From 88cb73f9235e2f9a8d8fcc38d023fd7f1ea8648a Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Fri, 10 Nov 2023 11:28:47 +0000 Subject: [PATCH] Updating workflows/epigenetics/consensus-peaks from 0.1 to 0.2 --- .../epigenetics/consensus-peaks/CHANGELOG.md | 8 +++++ .../consensus-peaks-chip-pe.ga | 34 ++++++++----------- 2 files changed, 23 insertions(+), 19 deletions(-) diff --git a/workflows/epigenetics/consensus-peaks/CHANGELOG.md b/workflows/epigenetics/consensus-peaks/CHANGELOG.md index faf930c95..2a1dc9f2a 100644 --- a/workflows/epigenetics/consensus-peaks/CHANGELOG.md +++ b/workflows/epigenetics/consensus-peaks/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog +## [0.2] 2023-11-10 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0` + ## [0.3] 2023-10-17 ### Automatic update diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga index b8ff5eaa6..4786c2d94 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Get Confident Peaks From ChIP_PE duplicates", "steps": { "0": { @@ -141,7 +141,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -217,15 +217,15 @@ "output_name": "output_treat_pileup" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "640d3af5d833", + "changeset_revision": "86e2413cf3f8", "name": "macs2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": true, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": true}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"No\", \"__current_case__\": 1}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"bdg\", \"peaks_tabular\"], \"treatment\": {\"t_multi_select\": \"No\", \"__current_case__\": 0, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.7.1+galaxy0", + "tool_version": "2.2.9.1+galaxy0", "type": "tool", "uuid": "8f2a3aa4-704e-4d90-a672-94b97996dd56", "when": null, @@ -517,7 +517,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "errors": null, "id": 11, "input_connections": { @@ -534,10 +534,6 @@ { "description": "runtime parameter for tool bigwigAverage", "name": "advancedOpt" - }, - { - "description": "runtime parameter for tool bigwigAverage", - "name": "bigwigs" } ], "label": "average coverage from both replicates", @@ -561,15 +557,15 @@ "output_name": "outFileName" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "f6f246438eda", + "changeset_revision": "4a53856a5b85", "name": "deeptools_bigwig_average", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"skipNAs\": false, \"scaleFactors\": \"1\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"bigwigs\": {\"__class__\": \"RuntimeValue\"}, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.5.2+galaxy0", + "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": {\"__class__\": \"ConnectedValue\"}, \"skipNAs\": false, \"scaleFactors\": \"1\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"bigwigs\": {\"__class__\": \"ConnectedValue\"}, \"outFileFormat\": \"bigwig\", \"region\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.5.4+galaxy0", "type": "tool", "uuid": "36059130-5f2a-4fe0-8b36-58073595fdd5", "when": null, @@ -671,7 +667,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -729,15 +725,15 @@ "output_name": "output_treat_pileup" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "640d3af5d833", + "changeset_revision": "86e2413cf3f8", "name": "macs2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"to_large\": false, \"nolambda\": false, \"spmr\": true, \"ratio\": null, \"slocal\": null, \"llocal\": null, \"broad_options\": {\"broad_options_selector\": \"nobroad\", \"__current_case__\": 1, \"call_summits\": true}, \"keep_dup_options\": {\"keep_dup_options_selector\": \"1\", \"__current_case__\": 1}, \"d_min\": \"20\", \"buffer_size\": \"100000\"}, \"control\": {\"c_select\": \"No\", \"__current_case__\": 1}, \"cutoff_options\": {\"cutoff_options_selector\": \"qvalue\", \"__current_case__\": 1, \"qvalue\": \"0.05\"}, \"effective_genome_size_options\": {\"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 4, \"gsize\": {\"__class__\": \"ConnectedValue\"}}, \"format\": \"BAMPE\", \"nomodel_type\": {\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0, \"mfold_lower\": \"5\", \"mfold_upper\": \"50\", \"band_width\": \"300\"}, \"outputs\": [\"peaks_tabular\"], \"treatment\": {\"t_multi_select\": \"Yes\", \"__current_case__\": 1, \"input_treatment_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.7.1+galaxy0", + "tool_version": "2.2.9.1+galaxy0", "type": "tool", "uuid": "e183ec20-d4ab-427a-9a0c-3e9bbced8793", "when": null, @@ -977,7 +973,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"