{ "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", "license": "MIT", "name": "Genetic 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": { "bottom": 223.87500762939453, "height": 80.4000015258789, "left": -1654.25, "right": -1454.25, "top": 143.47500610351562, "width": 200, "x": -1654.25, "y": 143.47500610351562 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"vcf\", \"vcf_bgzip\"], \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "5c74e419-3515-4cc9-9b91-b046a3b0400e", "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": { "bottom": 412.7000198364258, "height": 60.400001525878906, "left": -1655.1875, "right": -1455.1875, "top": 352.3000183105469, "width": 200, "x": -1655.1875, "y": 352.3000183105469 }, "tool_id": null, "tool_state": "{\"default\": 0.05, \"parameter_type\": \"float\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "da906498-2d6d-44f8-806b-488e0195d3f3", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "f2e5bf99-b8e0-4460-ab4d-8b4d4068f309" } ] }, "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": { "bottom": 562.7125015258789, "height": 60.400001525878906, "left": -1656.75, "right": -1456.75, "top": 502.3125, "width": 200, "x": -1656.75, "y": 502.3125 }, "tool_id": null, "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "6a0538a6-6033-4f51-806f-d2b54384de7d", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "51ae3970-82cc-4766-9a1d-bf6ae0133b7c" } ] }, "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": { "bottom": 776.2125015258789, "height": 60.400001525878906, "left": -1683.5, "right": -1483.5, "top": 715.8125, "width": 200, "x": -1683.5, "y": 715.8125 }, "tool_id": null, "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "02fda709-c82f-4113-8840-513df5927350", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "7d810904-38f9-4f08-9755-6950a9edc634" } ] }, "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": { "bottom": 413.67501068115234, "height": 111.20000457763672, "left": -1334.8375244140625, "right": -1134.8375244140625, "top": 302.4750061035156, "width": 200, "x": -1334.8375244140625, "y": 302.4750061035156 }, "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": "26a29579-cb45-496d-a4a5-0db6d7a56005", "workflow_outputs": [ { "label": "prefiltered_variants", "output_name": "output", "uuid": "0d8e2160-fcd2-4675-b5f2-2262bb505873" } ] }, "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": { "bottom": 717.9500122070312, "height": 291.20001220703125, "left": -1336.5, "right": -1136.5, "top": 426.75, "width": 200, "x": -1336.5, "y": 426.75 }, "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\": \"( ( 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": "9d23b640-6dd0-4572-8dd9-0871a229897a", "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" }, "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": { "bottom": 1025.425048828125, "height": 291.20001220703125, "left": -1339.7750244140625, "right": -1139.7750244140625, "top": 734.2250366210938, "width": 200, "x": -1339.7750244140625, "y": 734.2250366210938 }, "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": "fdbf97f5-9a3b-4bb4-95b5-858381cf5f60", "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" }, "filtering|add_filter": { "id": 6, "output_name": "out1" }, "input": { "id": 4, "output_name": "output" } }, "inputs": [], "label": null, "name": "SnpSift Filter", "outputs": [ { "name": "output", "type": "vcf" } ], "position": { "bottom": 783.6625213623047, "height": 191.1999969482422, "left": -1104.0875244140625, "right": -904.0875244140625, "top": 592.4625244140625, "width": 200, "x": -1104.0875244140625, "y": 592.4625244140625 }, "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": "22d9cceb-da11-42b5-9975-19cd46592077", "workflow_outputs": [ { "label": "filtered_variants", "output_name": "output", "uuid": "83d2f721-b94e-4699-8b81-dd2a50cb69e1" } ] }, "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": { "bottom": 660.6374969482422, "height": 171.1999969482422, "left": -868.0625, "right": -668.0625, "top": 489.4375, "width": 200, "x": -868.0625, "y": 489.4375 }, "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": "943b580c-ffaf-40cf-a143-f1b997bc1f31", "workflow_outputs": [ { "label": "filtered_extracted_variants", "output_name": "output", "uuid": "afa0a3fa-a72e-4d3b-8c51-825123b37b9d" } ] }, "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": { "bottom": 601.9375228881836, "height": 91.20000457763672, "left": -416.76251220703125, "right": -216.76251220703125, "top": 510.7375183105469, "width": 200, "x": -416.76251220703125, "y": 510.7375183105469 }, "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": "02026300aa45", "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": "ffed89eb-b103-424e-9d2b-ed9257d79fb2", "workflow_outputs": [ { "label": "af_recalculated", "output_name": "out_file1", "uuid": "5bf807a0-360e-4278-b545-366b916f413c" } ] }, "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": { "bottom": 402.17501068115234, "height": 111.20000457763672, "left": -250.33750915527344, "right": -50.33750915527344, "top": 290.9750061035156, "width": 200, "x": -250.33750915527344, "y": 290.9750061035156 }, "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": "679cd8d6-5957-4202-b3b8-d32d10a83604", "workflow_outputs": [ { "label": "collapsed_effects", "output_name": "out_file", "uuid": "b0e62d8e-8ce0-4f6b-a141-be353634a9eb" } ] }, "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": { "bottom": 578.2375106811523, "height": 111.20000457763672, "left": -127.1500015258789, "right": 72.8499984741211, "top": 467.0375061035156, "width": 200, "x": -127.1500015258789, "y": 467.0375061035156 }, "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": "ddf54b12c295", "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": "b6f6d8da-9863-4dde-b61a-efc63801a5d0", "workflow_outputs": [ { "label": "highest_impact_effects", "output_name": "outfile", "uuid": "a58460be-31e9-4fed-a7d8-7cbca5277373" } ] }, "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": { "bottom": 399.9124984741211, "height": 91.20000457763672, "left": 23.700000762939453, "right": 223.70000076293945, "top": 308.7124938964844, "width": 200, "x": 23.700000762939453, "y": 308.7124938964844 }, "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": "ddf54b12c295", "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": "24b34af0-8226-4d3b-90f5-8b16200c96ca", "workflow_outputs": [ { "label": "cleaned_header", "output_name": "outfile", "uuid": "96fdb8ed-9520-4531-aeef-e2cbe9897617" } ] }, "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": { "bottom": 604.5625152587891, "height": 131.1999969482422, "left": 142, "right": 342, "top": 473.3625183105469, "width": 200, "x": 142, "y": 473.3625183105469 }, "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": "ddf54b12c295", "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": "7c9880cd-02e1-4965-9ee0-4cb3991e6c4d", "workflow_outputs": [ { "label": "processed_variants_collection", "output_name": "outfile", "uuid": "9447307f-5187-4321-989f-13719af24829" } ] }, "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": { "bottom": 429.66249084472656, "height": 131.1999969482422, "left": 301.01251220703125, "right": 501.01251220703125, "top": 298.4624938964844, "width": 200, "x": 301.01251220703125, "y": 298.4624938964844 }, "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": "d6bec274-16bf-4299-bb35-affe81a3d9be", "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": { "bottom": 573.1624984741211, "height": 91.20000457763672, "left": 422.88751220703125, "right": 622.8875122070312, "top": 481.9624938964844, "width": 200, "x": 422.88751220703125, "y": 481.9624938964844 }, "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": "02026300aa45", "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": "4b0cbd30-ef99-4a72-a3b2-d61ff60e141f", "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": { "bottom": 573.9749984741211, "height": 91.20000457763672, "left": 646.4000244140625, "right": 846.4000244140625, "top": 482.7749938964844, "width": 200, "x": 646.4000244140625, "y": 482.7749938964844 }, "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": "02026300aa45", "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": "1b90828f-c84b-4e31-a815-83fecb0f0bb4", "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": { "bottom": 461.7625045776367, "height": 111.20000457763672, "left": 852.5750122070312, "right": 1052.5750122070312, "top": 350.5625, "width": 200, "x": 852.5750122070312, "y": 350.5625 }, "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": "ddf54b12c295", "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": "eee78c97-73f5-48d3-9282-cdd1e5b37f73", "workflow_outputs": [ { "label": "all_variants_all_samples", "output_name": "outfile", "uuid": "971a7b51-890f-4bf9-967c-2fd91e24dc56" } ] }, "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": { "bottom": 413.2000045776367, "height": 111.20000457763672, "left": 1103.8375244140625, "right": 1303.8375244140625, "top": 302, "width": 200, "x": 1103.8375244140625, "y": 302 }, "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": "d26c7ee7-3d12-4080-b07e-dc63428494ee", "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": { "bottom": 606.3250045776367, "height": 91.20000457763672, "left": 1096.6375732421875, "right": 1296.6375732421875, "top": 515.125, "width": 200, "x": 1096.6375732421875, "y": 515.125 }, "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": "fef0e498-4509-4d3b-9fe8-d884fe0fbca3", "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": { "bottom": 823.2499923706055, "height": 111.20000457763672, "left": 1387.5374755859375, "right": 1587.5374755859375, "top": 712.0499877929688, "width": 200, "x": 1387.5374755859375, "y": 712.0499877929688 }, "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/1.1.0", "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": "f85b85ae-1c88-4d66-8ec5-9e2af026a12b", "workflow_outputs": [] }, "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", "errors": null, "id": 21, "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": { "bottom": 443.5750045776367, "height": 121.20000457763672, "left": 1345.2249755859375, "right": 1545.2249755859375, "top": 322.375, "width": 200, "x": 1345.2249755859375, "y": 322.375 }, "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/1.1.2", "tool_shed_repository": { "changeset_revision": "ddf54b12c295", "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": "a222093d-b24a-45b5-be28-615074c9fbf6", "workflow_outputs": [] }, "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", "errors": null, "id": 22, "input_connections": { "in_file": { "id": 19, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Datamash", "outputs": [ { "name": "out_file", "type": "tabular" } ], "position": { "bottom": 693.7375411987305, "height": 111.20000457763672, "left": 1353.6500244140625, "right": 1553.6500244140625, "top": 582.5375366210938, "width": 200, "x": 1353.6500244140625, "y": 582.5375366210938 }, "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": "56e392b7-fb9d-4ed1-9d95-c852e2212b3f", "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": [ { "description": "runtime parameter for tool Datamash", "name": "in_file" } ], "label": null, "name": "Datamash", "outputs": [ { "name": "out_file", "type": "tabular" } ], "position": { "bottom": 1043.9999923706055, "height": 111.20000457763672, "left": 1212.1500244140625, "right": 1412.1500244140625, "top": 932.7999877929688, "width": 200, "x": 1212.1500244140625, "y": 932.7999877929688 }, "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__\": \"RuntimeValue\"}, \"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": "68d0d87e-8136-40f2-bfa2-7d3a0db0bfe5", "workflow_outputs": [] }, "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", "errors": null, "id": 24, "input_connections": { "in_file": { "id": 21, "output_name": "output" } }, "inputs": [], "label": null, "name": "Datamash", "outputs": [ { "name": "out_file", "type": "tabular" } ], "position": { "bottom": 396.7000045776367, "height": 111.20000457763672, "left": 1589.3375244140625, "right": 1789.3375244140625, "top": 285.5, "width": 200, "x": 1589.3375244140625, "y": 285.5 }, "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": "972805f1-c0d4-4cd6-80b7-cb81109fd725", "workflow_outputs": [] }, "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", "errors": null, "id": 25, "input_connections": { "infile1": { "id": 17, "output_name": "outfile" }, "infile2": { "id": 22, "output_name": "out_file" } }, "inputs": [], "label": null, "name": "Join", "outputs": [ { "name": "output", "type": "input" } ], "position": { "bottom": 616.2500228881836, "height": 121.20000457763672, "left": 1591.4000244140625, "right": 1791.4000244140625, "top": 495.0500183105469, "width": 200, "x": 1591.4000244140625, "y": 495.0500183105469 }, "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": "ddf54b12c295", "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": "ee129fff-a0e3-42c0-97ab-536ced597835", "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": 16, "output_name": "out_file1" }, "infile2": { "id": 23, "output_name": "out_file" } }, "inputs": [], "label": null, "name": "Join", "outputs": [ { "name": "output", "type": "input" } ], "position": { "bottom": 984.5125045776367, "height": 121.20000457763672, "left": 1549.4000244140625, "right": 1749.4000244140625, "top": 863.3125, "width": 200, "x": 1549.4000244140625, "y": 863.3125 }, "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": "ddf54b12c295", "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": "467474cd-6244-4bd6-b5bd-a04386c54669", "workflow_outputs": [] }, "27": { "annotation": "", "content_id": "Cut1", "errors": null, "id": 27, "input_connections": { "input": { "id": 24, "output_name": "out_file" } }, "inputs": [], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "bottom": 481.48751068115234, "height": 91.20000457763672, "left": 1813.4000244140625, "right": 2013.4000244140625, "top": 390.2875061035156, "width": 200, "x": 1813.4000244140625, "y": 390.2875061035156 }, "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": "3c3ab342-435e-421f-b006-07d3f97bdc85", "workflow_outputs": [] }, "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", "errors": null, "id": 28, "input_connections": { "infile1": { "id": 25, "output_name": "output" }, "infile2": { "id": 20, "output_name": "out_file" } }, "inputs": [], "label": null, "name": "Join", "outputs": [ { "name": "output", "type": "input" } ], "position": { "bottom": 709.4125289916992, "height": 121.20000457763672, "left": 1809.4375, "right": 2009.4375, "top": 588.2125244140625, "width": 200, "x": 1809.4375, "y": 588.2125244140625 }, "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/1.1.2", "tool_shed_repository": { "changeset_revision": "ddf54b12c295", "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": "bb7f635b-793d-49cf-9810-65d7e6a3df71", "workflow_outputs": [] }, "29": { "annotation": "", "content_id": "Cut1", "errors": null, "id": 29, "input_connections": { "input": { "id": 26, "output_name": "output" } }, "inputs": [], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "bottom": 890.2625045776367, "height": 91.20000457763672, "left": 1774.875, "right": 1974.875, "top": 799.0625, "width": 200, "x": 1774.875, "y": 799.0625 }, "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": "e5da0892-47f8-499e-9228-a35e8bdef4c7", "workflow_outputs": [] }, "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", "errors": null, "id": 30, "input_connections": { "infile": { "id": 27, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Replace", "outputs": [ { "name": "outfile", "type": "input" } ], "position": { "bottom": 380.92501068115234, "height": 91.20000457763672, "left": 2022.875, "right": 2222.875, "top": 289.7250061035156, "width": 200, "x": 2022.875, "y": 289.7250061035156 }, "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/1.1.3", "tool_shed_repository": { "changeset_revision": "ddf54b12c295", "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": "11445f8e-a61b-49bb-a57e-12ac7a2f54b8", "workflow_outputs": [] }, "31": { "annotation": "", "content_id": "Cut1", "errors": null, "id": 31, "input_connections": { "input": { "id": 28, "output_name": "output" } }, "inputs": [], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "bottom": 705.9125289916992, "height": 91.20000457763672, "left": 2026.6875, "right": 2226.6875, "top": 614.7125244140625, "width": 200, "x": 2026.6875, "y": 614.7125244140625 }, "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": "a3fe45b8-d062-4022-93b5-1985a4ff208d", "workflow_outputs": [] }, "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "errors": null, "id": 32, "input_connections": { "split_parms|input": { "id": 29, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Split file", "outputs": [ { "name": "list_output_tab", "type": "input" } ], "position": { "bottom": 910.4374923706055, "height": 111.20000457763672, "left": 1998.1375732421875, "right": 2198.1375732421875, "top": 799.2374877929688, "width": 200, "x": 1998.1375732421875, "y": 799.2374877929688 }, "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": "cb9acaf4-0054-40c1-abdf-fe926da04003", "workflow_outputs": [ { "label": "variants_for_plotting", "output_name": "list_output_tab", "uuid": "9913d7bc-0911-482a-a888-b647056b4971" } ] }, "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": 30, "output_name": "outfile" } }, "inputs": [], "label": null, "name": "Sort", "outputs": [ { "name": "outfile", "type": "input" } ], "position": { "bottom": 482.48751068115234, "height": 91.20000457763672, "left": 2245.400146484375, "right": 2445.400146484375, "top": 391.2875061035156, "width": 200, "x": 2245.400146484375, "y": 391.2875061035156 }, "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": "ddf54b12c295", "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": "e666cf10-78f5-417f-af95-b79bd2804fdf", "workflow_outputs": [ { "label": "by_variant_report", "output_name": "outfile", "uuid": "fdf8e687-5f1a-457e-b218-81f4ce4171a8" } ] }, "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": 31, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Sort", "outputs": [ { "name": "outfile", "type": "input" } ], "position": { "bottom": 712.1375045776367, "height": 111.20000457763672, "left": 2249.199951171875, "right": 2449.199951171875, "top": 600.9375, "width": 200, "x": 2249.199951171875, "y": 600.9375 }, "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": "ddf54b12c295", "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": "600ae2ca-48a5-444c-b4a5-0c674cf6ed78", "workflow_outputs": [ { "label": "combined_variant_report", "output_name": "outfile", "uuid": "ec73b845-937f-4b04-8184-08ce0b3fbc04" } ] } }, "tags": [ "mpvx", "generic" ], "uuid": "3201b9e8-0c63-40ad-a650-6613531e6f0b", "version": 3 }