From db21369bce92e6139a08c7f076632d34413ed347 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 23 Sep 2024 14:56:55 +0000 Subject: [PATCH] Updating workflows/variant-calling/variation-reporting from 0.1.1 to 0.1.2 --- .../variation-reporting/CHANGELOG.md | 10 + .../Generic-variation-analysis-reporting.ga | 3295 +++++++++-------- 2 files changed, 1682 insertions(+), 1623 deletions(-) diff --git a/workflows/variant-calling/variation-reporting/CHANGELOG.md b/workflows/variant-calling/variation-reporting/CHANGELOG.md index 46bfcc79c..8250d5b16 100644 --- a/workflows/variant-calling/variation-reporting/CHANGELOG.md +++ b/workflows/variant-calling/variation-reporting/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [0.1.2] 2024-09-23 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` +- `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1` + ## [0.1.1] 2023-11-20 - Fix author in dockstore 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 a3a763a4e..7f548d0f4 100644 --- a/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting.ga +++ b/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting.ga @@ -1,1641 +1,1690 @@ { - "a_galaxy_workflow": "true", - "annotation": "This workflow takes a VCF dataset of variants produced by any of the variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.", - "creator": [ - { - "class": "Person", - "identifier": "https://orcid.org/0000-0002-9464-6640", - "name": "Wolfgang Maier" - } - ], - "format-version": "0.1", - "release": "0.1.1", - "license": "MIT", - "name": "Generic variation analysis reporting", - "steps": { - "0": { - "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ + "a_galaxy_workflow": "true", + "annotation": "This workflow takes a VCF dataset of variants produced by any of the variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.", + "creator": [ { - "description": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", - "name": "Variation data to report" - } - ], - "label": "Variation data to report", - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 29.25, - "top": 0 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"vcf\", \"vcf_bgzip\"], \"tag\": \"\", \"collection_type\": \"list\"}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "900f58cd-3ac6-4371-9295-6596726b1ee9", - "workflow_outputs": [] - }, - "1": { - "annotation": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", - "name": "AF Filter" - } - ], - "label": "AF Filter", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 28.3125, - "top": 208.8203125 - }, - "tool_id": null, - "tool_state": "{\"default\": 0.05, \"parameter_type\": \"float\", \"optional\": true}", - "tool_version": null, - "type": "parameter_input", - "uuid": "664a4fe1-a981-4e22-b6c4-628c87baf28a", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "15fcff98-3e33-4deb-a083-a6c3c94b1b8d" - } - ] - }, - "2": { - "annotation": "Depth Filter. This is the minimum depth of all alignments at a variant site. ", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "Depth Filter. This is the minimum depth of all alignments at a variant site. ", - "name": "DP Filter" - } - ], - "label": "DP Filter", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 26.75, - "top": 358.8359375 - }, - "tool_id": null, - "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}", - "tool_version": null, - "type": "parameter_input", - "uuid": "8d6df2cd-f16c-476e-bc00-e83a5e568cdd", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a01b2b83-81d7-4cd5-a307-797046910821" - } - ] - }, - "3": { - "annotation": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.", - "content_id": null, - "errors": null, - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.", - "name": "DP_ALT Filter" - } - ], - "label": "DP_ALT Filter", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 0, - "top": 572.3359375 - }, - "tool_id": null, - "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}", - "tool_version": null, - "type": "parameter_input", - "uuid": "842ca5f3-acfd-4243-88cd-625d1834ad89", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "89133c97-8b6f-4c7b-abbd-799fd385ac6a" - } - ] - }, - "4": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", - "errors": null, - "id": 4, - "input_connections": { - "input": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SnpSift Filter", - "outputs": [ - { - "name": "output", - "type": "vcf" - } - ], - "position": { - "left": 348.65625, - "top": 159 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", - "tool_shed_repository": { - "changeset_revision": "2e497a770bca", - "name": "snpsift", - "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_version": "4.3+t.galaxy1", - "type": "tool", - "uuid": "8adcdaba-fea6-4cb1-9ec3-70972604145e", - "workflow_outputs": [ - { - "label": "prefiltered_variants", - "output_name": "output", - "uuid": "7e953ef0-9e3a-485b-8201-290512552269" - } - ] - }, - "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", - "errors": null, - "id": 5, - "input_connections": { - "components_1|param_type|component_value": { - "id": 1, - "output_name": "output" + "class": "Person", + "identifier": "https://orcid.org/0000-0002-9464-6640", + "name": "Wolfgang Maier" + } + ], + "format-version": "0.1", + "release": "0.1.2", + "license": "MIT", + "name": "Generic variation analysis reporting", + "steps": { + "0": { + "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", + "name": "Variation data to report" + } + ], + "label": "Variation data to report", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 29.25, + "top": 0 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"vcf\", \"vcf_bgzip\"], \"tag\": \"\", \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "900f58cd-3ac6-4371-9295-6596726b1ee9", + "when": null, + "workflow_outputs": [] }, - "components_3|param_type|component_value": { - "id": 2, - "output_name": "output" + "1": { + "annotation": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", + "name": "AF Filter" + } + ], + "label": "AF Filter", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 28.3125, + "top": 208.8203125 + }, + "tool_id": null, + "tool_state": "{\"default\": 0.05, \"parameter_type\": \"float\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "664a4fe1-a981-4e22-b6c4-628c87baf28a", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "15fcff98-3e33-4deb-a083-a6c3c94b1b8d" + } + ] }, - "components_5|param_type|component_value": { - "id": 3, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Compose text parameter value", - "outputs": [ - { - "name": "out1", - "type": "expression.json" - } - ], - "position": { - "left": 347, - "top": 283.2734375 - }, - "post_job_actions": { - "HideDatasetActionout1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out1" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", - "tool_shed_repository": { - "changeset_revision": "e188c9826e0f", - "name": "compose_text_param", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"( ( DP4[2] + DP4[3] ) < ( \"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" * DP ) ) | ( DP < \"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" ) | ( ( AF * DP ) < ( \"}}, {\"__index__\": 5, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" - 0.5 ) )\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.1", - "type": "tool", - "uuid": "7b42a044-ea48-4aae-82d0-7e134e47e6ee", - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", - "errors": null, - "id": 6, - "input_connections": { - "components_1|param_type|component_value": { - "id": 1, - "output_name": "output" + "2": { + "annotation": "Depth Filter. This is the minimum depth of all alignments at a variant site. ", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Depth Filter. This is the minimum depth of all alignments at a variant site. ", + "name": "DP Filter" + } + ], + "label": "DP Filter", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 26.75, + "top": 358.8359375 + }, + "tool_id": null, + "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "8d6df2cd-f16c-476e-bc00-e83a5e568cdd", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "a01b2b83-81d7-4cd5-a307-797046910821" + } + ] }, - "components_3|param_type|component_value": { - "id": 2, - "output_name": "output" + "3": { + "annotation": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.", + "name": "DP_ALT Filter" + } + ], + "label": "DP_ALT Filter", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0, + "top": 572.3359375 + }, + "tool_id": null, + "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "842ca5f3-acfd-4243-88cd-625d1834ad89", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "89133c97-8b6f-4c7b-abbd-799fd385ac6a" + } + ] }, - "components_5|param_type|component_value": { - "id": 3, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Compose text parameter value", - "outputs": [ - { - "name": "out1", - "type": "expression.json" - } - ], - "position": { - "left": 343.71875, - "top": 590.75 - }, - "post_job_actions": { - "HideDatasetActionout1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out1" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", - "tool_shed_repository": { - "changeset_revision": "e188c9826e0f", - "name": "compose_text_param", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"min_af_\"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"|min_dp_\"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"|min_dp_alt_\"}}, {\"__index__\": 5, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.1", - "type": "tool", - "uuid": "dd9b21a6-e2e1-4637-aca7-dd485b52ddf9", - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", - "errors": null, - "id": 7, - "input_connections": { - "filter_expression|expr": { - "id": 5, - "output_name": "out1" + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", + "errors": null, + "id": 4, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 348.65625, + "top": 159 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", + "tool_shed_repository": { + "changeset_revision": "5fab4f81391d", + "name": "snpsift", + "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_version": "4.3+t.galaxy1", + "type": "tool", + "uuid": "8adcdaba-fea6-4cb1-9ec3-70972604145e", + "when": null, + "workflow_outputs": [ + { + "label": "prefiltered_variants", + "output_name": "output", + "uuid": "7e953ef0-9e3a-485b-8201-290512552269" + } + ] }, - "filtering|add_filter": { - "id": 6, - "output_name": "out1" + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "errors": null, + "id": 5, + "input_connections": { + "components_1|param_type|component_value": { + "id": 1, + "output_name": "output" + }, + "components_3|param_type|component_value": { + "id": 2, + "output_name": "output" + }, + "components_5|param_type|component_value": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Compose text parameter value", + "outputs": [ + { + "name": "out1", + "type": "expression.json" + } + ], + "position": { + "left": 347, + "top": 283.2734375 + }, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "tool_shed_repository": { + "changeset_revision": "e188c9826e0f", + "name": "compose_text_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"( ( DP4[2] + DP4[3] ) < ( \"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" * DP ) ) | ( DP < \"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" ) | ( ( AF * DP ) < ( \"}}, {\"__index__\": 5, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 6, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" - 0.5 ) )\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.1", + "type": "tool", + "uuid": "7b42a044-ea48-4aae-82d0-7e134e47e6ee", + "when": null, + "workflow_outputs": [] }, - "input": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SnpSift Filter", - "outputs": [ - { - "name": "output", - "type": "vcf" - } - ], - "position": { - "left": 579.40625, - "top": 448.984375 - }, - "post_job_actions": { - "RenameDatasetActionoutput": { - "action_arguments": { - "newname": "Filtered variants" - }, - "action_type": "RenameDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", - "tool_shed_repository": { - "changeset_revision": "2e497a770bca", - "name": "snpsift", - "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_version": "4.3+t.galaxy1", - "type": "tool", - "uuid": "8c1888cd-fceb-45fc-add4-2e7edc582ca1", - "workflow_outputs": [ - { - "label": "filtered_variants", - "output_name": "output", - "uuid": "a923399c-9faa-40a7-be8d-caa2ca72c5be" - } - ] - }, - "8": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", - "errors": null, - "id": 8, - "input_connections": { - "input": { - "id": 7, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "SnpSift Extract Fields", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 815.4375, - "top": 345.9609375 - }, - "post_job_actions": { - "RenameDatasetActionoutput": { - "action_arguments": { - "newname": "Filtered extracted variants" - }, - "action_type": "RenameDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", - "tool_shed_repository": { - "changeset_revision": "2e497a770bca", - "name": "snpsift", - "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_version": "4.3+t.galaxy0", - "type": "tool", - "uuid": "dce57343-cb31-469a-b886-d62e7ce53bad", - "workflow_outputs": [ - { - "label": "filtered_extracted_variants", - "output_name": "output", - "uuid": "fb09ef77-9522-452a-a0e9-73a4a580b8aa" - } - ] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", - "errors": null, - "id": 9, - "input_connections": { - "input": { - "id": 8, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Compute", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1266.7265625, - "top": 367.2578125 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "Extracted variants with filtered and renamed effects and AF recalculated" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", - "tool_shed_repository": { - "changeset_revision": "427903d47026", - "name": "column_maker", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"avoid_scientific_notation\": \"false\", \"cond\": \"round((c17 + c18) / c6, 6)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"AFrecalc\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.6", - "type": "tool", - "uuid": "726b7b08-31a8-4ec7-b5b9-027b1f104eeb", - "workflow_outputs": [ - { - "label": "af_recalculated", - "output_name": "out_file1", - "uuid": "a47c05f5-0ea1-4649-a7c1-7b88cca0e6e5" - } - ] - }, - "10": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "errors": null, - "id": 10, - "input_connections": { - "in_file": { - "id": 9, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Datamash", - "outputs": [ - { - "name": "out_file", - "type": "tabular" - } - ], - "position": { - "left": 1433.15625, - "top": 147.5 - }, - "post_job_actions": { - "RenameDatasetActionout_file": { - "action_arguments": { - "newname": "Collapsed effects (Datamash on all variants)" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "tool_shed_repository": { - "changeset_revision": "562f3c677828", - "name": "datamash_ops", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "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\"}, \"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": "1.1.0", - "type": "tool", - "uuid": "a5100b84-498a-47fe-b408-fd159a8d729a", - "workflow_outputs": [ - { - "label": "collapsed_effects", - "output_name": "out_file", - "uuid": "407d9cee-4b7d-4855-b62c-a166ecf8f50e" - } - ] - }, - "11": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "errors": null, - "id": 11, - "input_connections": { - "infile": { - "id": 10, - "output_name": "out_file" - } - }, - "inputs": [], - "label": null, - "name": "Replace", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 1556.34375, - "top": 323.5625 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "Extracted variants with highest impact effects" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"caseinsensitive\": \"false\", \"find_pattern\": \"\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\s]+\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"\\\\t$1\\\\t$2\\\\t$3\\\\t$4\\\\t$5\\\\t$6\\\\t$7\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"true\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.3", - "type": "tool", - "uuid": "6e156bbc-a207-4941-bd6a-d654473fde37", - "workflow_outputs": [ - { - "label": "highest_impact_effects", - "output_name": "outfile", - "uuid": "aacf2235-fd9c-43e9-a886-dde7ccc7c691" - } - ] - }, - "12": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "errors": null, - "id": 12, - "input_connections": { - "infile": { - "id": 11, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Replace", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 1707.1953125, - "top": 165.234375 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "Variants with cleaned up header" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"caseinsensitive\": \"false\", \"find_pattern\": \"(GroupBy|collapse)\\\\(([^)]+)\\\\)\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"$2\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.3", - "type": "tool", - "uuid": "4d002a96-055c-4892-8ad4-d6266de51e4e", - "workflow_outputs": [ - { - "label": "cleaned_header", - "output_name": "outfile", - "uuid": "0bade229-08f2-491c-8361-77ec91ceed98" - } - ] - }, - "13": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "errors": null, - "id": 13, - "input_connections": { - "infile": { - "id": 12, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Replace", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 1825.5, - "top": 329.8828125 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "Fully processed variants collection for reporting" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"caseinsensitive\": \"false\", \"find_pattern\": \"AFrecalc\\\\tAF\", \"global\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"AF\\\\tAFcaller\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.3", - "type": "tool", - "uuid": "9ee0a745-0f40-4579-91ed-39aaa9895302", - "workflow_outputs": [ - { - "label": "processed_variants_collection", - "output_name": "outfile", - "uuid": "2707f4c6-dd54-44bb-adad-a3703d165823" - } - ] - }, - "14": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", - "errors": null, - "id": 14, - "input_connections": { - "input_list": { - "id": 13, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Collapse Collection", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 1984.5078125, - "top": 154.984375 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", - "tool_shed_repository": { - "changeset_revision": "90981f86000f", - "name": "collapse_collections", - "owner": "nml", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"filename\": {\"add_name\": \"true\", \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.1.0", - "type": "tool", - "uuid": "c8ad21ea-c72b-4063-9974-380869b87d58", - "workflow_outputs": [] - }, - "15": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", - "errors": null, - "id": 15, - "input_connections": { - "input": { - "id": 14, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Compute", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 2106.3828125, - "top": 338.484375 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", - "tool_shed_repository": { - "changeset_revision": "427903d47026", - "name": "column_maker", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"avoid_scientific_notation\": \"false\", \"cond\": \"str(c5) + '>' + str(c6)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"change\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.6", - "type": "tool", - "uuid": "61cc455a-4330-4518-bf8a-b099780bdb30", - "workflow_outputs": [] - }, - "16": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", - "errors": null, - "id": 16, - "input_connections": { - "input": { - "id": 15, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Compute", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 2329.8984375, - "top": 339.296875 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", - "tool_shed_repository": { - "changeset_revision": "427903d47026", - "name": "column_maker", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"avoid_scientific_notation\": \"false\", \"cond\": \"str(int(c3)) + ':' + str(c19)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"change_with_pos\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.6", - "type": "tool", - "uuid": "5a0297af-22c4-4550-8673-cbe044496410", - "workflow_outputs": [] - }, - "17": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "errors": null, - "id": 17, - "input_connections": { - "infile": { - "id": 16, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Replace", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 2536.0703125, - "top": 207.0859375 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "All variants of all samples" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"caseinsensitive\": \"false\", \"find_pattern\": \"EFF[*].\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"false\", \"replace_pattern\": \"\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.3", - "type": "tool", - "uuid": "23c73601-2fdb-4a1e-be60-ff0f1ec96be8", - "workflow_outputs": [ - { - "label": "all_variants_all_samples", - "output_name": "outfile", - "uuid": "c3bf5f59-3363-4305-ab99-7c38fceab34c" - } - ] - }, - "18": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "errors": null, - "id": 18, - "input_connections": { - "in_file": { - "id": 17, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Datamash", - "outputs": [ - { - "name": "out_file", - "type": "tabular" - } - ], - "position": { - "left": 2787.3359375, - "top": 158.5234375 - }, - "post_job_actions": { - "HideDatasetActionout_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "tool_shed_repository": { - "changeset_revision": "562f3c677828", - "name": "datamash_ops", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"grouping\": \"20\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"min\", \"op_column\": \"8\"}, {\"__index__\": 2, \"op_name\": \"max\", \"op_column\": \"8\"}, {\"__index__\": 3, \"op_name\": \"collapse\", \"op_column\": \"1\"}, {\"__index__\": 4, \"op_name\": \"collapse\", \"op_column\": \"8\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0", - "type": "tool", - "uuid": "61adea76-ce05-489d-af2b-1ad74bd141fa", - "workflow_outputs": [] - }, - "19": { - "annotation": "", - "content_id": "Filter1", - "errors": null, - "id": 19, - "input_connections": { - "input": { - "id": 17, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Filter", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 2780.1328125, - "top": 371.6484375 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "Filter1", - "tool_state": "{\"cond\": \"c4=='PASS' or c4=='.'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.1", - "type": "tool", - "uuid": "c5568630-a6f4-468c-b320-5f28547f7c14", - "workflow_outputs": [] - }, - "20": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "errors": null, - "id": 20, - "input_connections": { - "in_file": { - "id": 17, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Datamash", - "outputs": [ - { - "name": "out_file", - "type": "tabular" - } - ], - "position": { - "left": 3071.03125, - "top": 568.5703125 - }, - "post_job_actions": { - "HideDatasetActionout_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file" + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "errors": null, + "id": 6, + "input_connections": { + "components_1|param_type|component_value": { + "id": 1, + "output_name": "output" + }, + "components_3|param_type|component_value": { + "id": 2, + "output_name": "output" + }, + "components_5|param_type|component_value": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Compose text parameter value", + "outputs": [ + { + "name": "out1", + "type": "expression.json" + } + ], + "position": { + "left": 343.71875, + "top": 590.75 + }, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "tool_shed_repository": { + "changeset_revision": "e188c9826e0f", + "name": "compose_text_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"min_af_\"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"|min_dp_\"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"|min_dp_alt_\"}}, {\"__index__\": 5, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.1", + "type": "tool", + "uuid": "dd9b21a6-e2e1-4637-aca7-dd485b52ddf9", + "when": null, + "workflow_outputs": [] }, - "RenameDatasetActionout_file": { - "action_arguments": { - "newname": "Cross-sample variant stats (Datamash)" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "tool_shed_repository": { - "changeset_revision": "562f3c677828", - "name": "datamash_ops", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"grouping\": \"3\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"min\", \"op_column\": \"8\"}, {\"__index__\": 2, \"op_name\": \"max\", \"op_column\": \"8\"}, {\"__index__\": 3, \"op_name\": \"countunique\", \"op_column\": \"19\"}, {\"__index__\": 4, \"op_name\": \"countunique\", \"op_column\": \"13\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0", - "type": "tool", - "uuid": "517d8ba6-1df6-417c-96e9-f297b3b8f51f", - "workflow_outputs": [] - }, - "21": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "errors": null, - "id": 21, - "input_connections": { - "in_file": { - "id": 19, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Datamash", - "outputs": [ - { - "name": "out_file", - "type": "tabular" - } - ], - "position": { - "left": 2895.6484375, - "top": 789.3203125 - }, - "post_job_actions": { - "HideDatasetActionout_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "tool_shed_repository": { - "changeset_revision": "562f3c677828", - "name": "datamash_ops", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"grouping\": \"20\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0", - "type": "tool", - "uuid": "6f97bd54-aeea-4615-b6f0-b9cc8e99b519", - "workflow_outputs": [] - }, - "22": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "errors": null, - "id": 22, - "input_connections": { - "infile1": { - "id": 19, - "output_name": "out_file1" + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", + "errors": null, + "id": 7, + "input_connections": { + "filter_expression|expr": { + "id": 5, + "output_name": "out1" + }, + "filtering|add_filter": { + "id": 6, + "output_name": "out1" + }, + "input": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "filter_expression" + }, + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "filtering" + } + ], + "label": null, + "name": "SnpSift Filter", + "outputs": [ + { + "name": "output", + "type": "vcf" + } + ], + "position": { + "left": 579.40625, + "top": 448.984375 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "Filtered variants" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", + "tool_shed_repository": { + "changeset_revision": "5fab4f81391d", + "name": "snpsift", + "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_version": "4.3+t.galaxy1", + "type": "tool", + "uuid": "8c1888cd-fceb-45fc-add4-2e7edc582ca1", + "when": null, + "workflow_outputs": [ + { + "label": "filtered_variants", + "output_name": "output", + "uuid": "a923399c-9faa-40a7-be8d-caa2ca72c5be" + } + ] }, - "infile2": { - "id": 18, - "output_name": "out_file" - } - }, - "inputs": [], - "label": null, - "name": "Join", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 3028.71875, - "top": 178.8984375 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", + "errors": null, + "id": 8, + "input_connections": { + "input": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "SnpSift Extract Fields", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 815.4375, + "top": 345.9609375 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "Filtered extracted variants" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", + "tool_shed_repository": { + "changeset_revision": "5fab4f81391d", + "name": "snpsift", + "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_version": "4.3+t.galaxy0", + "type": "tool", + "uuid": "dce57343-cb31-469a-b886-d62e7ce53bad", + "when": null, + "workflow_outputs": [ + { + "label": "filtered_extracted_variants", + "output_name": "output", + "uuid": "fb09ef77-9522-452a-a0e9-73a4a580b8aa" + } + ] }, - "RenameDatasetActionoutput": { - "action_arguments": { - "newname": "Filtered variants of all samples with stats" - }, - "action_type": "RenameDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "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": "ce58eb8c-118f-467e-80e4-b0bf35c2919f", - "workflow_outputs": [] - }, - "23": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "errors": null, - "id": 23, - "input_connections": { - "in_file": { - "id": 19, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Datamash", - "outputs": [ - { - "name": "out_file", - "type": "tabular" - } - ], - "position": { - "left": 3037.1484375, - "top": 439.0625 - }, - "post_job_actions": { - "HideDatasetActionout_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "tool_shed_repository": { - "changeset_revision": "562f3c677828", - "name": "datamash_ops", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"grouping\": \"3\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0", - "type": "tool", - "uuid": "aee9b1d2-a707-4101-8b22-23ebaa3a32a1", - "workflow_outputs": [] - }, - "24": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "errors": null, - "id": 24, - "input_connections": { - "infile1": { - "id": 16, - "output_name": "out_file1" + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "errors": null, + "id": 9, + "input_connections": { + "input": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Compute", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1266.7265625, + "top": 367.2578125 + }, + "post_job_actions": { + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "Extracted variants with filtered and renamed effects and AF recalculated" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "tool_shed_repository": { + "changeset_revision": "aff5135563c6", + "name": "column_maker", + "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_version": "2.1", + "type": "tool", + "uuid": "726b7b08-31a8-4ec7-b5b9-027b1f104eeb", + "when": null, + "workflow_outputs": [ + { + "label": "af_recalculated", + "output_name": "out_file1", + "uuid": "a47c05f5-0ea1-4649-a7c1-7b88cca0e6e5" + } + ] }, - "infile2": { - "id": 21, - "output_name": "out_file" - } - }, - "inputs": [], - "label": null, - "name": "Join", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 3232.8984375, - "top": 719.8359375 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "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", - "workflow_outputs": [] - }, - "25": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "errors": null, - "id": 25, - "input_connections": { - "in_file": { - "id": 22, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Datamash", - "outputs": [ - { - "name": "out_file", - "type": "tabular" - } - ], - "position": { - "left": 3272.8359375, - "top": 142.0234375 - }, - "post_job_actions": { - "HideDatasetActionout_file": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", - "tool_shed_repository": { - "changeset_revision": "562f3c677828", - "name": "datamash_ops", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"grouping\": \"1\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"unique\", \"op_column\": \"2\"}], \"print_full_line\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.0", - "type": "tool", - "uuid": "74886968-16db-41a0-9d2a-98475d1d163e", - "workflow_outputs": [] - }, - "26": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "errors": null, - "id": 26, - "input_connections": { - "infile1": { - "id": 17, - "output_name": "outfile" + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "errors": null, + "id": 10, + "input_connections": { + "in_file": { + "id": 9, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 1433.15625, + "top": 147.5 + }, + "post_job_actions": { + "RenameDatasetActionout_file": { + "action_arguments": { + "newname": "Collapsed effects (Datamash on all variants)" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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", + "output_name": "out_file", + "uuid": "407d9cee-4b7d-4855-b62c-a166ecf8f50e" + } + ] }, - "infile2": { - "id": 23, - "output_name": "out_file" - } - }, - "inputs": [], - "label": null, - "name": "Join", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 3274.8984375, - "top": 351.5703125 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "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", - "workflow_outputs": [] - }, - "27": { - "annotation": "", - "content_id": "Cut1", - "errors": null, - "id": 27, - "input_connections": { - "input": { - "id": 24, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Cut", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 3458.375, - "top": 655.5859375 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c2,c3,c4,c5,c6,c7,c8,c9,c11,c12,c13,c14,c15,c16,c17,c18,c19\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.2", - "type": "tool", - "uuid": "c74fc520-a76c-4b7b-b846-8cd8310ead70", - "workflow_outputs": [] - }, - "28": { - "annotation": "", - "content_id": "Cut1", - "errors": null, - "id": 28, - "input_connections": { - "input": { - "id": 25, - "output_name": "out_file" - } - }, - "inputs": [], - "label": null, - "name": "Cut", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 3496.8984375, - "top": 246.8125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c4,c6,c7,c13,c14,c15,c16,c17,c18,c19,c21,c22,c23,c26,c24,c25,c20\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.2", - "type": "tool", - "uuid": "102b3ed6-1c6c-4545-9985-dfd3ac735acf", - "workflow_outputs": [] - }, - "29": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "errors": null, - "id": 29, - "input_connections": { - "infile1": { - "id": 26, - "output_name": "output" + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 11, + "input_connections": { + "infile": { + "id": 10, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 1556.34375, + "top": 323.5625 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Extracted variants with highest impact effects" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"caseinsensitive\": \"false\", \"find_and_replace\": [], \"find_pattern\": \"\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\s]+\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"\\\\t$1\\\\t$2\\\\t$3\\\\t$4\\\\t$5\\\\t$6\\\\t$7\", \"searchwhere\": {\"__current_case__\": 0, \"searchwhere_select\": \"line\"}, \"skip_first_line\": \"true\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "6e156bbc-a207-4941-bd6a-d654473fde37", + "when": null, + "workflow_outputs": [ + { + "label": "highest_impact_effects", + "output_name": "outfile", + "uuid": "aacf2235-fd9c-43e9-a886-dde7ccc7c691" + } + ] }, - "infile2": { - "id": 20, - "output_name": "out_file" - } - }, - "inputs": [], - "label": null, - "name": "Join", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 3492.9375, - "top": 444.734375 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 12, + "input_connections": { + "infile": { + "id": 11, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 1707.1953125, + "top": 165.234375 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Variants with cleaned up header" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"caseinsensitive\": \"false\", \"find_and_replace\": [], \"find_pattern\": \"(GroupBy|collapse)\\\\(([^)]+)\\\\)\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"$2\", \"searchwhere\": {\"__current_case__\": 0, \"searchwhere_select\": \"line\"}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "4d002a96-055c-4892-8ad4-d6266de51e4e", + "when": null, + "workflow_outputs": [ + { + "label": "cleaned_header", + "output_name": "outfile", + "uuid": "0bade229-08f2-491c-8361-77ec91ceed98" + } + ] }, - "RenameDatasetActionoutput": { - "action_arguments": { - "newname": "Filtered variants of all samples with per-position stats" - }, - "action_type": "RenameDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "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_version": "1.1.2", - "type": "tool", - "uuid": "95dcccd0-0323-4448-b8ca-ad1fce8d2a45", - "workflow_outputs": [] - }, - "30": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", - "errors": null, - "id": 30, - "input_connections": { - "split_parms|input": { - "id": 27, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Split file", - "outputs": [ - { - "name": "list_output_tab", - "type": "input" - } - ], - "position": { - "left": 3681.6328125, - "top": 655.7578125 - }, - "post_job_actions": { - "RenameDatasetActionlist_output_tab": { - "action_arguments": { - "newname": "Per-sample variants for plotting" - }, - "action_type": "RenameDatasetAction", - "output_name": "list_output_tab" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", - "tool_shed_repository": { - "changeset_revision": "6cbe2f30c2d7", - "name": "split_file_to_collection", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"split_parms\": {\"select_ftype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"top\": \"1\", \"split_by\": {\"select_split_by\": \"col\", \"__current_case__\": 0, \"id_col\": \"1\", \"match_regex\": \"(.*)\", \"sub_regex\": \"\\\\1\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.5.0", - "type": "tool", - "uuid": "c0accd6f-76af-46f7-a5f0-647000d54444", - "workflow_outputs": [ - { - "label": "variants_for_plotting", - "output_name": "list_output_tab", - "uuid": "e62f958f-e749-43b4-9c02-17fced624689" - } - ] - }, - "31": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "errors": null, - "id": 31, - "input_connections": { - "infile": { - "id": 28, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Replace", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 3706.375, - "top": 146.25 - }, - "post_job_actions": { - "HideDatasetActionoutfile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outfile" + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 13, + "input_connections": { + "infile": { + "id": 12, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 1825.5, + "top": 329.8828125 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Fully processed variants collection for reporting" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"caseinsensitive\": \"false\", \"find_and_replace\": [], \"find_pattern\": \"AFrecalc\\\\tAF\", \"global\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"AF\\\\tAFcaller\", \"searchwhere\": {\"__current_case__\": 0, \"searchwhere_select\": \"line\"}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "9ee0a745-0f40-4579-91ed-39aaa9895302", + "when": null, + "workflow_outputs": [ + { + "label": "processed_variants_collection", + "output_name": "outfile", + "uuid": "2707f4c6-dd54-44bb-adad-a3703d165823" + } + ] }, - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "All variants of all samples" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"caseinsensitive\": \"false\", \"find_pattern\": \"unique\\\\(Sample\\\\)\\\\tcollapse\\\\(Sample\\\\)\\\\tcollapse\\\\(AF\\\\)\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"SAMPLES(above-thresholds)\\\\tSAMPLES(all)\\\\tAFs(all)\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.3", - "type": "tool", - "uuid": "cf84a2f6-689b-4bed-bc0d-324d40f46dd7", - "workflow_outputs": [] - }, - "32": { - "annotation": "", - "content_id": "Cut1", - "errors": null, - "id": 32, - "input_connections": { - "input": { - "id": 29, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Cut", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 3710.1875, - "top": 471.234375 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c2,c1,c4,c5,c6,c7,c8,c9,c11,c10,c12,c13,c14,c15,c16,c17,c18,c23,c24,c25,c26,c19\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.2", - "type": "tool", - "uuid": "3d0237fc-33b6-4305-b6e8-2502175f624f", - "workflow_outputs": [] - }, - "33": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", - "errors": null, - "id": 33, - "input_connections": { - "infile": { - "id": 31, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Sort", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 3928.8984375, - "top": 247.8125 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "Combined Variant Report by Variant" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "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_version": "1.1.1", - "type": "tool", - "uuid": "6edca54f-9af8-4305-bd11-4c74251af900", - "workflow_outputs": [ - { - "label": "by_variant_report", - "output_name": "outfile", - "uuid": "30808300-2789-48b0-9073-98ec1bddcb3f" + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", + "errors": null, + "id": 14, + "input_connections": { + "input_list": { + "id": 13, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Collapse Collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1984.5078125, + "top": 154.984375 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", + "tool_shed_repository": { + "changeset_revision": "90981f86000f", + "name": "collapse_collections", + "owner": "nml", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.1.0", + "type": "tool", + "uuid": "c8ad21ea-c72b-4063-9974-380869b87d58", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "errors": null, + "id": 15, + "input_connections": { + "input": { + "id": 14, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Compute", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 2106.3828125, + "top": 338.484375 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "tool_shed_repository": { + "changeset_revision": "aff5135563c6", + "name": "column_maker", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"avoid_scientific_notation\": false, \"cond\": \"str(c5) + '>' + str(c6)\", \"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\": \"change\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": []}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.1", + "type": "tool", + "uuid": "61cc455a-4330-4518-bf8a-b099780bdb30", + "when": null, + "workflow_outputs": [] + }, + "16": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "errors": null, + "id": 16, + "input_connections": { + "input": { + "id": 15, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Compute", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 2329.8984375, + "top": 339.296875 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", + "tool_shed_repository": { + "changeset_revision": "aff5135563c6", + "name": "column_maker", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"avoid_scientific_notation\": false, \"cond\": \"str(int(c3)) + ':' + str(c19)\", \"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\": \"change_with_pos\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": []}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.1", + "type": "tool", + "uuid": "5a0297af-22c4-4550-8673-cbe044496410", + "when": null, + "workflow_outputs": [] + }, + "17": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 17, + "input_connections": { + "infile": { + "id": 16, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 2536.0703125, + "top": 207.0859375 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "All variants of all samples" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"caseinsensitive\": \"false\", \"find_and_replace\": [], \"find_pattern\": \"EFF[*].\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"false\", \"replace_pattern\": \"\", \"searchwhere\": {\"__current_case__\": 0, \"searchwhere_select\": \"line\"}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "23c73601-2fdb-4a1e-be60-ff0f1ec96be8", + "when": null, + "workflow_outputs": [ + { + "label": "all_variants_all_samples", + "output_name": "outfile", + "uuid": "c3bf5f59-3363-4305-ab99-7c38fceab34c" + } + ] + }, + "18": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "errors": null, + "id": 18, + "input_connections": { + "in_file": { + "id": 17, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 2787.3359375, + "top": 158.5234375 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"grouping\": \"20\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"min\", \"op_column\": \"8\"}, {\"__index__\": 2, \"op_name\": \"max\", \"op_column\": \"8\"}, {\"__index__\": 3, \"op_name\": \"collapse\", \"op_column\": \"1\"}, {\"__index__\": 4, \"op_name\": \"collapse\", \"op_column\": \"8\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", + "type": "tool", + "uuid": "61adea76-ce05-489d-af2b-1ad74bd141fa", + "when": null, + "workflow_outputs": [] + }, + "19": { + "annotation": "", + "content_id": "Filter1", + "errors": null, + "id": 19, + "input_connections": { + "input": { + "id": 17, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Filter", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 2780.1328125, + "top": 371.6484375 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Filter1", + "tool_state": "{\"cond\": \"c4=='PASS' or c4=='.'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.1", + "type": "tool", + "uuid": "c5568630-a6f4-468c-b320-5f28547f7c14", + "when": null, + "workflow_outputs": [] + }, + "20": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "errors": null, + "id": 20, + "input_connections": { + "in_file": { + "id": 17, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 3071.03125, + "top": 568.5703125 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + }, + "RenameDatasetActionout_file": { + "action_arguments": { + "newname": "Cross-sample variant stats (Datamash)" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"grouping\": \"3\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"min\", \"op_column\": \"8\"}, {\"__index__\": 2, \"op_name\": \"max\", \"op_column\": \"8\"}, {\"__index__\": 3, \"op_name\": \"countunique\", \"op_column\": \"19\"}, {\"__index__\": 4, \"op_name\": \"countunique\", \"op_column\": \"13\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", + "type": "tool", + "uuid": "517d8ba6-1df6-417c-96e9-f297b3b8f51f", + "when": null, + "workflow_outputs": [] + }, + "21": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "errors": null, + "id": 21, + "input_connections": { + "in_file": { + "id": 19, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 2895.6484375, + "top": 789.3203125 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"grouping\": \"20\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", + "type": "tool", + "uuid": "6f97bd54-aeea-4615-b6f0-b9cc8e99b519", + "when": null, + "workflow_outputs": [] + }, + "22": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "errors": null, + "id": 22, + "input_connections": { + "infile1": { + "id": 19, + "output_name": "out_file1" + }, + "infile2": { + "id": 18, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Join", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3028.71875, + "top": 178.8984375 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "Filtered variants of all samples with stats" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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": "9.3+galaxy1", + "type": "tool", + "uuid": "ce58eb8c-118f-467e-80e4-b0bf35c2919f", + "when": null, + "workflow_outputs": [] + }, + "23": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "errors": null, + "id": 23, + "input_connections": { + "in_file": { + "id": 19, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 3037.1484375, + "top": 439.0625 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"grouping\": \"3\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"1\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", + "type": "tool", + "uuid": "aee9b1d2-a707-4101-8b22-23ebaa3a32a1", + "when": null, + "workflow_outputs": [] + }, + "24": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "errors": null, + "id": 24, + "input_connections": { + "infile1": { + "id": 16, + "output_name": "out_file1" + }, + "infile2": { + "id": 21, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Join", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3232.8984375, + "top": 719.8359375 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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": "9.3+galaxy1", + "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/1.8+galaxy0", + "errors": null, + "id": 25, + "input_connections": { + "in_file": { + "id": 22, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Datamash", + "outputs": [ + { + "name": "out_file", + "type": "input" + } + ], + "position": { + "left": 3272.8359375, + "top": 142.0234375 + }, + "post_job_actions": { + "HideDatasetActionout_file": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", + "tool_shed_repository": { + "changeset_revision": "4c07ddedc198", + "name": "datamash_ops", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"grouping\": \"1\", \"header_in\": true, \"header_out\": true, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": true, \"operations\": [{\"__index__\": 0, \"op_name\": \"unique\", \"op_column\": \"2\"}], \"print_full_line\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8+galaxy0", + "type": "tool", + "uuid": "74886968-16db-41a0-9d2a-98475d1d163e", + "when": null, + "workflow_outputs": [] + }, + "26": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "errors": null, + "id": 26, + "input_connections": { + "infile1": { + "id": 17, + "output_name": "outfile" + }, + "infile2": { + "id": 23, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Join", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3274.8984375, + "top": 351.5703125 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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": "9.3+galaxy1", + "type": "tool", + "uuid": "9c3e2d08-a103-497b-b22c-667f1ca23152", + "when": null, + "workflow_outputs": [] + }, + "27": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 27, + "input_connections": { + "input": { + "id": 24, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 3458.375, + "top": 655.5859375 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c2,c3,c4,c5,c6,c7,c8,c9,c11,c12,c13,c14,c15,c16,c17,c18,c19\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "c74fc520-a76c-4b7b-b846-8cd8310ead70", + "when": null, + "workflow_outputs": [] + }, + "28": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 28, + "input_connections": { + "input": { + "id": 25, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 3496.8984375, + "top": 246.8125 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c4,c6,c7,c13,c14,c15,c16,c17,c18,c19,c21,c22,c23,c26,c24,c25,c20\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "102b3ed6-1c6c-4545-9985-dfd3ac735acf", + "when": null, + "workflow_outputs": [] + }, + "29": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "errors": null, + "id": 29, + "input_connections": { + "infile1": { + "id": 26, + "output_name": "output" + }, + "infile2": { + "id": 20, + "output_name": "out_file" + } + }, + "inputs": [], + "label": null, + "name": "Join", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 3492.9375, + "top": 444.734375 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + }, + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "Filtered variants of all samples with per-position stats" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "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_version": "9.3+galaxy1", + "type": "tool", + "uuid": "95dcccd0-0323-4448-b8ca-ad1fce8d2a45", + "when": null, + "workflow_outputs": [] + }, + "30": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "errors": null, + "id": 30, + "input_connections": { + "split_parms|input": { + "id": 27, + "output_name": "out_file1" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Split file", + "name": "split_parms" + } + ], + "label": null, + "name": "Split file", + "outputs": [ + { + "name": "list_output_tab", + "type": "input" + } + ], + "position": { + "left": 3681.6328125, + "top": 655.7578125 + }, + "post_job_actions": { + "RenameDatasetActionlist_output_tab": { + "action_arguments": { + "newname": "Per-sample variants for plotting" + }, + "action_type": "RenameDatasetAction", + "output_name": "list_output_tab" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", + "tool_shed_repository": { + "changeset_revision": "2dae863c8f42", + "name": "split_file_to_collection", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"split_parms\": {\"select_ftype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"top\": \"1\", \"split_by\": {\"select_split_by\": \"col\", \"__current_case__\": 0, \"id_col\": \"1\", \"match_regex\": \"(.*)\", \"sub_regex\": \"\\\\1\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.5.2", + "type": "tool", + "uuid": "c0accd6f-76af-46f7-a5f0-647000d54444", + "when": null, + "workflow_outputs": [ + { + "label": "variants_for_plotting", + "output_name": "list_output_tab", + "uuid": "e62f958f-e749-43b4-9c02-17fced624689" + } + ] + }, + "31": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "errors": null, + "id": 31, + "input_connections": { + "infile": { + "id": 28, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Replace", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 3706.375, + "top": 146.25 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + }, + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "All variants of all samples" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"caseinsensitive\": \"false\", \"find_and_replace\": [], \"find_pattern\": \"unique\\\\(Sample\\\\)\\\\tcollapse\\\\(Sample\\\\)\\\\tcollapse\\\\(AF\\\\)\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"true\", \"replace_pattern\": \"SAMPLES(above-thresholds)\\\\tSAMPLES(all)\\\\tAFs(all)\", \"searchwhere\": {\"__current_case__\": 0, \"searchwhere_select\": \"line\"}, \"skip_first_line\": \"false\", \"wholewords\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "cf84a2f6-689b-4bed-bc0d-324d40f46dd7", + "when": null, + "workflow_outputs": [] + }, + "32": { + "annotation": "", + "content_id": "Cut1", + "errors": null, + "id": 32, + "input_connections": { + "input": { + "id": 29, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Cut", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 3710.1875, + "top": 471.234375 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Cut1", + "tool_state": "{\"columnList\": \"c2,c1,c4,c5,c6,c7,c8,c9,c11,c10,c12,c13,c14,c15,c16,c17,c18,c23,c24,c25,c26,c19\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.2", + "type": "tool", + "uuid": "3d0237fc-33b6-4305-b6e8-2502175f624f", + "when": null, + "workflow_outputs": [] + }, + "33": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", + "errors": null, + "id": 33, + "input_connections": { + "infile": { + "id": 31, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Sort", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 3928.8984375, + "top": 247.8125 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Combined Variant Report by Variant" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "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_version": "9.3+galaxy1", + "type": "tool", + "uuid": "6edca54f-9af8-4305-bd11-4c74251af900", + "when": null, + "workflow_outputs": [ + { + "label": "by_variant_report", + "output_name": "outfile", + "uuid": "30808300-2789-48b0-9073-98ec1bddcb3f" + } + ] + }, + "34": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", + "errors": null, + "id": 34, + "input_connections": { + "infile": { + "id": 32, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Sort", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 3932.6953125, + "top": 457.4609375 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "Combined Variant Report by Sample" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "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_version": "9.3+galaxy1", + "type": "tool", + "uuid": "eb754361-9ec5-46c8-80b5-6bb040345719", + "when": null, + "workflow_outputs": [ + { + "label": "combined_variant_report", + "output_name": "outfile", + "uuid": "2f0680a4-d809-4f85-8df9-4fcd6c4f3d80" + } + ] } - ] }, - "34": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", - "errors": null, - "id": 34, - "input_connections": { - "infile": { - "id": 32, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Sort", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 3932.6953125, - "top": 457.4609375 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "Combined Variant Report by Sample" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", - "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "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_version": "1.1.1", - "type": "tool", - "uuid": "eb754361-9ec5-46c8-80b5-6bb040345719", - "workflow_outputs": [ - { - "label": "combined_variant_report", - "output_name": "outfile", - "uuid": "2f0680a4-d809-4f85-8df9-4fcd6c4f3d80" - } - ] - } - }, - "tags": [ - "mpvx", - "generic" - ], - "uuid": "9e94da53-d8ab-4713-8aac-7c6674fa1d39", - "version": 2 -} + "tags": [ + "mpvx", + "generic" + ], + "uuid": "9e94da53-d8ab-4713-8aac-7c6674fa1d39", + "version": 2 +} \ No newline at end of file