{ "a_galaxy_workflow": "true", "annotation": "Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold.\nHard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.", "creator": [ { "class": "Person", "identifier": "https://orcid.org/0000-0002-9464-6640", "name": "Wolfgang Maier" } ], "format-version": "0.1", "license": "MIT", "name": "COVID-19: consensus construction", "release": "0.4.3", "steps": { "0": { "annotation": "Collection of VCFs produced by upstream workflows for variation analysis", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "Collection of VCFs produced by upstream workflows for variation analysis", "name": "Variant calls" } ], "label": "Variant calls", "name": "Input dataset collection", "outputs": [], "position": { "left": 0.0, "top": 306.13330078125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "fca4e710-87a7-4cb6-9ff1-f9a8dc84ca37", "when": null, "workflow_outputs": [] }, "1": { "annotation": "Only variant calls with an allele-frequency greater this value will be considered consensus variants.", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "Only variant calls with an allele-frequency greater this value will be considered consensus variants.", "name": "min-AF for consensus variant" } ], "label": "min-AF for consensus variant", "name": "Input parameter", "outputs": [], "position": { "left": 0.45001220703125, "top": 469.0 }, "tool_id": null, "tool_state": "{\"default\": 0.75, \"validators\": [], \"parameter_type\": \"float\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5", "when": null, "workflow_outputs": [ { "label": "consensus_af_threshold", "output_name": "output", "uuid": "0d802d31-bb4c-41e3-8e84-c1d99b914ee9" } ] }, "2": { "annotation": "Variant calls with an allele frequency higher than this value, but lower than the AF threshold for consensus variants will be considered questionable and the respective sites be masked (with Ns) in the consensus sequence.", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { "description": "Variant calls with an allele frequency higher than this value, but lower than the AF threshold for consensus variants will be considered questionable and the respective sites be masked (with Ns) in the consensus sequence.", "name": "min-AF for failed variants" } ], "label": "min-AF for failed variants", "name": "Input parameter", "outputs": [], "position": { "left": 0.45001220703125, "top": 640.6500244140625 }, "tool_id": null, "tool_state": "{\"default\": 0.25, \"validators\": [], \"parameter_type\": \"float\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "a2a15cce-94ec-4a76-a3ff-3ea898e9c678", "when": null, "workflow_outputs": [ { "label": "non_consensus_af_threshold", "output_name": "output", "uuid": "16c62493-ad4b-46da-8790-a8094d01a130" } ] }, "3": { "annotation": "Fully processed BAMs as generated by upstream workflows for variation analysis. Note: for ARTIC data, these BAMs should NOT have undergone processing with ivar removereads.", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { "description": "Fully processed BAMs as generated by upstream workflows for variation analysis. Note: for ARTIC data, these BAMs should NOT have undergone processing with ivar removereads.", "name": "aligned reads data for depth calculation" } ], "label": "aligned reads data for depth calculation", "name": "Input dataset collection", "outputs": [], "position": { "left": 581.3167114257812, "top": 395.16668701171875 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "23ae69ea-f9a7-4d5f-85f5-63b9d2bd2c50", "when": null, "workflow_outputs": [] }, "4": { "annotation": "Sites in the viral genome covered by less than this number of reads are considered questionable and will be masked (with Ns) in the consensus sequence independent of whether a variant has been called at them or not.", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { "description": "Sites in the viral genome covered by less than this number of reads are considered questionable and will be masked (with Ns) in the consensus sequence independent of whether a variant has been called at them or not.", "name": "Depth-threshold for masking" } ], "label": "Depth-threshold for masking", "name": "Input parameter", "outputs": [], "position": { "left": 585.25, "top": 557.8499755859375 }, "tool_id": null, "tool_state": "{\"default\": 5, \"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "cfdc65b0-8393-4ee3-9e27-16b23135fbec", "when": null, "workflow_outputs": [ { "label": "depth_threshold", "output_name": "output", "uuid": "f677edfd-5faf-44af-8e20-c5e6d72ba24a" } ] }, "5": { "annotation": "The SARS-CoV-2 reference genome", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [ { "description": "The SARS-CoV-2 reference genome", "name": "Reference genome" } ], "label": "Reference genome", "name": "Input dataset", "outputs": [], "position": { "left": 2283.8167114257812, "top": 346.1500244140625 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "4a2c6df2-fb1e-42d8-96d5-6765ca85c214", "when": null, "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" } }, "inputs": [], "label": null, "name": "Compose text parameter value", "outputs": [ { "name": "out1", "type": "expression.json" } ], "position": { "left": 282.79998779296875, "top": 285.3500061035156 }, "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\": \"( ( FILTER = 'PASS' ) | ( na FILTER ) ) & ( ( 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 ) )\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.1", "type": "tool", "uuid": "8ec54933-36d6-404c-b0a6-5a14b04eb30e", "when": null, "workflow_outputs": [] }, "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, "id": 7, "input_connections": { "components_1|param_type|component_value": { "id": 2, "output_name": "output" }, "components_3|param_type|component_value": { "id": 1, "output_name": "output" } }, "inputs": [], "label": null, "name": "Compose text parameter value", "outputs": [ { "name": "out1", "type": "expression.json" } ], "position": { "left": 233.0, "top": 802.0166625976562 }, "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 ) ) & ( ( DP4[2] + DP4[3] ) < ( \"}}, {\"__index__\": 3, \"param_type\": {\"select_param_type\": \"float\", \"__current_case__\": 2, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 4, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \" * DP ) ) & ( ( FILTER = 'PASS' ) | ( na FILTER ) )\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.1", "type": "tool", "uuid": "51ac3588-c801-4551-8345-b04cc3571fea", "when": null, "workflow_outputs": [] }, "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1", "errors": null, "id": 8, "input_connections": { "input_type|input": { "id": 3, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool bedtools Genome Coverage", "name": "input_type" } ], "label": null, "name": "bedtools Genome Coverage", "outputs": [ { "name": "output", "type": "bedgraph" } ], "position": { "left": 880.7999877929688, "top": 403.3499755859375 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Depth of coverage" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1", "tool_shed_repository": { "changeset_revision": "2892111d91f8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"d\": false, \"dz\": false, \"five\": false, \"input_type\": {\"input_type_select\": \"bam\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"report\": {\"report_select\": \"bg\", \"__current_case__\": 0, \"zero_regions\": true, \"scale\": \"1.0\"}, \"split\": true, \"strand\": \"\", \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.31.1", "type": "tool", "uuid": "d89684f5-5a49-4b4c-821b-6c8a87f3a46e", "when": null, "workflow_outputs": [ { "label": "coverage_depth", "output_name": "output", "uuid": "df923e92-8241-4c8b-9983-4773b753a144" } ] }, "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, "id": 9, "input_connections": { "components_1|param_type|component_value": { "id": 4, "output_name": "output" } }, "inputs": [], "label": null, "name": "Compose text parameter value", "outputs": [ { "name": "out1", "type": "expression.json" } ], "position": { "left": 879.3167114257812, "top": 559.8499755859375 }, "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\": \"c4 < \"}}, {\"__index__\": 1, \"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": "089b2659-d4c8-44c8-9ecc-ffe71676e650", "when": null, "workflow_outputs": [] }, "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", "errors": null, "id": 10, "input_connections": { "filter_expression|expr": { "id": 6, "output_name": "out1" }, "input": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool SnpSift Filter", "name": "filter_expression" } ], "label": null, "name": "SnpSift Filter", "outputs": [ { "name": "output", "type": "vcf" } ], "position": { "left": 485.2833251953125, "top": 0.0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Consensus 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\": \"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": "3673b687-1ba0-42f2-ba13-fa3130462079", "when": null, "workflow_outputs": [ { "label": "consensus_variants", "output_name": "output", "uuid": "1db759fb-634a-4b5f-abd9-a0579a003570" } ] }, "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", "errors": null, "id": 11, "input_connections": { "filter_expression|expr": { "id": 7, "output_name": "out1" }, "input": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool SnpSift Filter", "name": "filter_expression" } ], "label": null, "name": "SnpSift Filter", "outputs": [ { "name": "output", "type": "vcf" } ], "position": { "left": 456.66668701171875, "top": 733.3499755859375 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Filter-failed 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\": \"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": "fb232cba-e3b2-43f9-bb1f-a9ebc69c9b97", "when": null, "workflow_outputs": [ { "label": "filter_failed_variants", "output_name": "output", "uuid": "73373a44-4651-49c2-813d-e4ea0ffd46cf" } ] }, "12": { "annotation": "", "content_id": "Filter1", "errors": null, "id": 12, "input_connections": { "cond": { "id": 9, "output_name": "out1" }, "input": { "id": 8, "output_name": "output" } }, "inputs": [], "label": null, "name": "Filter", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1213.8333129882812, "top": 427.3499755859375 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Low-coverage regions" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" } }, "tool_id": "Filter1", "tool_state": "{\"cond\": {\"__class__\": \"ConnectedValue\"}, \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.1", "type": "tool", "uuid": "8ac27ee3-9e9e-4d6f-b424-2c21f80c87ef", "when": null, "workflow_outputs": [ { "label": "low_cov_regions", "output_name": "out_file1", "uuid": "20b0e19e-6916-4709-b8db-8c828ccde324" } ] }, "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", "errors": null, "id": 13, "input_connections": { "input": { "id": 10, "output_name": "output" } }, "inputs": [], "label": null, "name": "SnpSift Extract Fields", "outputs": [ { "name": "output", "type": "tabular" } ], "position": { "left": 807.4500122070312, "top": 183.0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Called variants - CHROM_POS_REF" }, "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 REF\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": false, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.3+t.galaxy0", "type": "tool", "uuid": "5aca2952-a87c-4c77-a259-a22daceab557", "when": null, "workflow_outputs": [ { "label": "chrom_pos_ref_called_variants", "output_name": "output", "uuid": "555dff08-7ce6-4d48-b00f-2c4143f83489" } ] }, "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", "errors": null, "id": 14, "input_connections": { "input": { "id": 11, "output_name": "output" } }, "inputs": [], "label": null, "name": "SnpSift Extract Fields", "outputs": [ { "name": "output", "type": "tabular" } ], "position": { "left": 673.9500122070312, "top": 899.0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Filter-failed variants - CHROM_POS_REF" }, "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 REF\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": false, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.3+t.galaxy0", "type": "tool", "uuid": "d99d1a1a-24a7-4379-a7d1-1980303ee08a", "when": null, "workflow_outputs": [ { "label": "chrom_pos_ref_failed_variants", "output_name": "output", "uuid": "13574d4b-8c55-4c2f-a5da-76b82ed31deb" } ] }, "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": 13, "output_name": "output" } }, "inputs": [], "label": null, "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1148.1333618164062, "top": 249.64999389648438 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "bed" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Called variant sites" }, "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, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.1", "type": "tool", "uuid": "fd260e32-723d-4a22-8d64-4795557f8159", "when": null, "workflow_outputs": [ { "label": "called_variant_sites", "output_name": "out_file1", "uuid": "0033def6-7531-40b6-8b01-d16a18726fe4" } ] }, "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": 14, "output_name": "output" } }, "inputs": [], "label": null, "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 901.6166381835938, "top": 919.1500244140625 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "bed" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Filter-failed variant sites" }, "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, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.1", "type": "tool", "uuid": "116e8e99-53ca-4366-a7e1-e3a9fb0bcfc3", "when": null, "workflow_outputs": [ { "label": "failed_variant_sites", "output_name": "out_file1", "uuid": "8ba74008-5f23-4b79-993b-ae8ddac44456" } ] }, "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1", "errors": null, "id": 17, "input_connections": { "input1": { "id": 12, "output_name": "out_file1" }, "input2": { "id": 16, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Concatenate", "outputs": [ { "name": "output", "type": "input" } ], "position": { "left": 1468.8833618164062, "top": 537.4166870117188 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Cocatenated low-coverage regions and filter-failed sites" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1", "tool_shed_repository": { "changeset_revision": "73ca13a7ec5f", "name": "concat", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"sameformat\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "uuid": "2b7570fb-9ce5-4a9a-863c-e33efbc88912", "when": null, "workflow_outputs": [ { "label": "low_cov_regions_plus_filter_failed", "output_name": "output", "uuid": "aff4b045-799f-4337-a8e6-af87be35bda3" } ] }, "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0", "errors": null, "id": 18, "input_connections": { "input1": { "id": 17, "output_name": "output" } }, "inputs": [], "label": null, "name": "Merge", "outputs": [ { "name": "output", "type": "input" } ], "position": { "left": 1703.3167114257812, "top": 533.6666870117188 }, "post_job_actions": { "ChangeDatatypeActionoutput": { "action_arguments": { "newtype": "bed" }, "action_type": "ChangeDatatypeAction", "output_name": "output" }, "RenameDatasetActionoutput": { "action_arguments": { "newname": "Combined low-coverage regions and filter-failed sites" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0", "tool_shed_repository": { "changeset_revision": "debffd27642d", "name": "merge", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"returntype\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "3e63167b-6560-4b6d-a409-7d3707039222", "when": null, "workflow_outputs": [ { "label": "low_cov_regions_plus_filter_failed_combined", "output_name": "output", "uuid": "8db1e8f6-9f76-4fd0-b6c9-10eeada9f8c4" } ] }, "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0", "errors": null, "id": 19, "input_connections": { "input1": { "id": 18, "output_name": "output" }, "input2": { "id": 15, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Subtract", "outputs": [ { "name": "output", "type": "input" } ], "position": { "left": 1959.4666137695312, "top": 408.0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Masking regions" }, "action_type": "RenameDatasetAction", "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0", "tool_shed_repository": { "changeset_revision": "0427ca314f3d", "name": "subtract", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"min\": \"1\", \"returntype\": \"-p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "51b26960-4ee7-4a3d-96cb-a6b3950c173e", "when": null, "workflow_outputs": [ { "label": "masking_regions", "output_name": "output", "uuid": "1bdf0a04-75d5-4b7b-bd52-880a869548a1" } ] }, "20": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "errors": null, "id": 20, "input_connections": { "input": { "id": 19, "output_name": "output" } }, "inputs": [], "label": null, "name": "Compute", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 2144.8333129882812, "top": 585.6666870117188 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { "action_arguments": { "newtype": "interval" }, "action_type": "ChangeDatatypeAction", "output_name": "out_file1" }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "1-based masking regions" }, "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, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) + 1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.1", "type": "tool", "uuid": "e06fe045-f0f0-4c32-80ad-a8e070946a2f", "when": null, "workflow_outputs": [ { "label": "1_based_masking_regions", "output_name": "out_file1", "uuid": "dc85cc18-db50-4c90-97d7-58eb5dcad70b" } ] }, "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "errors": null, "id": 21, "input_connections": { "input_file": { "id": 10, "output_name": "output" }, "reference_source|fasta_ref": { "id": 5, "output_name": "output" }, "sec_default|mask": { "id": 20, "output_name": "out_file1" } }, "inputs": [ { "description": "runtime parameter for tool bcftools consensus", "name": "reference_source" }, { "description": "runtime parameter for tool bcftools consensus", "name": "sec_default" } ], "label": null, "name": "bcftools consensus", "outputs": [ { "name": "output_file", "type": "fasta" } ], "position": { "left": 2603.8333129882812, "top": 243.66668701171875 }, "post_job_actions": { "RenameDatasetActionoutput_file": { "action_arguments": { "newname": "Consensus sequence with masking" }, "action_type": "RenameDatasetAction", "output_name": "output_file" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "tool_shed_repository": { "changeset_revision": "8aa352093d73", "name": "bcftools_consensus", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": true, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": \"\", \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": \"\", \"exclude\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.15.1+galaxy4", "type": "tool", "uuid": "698a9a8c-f6fe-430b-a7e0-cf9e1d058d02", "when": null, "workflow_outputs": [ { "label": "consensus", "output_name": "output_file", "uuid": "5e1e40be-fab7-4592-82b4-a02536f618ef" } ] }, "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", "errors": null, "id": 22, "input_connections": { "input_list": { "id": 21, "output_name": "output_file" } }, "inputs": [], "label": null, "name": "Collapse Collection", "outputs": [ { "name": "output", "type": "input" } ], "position": { "left": 2863.5000610351562, "top": 267.5 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Multisample consensus FASTA" }, "action_type": "RenameDatasetAction", "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\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.1.0", "type": "tool", "uuid": "acae0f3e-448b-483e-a44a-3e09ce9b3e77", "when": null, "workflow_outputs": [ { "label": "multisample_consensus_fasta", "output_name": "output", "uuid": "105f13c3-9c94-4924-b950-9526d680562f" } ] } }, "tags": [ "COVID-19", "covid19.galaxyproject.org" ], "uuid": "06dc40a7-99f2-4b3c-ae21-b3dcb239306f" }