Mercurial > repos > jjohnson > mmuflr
view Galaxy-Workflow-MMuFLR_Human_germline_v1.4.ga @ 0:4f70b23c497a
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author | jjohnson |
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date | Tue, 04 Jun 2013 09:51:17 -0400 |
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{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "MMuFLR_Human_germline_v1.4", "steps": { "0": { "annotation": "Human RNA-seq paired reads left mates", "id": 0, "input_connections": {}, "inputs": [ { "description": "Human RNA-seq paired reads left mates", "name": "Forward reads fastq" } ], "name": "Input dataset", "outputs": [], "position": { "left": 240, "top": 287 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Forward reads fastq\"}", "tool_version": null, "type": "data_input", "user_outputs": [] }, "1": { "annotation": "Human RNA-seq paired reads right mates", "id": 1, "input_connections": {}, "inputs": [ { "description": "Human RNA-seq paired reads right mates", "name": "Reverse reads fastq" } ], "name": "Input dataset", "outputs": [], "position": { "left": 249, "top": 383 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Reverse reads fastq\"}", "tool_version": null, "type": "data_input", "user_outputs": [] 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\\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", "tool_version": "1.0.4", "type": "tool", "user_outputs": [] }, "5": { "annotation": "Map paired reads to reference genome", "id": 5, "input_connections": { "input1": { "id": 3, "output_name": "output_file" }, "singlePaired|input2": { "id": 4, "output_name": "output_file" } }, "inputs": [ { "description": "runtime parameter for tool Tophat for Illumina", "name": "singlePaired" } ], "name": "Tophat for Illumina", "outputs": [ { "name": "insertions", "type": "bed" }, { "name": "deletions", "type": "bed" }, { "name": "junctions", "type": "bed" }, { "name": "accepted_hits", "type": "bam" } ], "position": { "left": 884, "top": 305 }, "post_job_actions": { "HideDatasetActiondeletions": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "deletions" }, "HideDatasetActioninsertions": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "insertions" }, 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\"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", "tool_version": "1.56.0", "type": "tool", "user_outputs": [] }, "9": { "annotation": "Synchronize paired reads", "id": 9, "input_connections": { "input_file": { "id": 8, "output_name": "outFile" } }, "inputs": [], "name": "Paired Read Mate Fixer", "outputs": [ { "name": "out_file", "type": "bam" } ], "position": { "left": 1841, "top": 348 }, "post_job_actions": { "HideDatasetActionout_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": 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[], "name": "Mark Duplicate reads", "outputs": [ { "name": "out_file", "type": "bam" }, { "name": "html_file", "type": "html" } ], "position": { "left": 3174, "top": 291 }, "post_job_actions": { "HideDatasetActionhtml_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "html_file" }, "HideDatasetActionout_file": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", "tool_version": "1.56.0", "type": "tool", "user_outputs": [] }, 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\\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", "tool_version": "0.0.1", "type": "tool", "user_outputs": [] }, "16": { "annotation": "Minimum Base Quality: 30\nMinimum 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} } }