From 1149faeefee1638e0a3f3b5e27753d349e705e41 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 17 Apr 2023 07:57:12 +0000 Subject: [PATCH] Updating workflows/variant-calling/variation-reporting from 0.2 to 0.3 --- .../Generic-variation-analysis-reporting.ga | 123 +++++++++++------- 1 file changed, 79 insertions(+), 44 deletions(-) diff --git a/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting.ga b/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting.ga index 8977cc5d9..669f5d22d 100644 --- a/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting.ga +++ b/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting.ga @@ -8,7 +8,7 @@ "name": "Wolfgang Maier" } ], - "release": "0.2", + "release": "0.3", "format-version": "0.1", "license": "MIT", "name": "Generic variation analysis reporting", @@ -37,6 +37,7 @@ "tool_version": null, "type": "data_collection_input", "uuid": "900f58cd-3ac6-4371-9295-6596726b1ee9", + "when": null, "workflow_outputs": [] }, "1": { @@ -63,6 +64,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "664a4fe1-a981-4e22-b6c4-628c87baf28a", + "when": null, "workflow_outputs": [ { "label": null, @@ -95,6 +97,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "8d6df2cd-f16c-476e-bc00-e83a5e568cdd", + "when": null, "workflow_outputs": [ { "label": null, @@ -127,6 +130,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "842ca5f3-acfd-4243-88cd-625d1834ad89", + "when": null, "workflow_outputs": [ { "label": null, @@ -167,10 +171,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": \"DP >= 1\"}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": \"DP >= 1\"}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.3+t.galaxy1", "type": "tool", "uuid": "8adcdaba-fea6-4cb1-9ec3-70972604145e", + "when": null, "workflow_outputs": [ { "label": "prefiltered_variants", @@ -229,6 +234,7 @@ "tool_version": "0.1.1", "type": "tool", "uuid": "7b42a044-ea48-4aae-82d0-7e134e47e6ee", + "when": null, "workflow_outputs": [] }, "6": { @@ -281,6 +287,7 @@ "tool_version": "0.1.1", "type": "tool", "uuid": "dd9b21a6-e2e1-4637-aca7-dd485b52ddf9", + "when": null, "workflow_outputs": [] }, "7": { @@ -331,10 +338,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"add_filter\", \"__current_case__\": 3, \"add_filter\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"add_filter\", \"__current_case__\": 3, \"add_filter\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.3+t.galaxy1", "type": "tool", "uuid": "8c1888cd-fceb-45fc-add4-2e7edc582ca1", + "when": null, "workflow_outputs": [ { "label": "filtered_variants", @@ -383,10 +391,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID DP4[2] DP4[3]\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"true\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID DP4[2] DP4[3]\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": true, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.3+t.galaxy0", "type": "tool", "uuid": "dce57343-cb31-469a-b886-d62e7ce53bad", + "when": null, "workflow_outputs": [ { "label": "filtered_extracted_variants", @@ -435,10 +444,11 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": \"false\", \"cond\": \"round((c17 + c18) / c6, 6)\", \"error_handling\": {\"auto_col_types\": \"true\", \"fail_on_non_existent_columns\": \"true\", \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"header_lines_conditional\": {\"__current_case__\": 1, \"header_lines_select\": \"yes\", \"header_new_column_name\": \"AFrecalc\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": []}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": false, \"cond\": \"round((c17 + c18) / c6, 6)\", \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"header_lines_conditional\": {\"__current_case__\": 1, \"header_lines_select\": \"yes\", \"header_new_column_name\": \"AFrecalc\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": []}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "726b7b08-31a8-4ec7-b5b9-027b1f104eeb", + "when": null, "workflow_outputs": [ { "label": "af_recalculated", @@ -449,7 +459,7 @@ }, "10": { "annotation": "", - 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"tool_version": "1.1.0+galaxy2", + "tool_state": "{\"grouping\": \"1,2,3,4,5,6,19,7,8,9\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"collapse\", \"op_column\": \"10\"}, {\"__index__\": 1, \"op_name\": \"collapse\", \"op_column\": \"11\"}, {\"__index__\": 2, \"op_name\": \"collapse\", \"op_column\": \"12\"}, {\"__index__\": 3, \"op_name\": \"collapse\", \"op_column\": \"13\"}, {\"__index__\": 4, \"op_name\": \"collapse\", \"op_column\": \"14\"}, {\"__index__\": 5, \"op_name\": \"collapse\", \"op_column\": \"15\"}, {\"__index__\": 6, \"op_name\": \"collapse\", \"op_column\": \"16\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", "type": "tool", "uuid": "a5100b84-498a-47fe-b408-fd159a8d729a", + "when": null, "workflow_outputs": [ { "label": "collapsed_effects", @@ -543,6 +554,7 @@ "tool_version": "1.1.4", "type": "tool", "uuid": "6e156bbc-a207-4941-bd6a-d654473fde37", + "when": null, "workflow_outputs": [ { "label": "highest_impact_effects", @@ -595,6 +607,7 @@ "tool_version": "1.1.4", "type": "tool", "uuid": "4d002a96-055c-4892-8ad4-d6266de51e4e", + "when": null, "workflow_outputs": [ { "label": "cleaned_header", @@ -647,6 +660,7 @@ "tool_version": "1.1.4", "type": "tool", "uuid": "9ee0a745-0f40-4579-91ed-39aaa9895302", + "when": null, "workflow_outputs": [ { "label": "processed_variants_collection", @@ -693,10 +707,11 @@ "owner": "nml", "tool_shed": "toolshed.g2.bx.psu.edu" }, - 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"tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.2", "type": "tool", "uuid": "9aeb39d3-d040-43ee-a3fa-2a65eb1a7c34", + "when": null, "workflow_outputs": [] }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "errors": null, "id": 25, "input_connections": { @@ -1194,17 +1219,18 @@ "output_name": "out_file" } }, - 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"tool_state": "{\"column1\": \"3\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"column1\": \"3\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.2", "type": "tool", "uuid": "9c3e2d08-a103-497b-b22c-667f1ca23152", + "when": null, "workflow_outputs": [] }, "27": { @@ -1291,6 +1318,7 @@ "tool_version": "1.0.2", "type": "tool", "uuid": "c74fc520-a76c-4b7b-b846-8cd8310ead70", + "when": null, "workflow_outputs": [] }, "28": { @@ -1329,6 +1357,7 @@ "tool_version": "1.0.2", "type": "tool", "uuid": "102b3ed6-1c6c-4545-9985-dfd3ac735acf", + "when": null, "workflow_outputs": [] }, "29": { @@ -1380,10 +1409,11 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.2", "type": "tool", "uuid": "95dcccd0-0323-4448-b8ca-ad1fce8d2a45", + "when": null, "workflow_outputs": [] }, "30": { @@ -1430,6 +1460,7 @@ "tool_version": "0.5.0", "type": "tool", "uuid": "c0accd6f-76af-46f7-a5f0-647000d54444", + "when": null, "workflow_outputs": [ { "label": "variants_for_plotting", @@ -1487,6 +1518,7 @@ "tool_version": "1.1.4", "type": "tool", "uuid": "cf84a2f6-689b-4bed-bc0d-324d40f46dd7", + "when": null, "workflow_outputs": [] }, "32": { @@ -1525,6 +1557,7 @@ "tool_version": "1.0.2", "type": "tool", "uuid": "3d0237fc-33b6-4305-b6e8-2502175f624f", + "when": null, "workflow_outputs": [] }, "33": { @@ -1567,10 +1600,11 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.1", "type": "tool", "uuid": "6edca54f-9af8-4305-bd11-4c74251af900", + "when": null, "workflow_outputs": [ { "label": "by_variant_report", @@ -1619,10 +1653,11 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.1", "type": "tool", "uuid": "eb754361-9ec5-46c8-80b5-6bb040345719", + "when": null, "workflow_outputs": [ { "label": "combined_variant_report",