Mercurial > repos > wolma > mimodd_workflows
view Galaxy-Workflow-MiModD_example_workflow_2.ga @ 1:87bfe31ce878 default tip
workflows for MiModD 0.1.6
author | Wolfgang Maier |
---|---|
date | Thu, 04 Jun 2015 18:19:52 +0200 |
parents | 9f64313f2ccb |
children |
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{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "MiModD example workflow 2", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 172, "top": 174 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "user_outputs": [], "uuid": "None" }, "1": { "annotation": "", "id": 1, "input_connections": { "ref_genome": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "SNAP Read Alignment", "outputs": [ { "name": "outputfile", "type": "bam" } ], "position": { "left": 359, "top": 366 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "read_alignment", "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": 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\\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [], "uuid": "None" }, "2": { "annotation": "", "id": 2, "input_connections": { "list_input_0|inputfile": { "id": 1, "output_name": "outputfile" }, "ref_genome": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "Variant Calling", "outputs": [ { "name": "output_vcf", "type": "bcf" } ], "position": { "left": 708, "top": 362 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "variant_calling", "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", 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"tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [], "uuid": "None" }, "5": { "annotation": "", "id": 5, "input_connections": { "covfile": { "id": 2, "output_name": "output_vcf" }, "list_input_0|bamfile": { "id": 1, "output_name": "outputfile" } }, "inputs": [], "label": null, "name": "Deletion Prediction for paired-end data", "outputs": [ { "name": "outputfile", "type": "gff" } ], "position": { "left": 1064, "top": 665 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "deletion_prediction", "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"False\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [], "uuid": "None" } }, "uuid": "ebf4ae7e-e823-4b67-a0aa-2a0e70b48db8" }