Mercurial > repos > scisjnu123 > ngsap_vc
view ngsap-vc/SAMTools.ga @ 3:0d10255b5434 draft default tip
Uploaded
author | scisjnu123 |
---|---|
date | Thu, 03 Oct 2019 10:42:15 -0400 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "SAMTools workflow", "format-version": "0.1", "name": "SAMTools", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 162, "top": 169 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "user_outputs": [], "uuid": "1eec712c-2fe0-43a8-b033-f027a74c6a48" }, "1": { "annotation": "", "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Input Dataset" } ], "label": null, "name": "Input dataset", "outputs": [], "position": { "left": 273.83331298828125, "top": 341.83331298828125 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Input Dataset\"}", "tool_version": null, "type": "data_input", "user_outputs": [], "uuid": "98d5e3bf-4715-48a2-9b2b-29b21179c425" }, "2": { "annotation": "", "id": 2, "input_connections": { "input1": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "Sort", "outputs": [ { "name": "output1", "type": "bam" } ], "position": { "left": 330, "top": 222 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}", "tool_version": "2.0", "type": "tool", "user_outputs": [], "uuid": "5e9aef3e-c2ad-43d1-b248-7d94d6a974bc" }, "3": { "annotation": "", "id": 3, "input_connections": { "reference_source|input_bams_0|input_bam": { "id": 2, "output_name": "output1" }, "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": 484.83331298828125, "top": 313.83331298828125 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0", "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"output_mapping_quality\\\": \\\"False\\\", \\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1, \\\"base_position_on_reads\\\": \\\"False\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}", "tool_version": "2.0", "type": "tool", "user_outputs": [], "uuid": "84c6d18e-1930-4eef-b58a-46c88a35339e" }, "4": { "annotation": "", "id": 4, "input_connections": { "input_file": { "id": 3, "output_name": "output_mpileup" } }, "inputs": [], "label": null, "name": "Pileup to VCF", "outputs": [ { "name": "output_file", "type": "vcf" } ], "position": { "left": 562.8333129882812, "top": 469.83331298828125 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.2", "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"False\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"\\\"20\\\"\", \"min_var_pct\": \"\\\"0.5\\\"\"}", "tool_version": "2.2", "type": "tool", "user_outputs": [], "uuid": "335581bc-838e-431d-8247-1e1580260275" } }, "uuid": "0c40a63d-b349-49b8-90b0-c927a05253ef" }