Mercurial > repos > scisjnu123 > test
view Galaxy-Workflow-SAMTools.ga @ 7:ab331b4507fd draft
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| author | scisjnu123 |
|---|---|
| date | Thu, 12 Sep 2019 12:39:24 -0400 |
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{ "a_galaxy_workflow": "true", "annotation": "This workflow uses SAMTools to call SNPs and INDELs.", "format-version": "0.1", "name": "SAMTools", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": ".bam file" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 200, "top": 156 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \".bam file\"}", "tool_version": null, "type": "data_input", "user_outputs": [], "uuid": "955f71da-3fad-46c4-a1d9-b0b1cb484569" }, "1": { "annotation": "", "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Reference genome." } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 512, "top": 285 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Reference genome.\"}", "tool_version": null, "type": "data_input", "user_outputs": [], "uuid": "7069b8d2-a89a-472a-8e18-b5b8f076de33" }, "2": { "annotation": "", "id": 2, "input_connections": { "inputFile": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "SortSam", "outputs": [ { "name": "outFile", "type": "bam" } ], "position": { "left": 436.5, "top": 121 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_SortSam/1.135", "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"coordinate\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", "tool_version": "1.135", "type": "tool", "user_outputs": [], "uuid": "b06955b6-6bba-4aaa-a919-fbb2aba9fdf5" }, "3": { "annotation": "", "id": 3, "input_connections": { "reference_source|input_bams_0|input_bam": { "id": 2, "output_name": "outFile" }, "reference_source|ref_file": { "id": 1, "output_name": "output" } }, "inputs": [], "label": null, "name": "MPileup", "outputs": [ { "name": "output_mpileup", "type": "pileup" }, { "name": "output_log", "type": "txt" } ], "position": { "left": 746, "top": 192 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", "tool_version": "0.0.3", "type": "tool", "user_outputs": [], "uuid": "99b58983-e355-4357-b77e-8e29afcdc866" } }, "uuid": "6b217aca-887a-4cca-91e4-446a7cc50726" }
