Mercurial > repos > bgruening > deeptools
view Galaxy-Workflow-Compute_and_correct_GC_bias.ga @ 25:d2898b81b912 draft
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author | bgruening |
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date | Tue, 04 Feb 2014 13:45:17 -0500 |
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{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Compute and correct GC bias", "steps": { "0": { "annotation": "must be a sorted BAM file", "id": 0, "input_connections": {}, "inputs": [ { "description": "must be a sorted BAM file", "name": "BAM file to be checked for GC bias" } ], "name": "Input dataset", "outputs": [], "position": { "left": 111, "top": 420 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"BAM file to be checked for GC bias\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "**Computationall;y intensive**", "id": 1, "input_connections": { "bamInput": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool computeGCBias", "name": "region" }, { "description": "runtime parameter for tool computeGCBias", "name": "source" }, { "description": "runtime parameter for tool computeGCBias", "name": "effectiveGenomeSize" }, { "description": "runtime parameter for tool computeGCBias", "name": "image_format" }, { "description": "runtime parameter for tool computeGCBias", "name": "fragmentLength" } ], "name": "computeGCBias", "outputs": [ { "name": "outFileName", "type": "tabular" }, { "name": "outImageName", "type": "png" } ], "position": { "left": 383.6166687011719, "top": 270.1166687011719 }, "post_job_actions": { "HideDatasetActionoutFileName": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outFileName" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeGCBias/1.0.3", "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"filterOut\\\": null, \\\"extraSampling\\\": null, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"sampleSize\\\": \\\"50000000\\\", \\\"__current_case__\\\": 1, \\\"regionSize\\\": \\\"300\\\"}\", \"image_format\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.0.3", "type": "tool", "user_outputs": [] }, "2": { "annotation": "", "id": 2, "input_connections": { "GCbiasFrequenciesFile": { "id": 1, "output_name": "outFileName" }, "bamInput": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool correctGCBias", "name": "region" }, { "description": "runtime parameter for tool correctGCBias", "name": "source" }, { "description": "runtime parameter for tool correctGCBias", "name": "effectiveGenomeSize" } ], "name": "correctGCBias", "outputs": [ { "name": "outFileName", "type": "bam" } ], "position": { "left": 779.61669921875, "top": 334.1166687011719 }, "post_job_actions": { "RenameDatasetActionoutFileName": { "action_arguments": { "newname": "GCcorrected BAM file" }, "action_type": "RenameDatasetAction", "output_name": "outFileName" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_correctGCBias/1.0.3", "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"GCbiasFrequenciesFile\": \"null\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"binSize\\\": \\\"50\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.3", "type": "tool", "user_outputs": [] } } }