connections": { @@ -1608,15 +1608,15 @@ "top": 1800.0079752861873 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a1a923cd89e8", + "changeset_revision": "64e2edfe7a2c", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": false, \"nameOnly\": false, \"split\": false, \"strand\": false, \"tab\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.30.0+galaxy1", + "tool_version": "2.31.1+galaxy0", "type": "tool", "uuid": "d9d6c096-58e0-4a33-af38-e94709c9af3b", "when": null, @@ -1822,7 +1822,7 @@ }, "43": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "errors": null, "id": 43, "input_connections": { @@ -1862,15 +1862,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a1a923cd89e8", + "changeset_revision": "64e2edfe7a2c", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": false, \"nameOnly\": false, \"split\": false, \"strand\": false, \"tab\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.30.0+galaxy1", + "tool_version": "2.31.1+galaxy0", "type": "tool", "uuid": "7283594d-0455-4f60-98f5-d9c315e28ee4", "when": null, @@ -3086,4 +3086,4 @@ ], "uuid": "cb26018e-9d2f-4513-a372-122474df703e", "version": 58 -} +} \ No newline at end of file From 30b73f282a84b9d7aab563dc89a57f5b488d3674 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 3 Jul 2024 13:05:04 +0200 Subject: [PATCH 2/2] Update Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga --- ...ection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga index 0387866c6..5021fde99 100644 --- a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga +++ b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga @@ -191,7 +191,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { @@ -3086,4 +3086,4 @@ ], "uuid": "cb26018e-9d2f-4513-a372-122474df703e", "version": 58 -} \ No newline at end of file +}