Mercurial > repos > scisjnu123 > test
comparison Galaxy-Workflow-SAMTools.ga @ 7:ab331b4507fd draft
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| author | scisjnu123 |
|---|---|
| date | Thu, 12 Sep 2019 12:39:24 -0400 |
| parents | |
| children |
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| 6:ebc5e82e6ae5 | 7:ab331b4507fd |
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| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "This workflow uses SAMTools to call SNPs and INDELs.", | |
| 4 "format-version": "0.1", | |
| 5 "name": "SAMTools", | |
| 6 "steps": { | |
| 7 "0": { | |
| 8 "annotation": "", | |
| 9 "id": 0, | |
| 10 "input_connections": {}, | |
| 11 "inputs": [ | |
| 12 { | |
| 13 "description": "", | |
| 14 "name": ".bam file" | |
| 15 } | |
| 16 ], | |
| 17 "label": null, | |
| 18 "name": "Input dataset", | |
| 19 "outputs": [], | |
| 20 "position": { | |
| 21 "left": 200, | |
| 22 "top": 156 | |
| 23 }, | |
| 24 "tool_errors": null, | |
| 25 "tool_id": null, | |
| 26 "tool_state": "{\"name\": \".bam file\"}", | |
| 27 "tool_version": null, | |
| 28 "type": "data_input", | |
| 29 "user_outputs": [], | |
| 30 "uuid": "955f71da-3fad-46c4-a1d9-b0b1cb484569" | |
| 31 }, | |
| 32 "1": { | |
| 33 "annotation": "", | |
| 34 "id": 1, | |
| 35 "input_connections": {}, | |
| 36 "inputs": [ | |
| 37 { | |
| 38 "description": "", | |
| 39 "name": "Reference genome." | |
| 40 } | |
| 41 ], | |
| 42 "label": null, | |
| 43 "name": "Input dataset", | |
| 44 "outputs": [], | |
| 45 "position": { | |
| 46 "left": 512, | |
| 47 "top": 285 | |
| 48 }, | |
| 49 "tool_errors": null, | |
| 50 "tool_id": null, | |
| 51 "tool_state": "{\"name\": \"Reference genome.\"}", | |
| 52 "tool_version": null, | |
| 53 "type": "data_input", | |
| 54 "user_outputs": [], | |
| 55 "uuid": "7069b8d2-a89a-472a-8e18-b5b8f076de33" | |
| 56 }, | |
| 57 "2": { | |
| 58 "annotation": "", | |
| 59 "id": 2, | |
| 60 "input_connections": { | |
| 61 "inputFile": { | |
| 62 "id": 0, | |
| 63 "output_name": "output" | |
| 64 } | |
| 65 }, | |
| 66 "inputs": [], | |
| 67 "label": null, | |
| 68 "name": "SortSam", | |
| 69 "outputs": [ | |
| 70 { | |
| 71 "name": "outFile", | |
| 72 "type": "bam" | |
| 73 } | |
| 74 ], | |
| 75 "position": { | |
| 76 "left": 436.5, | |
| 77 "top": 121 | |
| 78 }, | |
| 79 "post_job_actions": {}, | |
| 80 "tool_errors": null, | |
| 81 "tool_id": "toolshed.g2.bx.psu.edu/repos/avowinkel/picard/picard_SortSam/1.135", | |
| 82 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"coordinate\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", | |
| 83 "tool_version": "1.135", | |
| 84 "type": "tool", | |
| 85 "user_outputs": [], | |
| 86 "uuid": "b06955b6-6bba-4aaa-a919-fbb2aba9fdf5" | |
| 87 }, | |
| 88 "3": { | |
| 89 "annotation": "", | |
| 90 "id": 3, | |
| 91 "input_connections": { | |
| 92 "reference_source|input_bams_0|input_bam": { | |
| 93 "id": 2, | |
| 94 "output_name": "outFile" | |
| 95 }, | |
| 96 "reference_source|ref_file": { | |
| 97 "id": 1, | |
| 98 "output_name": "output" | |
| 99 } | |
| 100 }, | |
| 101 "inputs": [], | |
| 102 "label": null, | |
| 103 "name": "MPileup", | |
| 104 "outputs": [ | |
| 105 { | |
| 106 "name": "output_mpileup", | |
| 107 "type": "pileup" | |
| 108 }, | |
| 109 { | |
| 110 "name": "output_log", | |
| 111 "type": "txt" | |
| 112 } | |
| 113 ], | |
| 114 "position": { | |
| 115 "left": 746, | |
| 116 "top": 192 | |
| 117 }, | |
| 118 "post_job_actions": {}, | |
| 119 "tool_errors": null, | |
| 120 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3", | |
| 121 "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}\"}", | |
| 122 "tool_version": "0.0.3", | |
| 123 "type": "tool", | |
| 124 "user_outputs": [], | |
| 125 "uuid": "99b58983-e355-4357-b77e-8e29afcdc866" | |
| 126 } | |
| 127 }, | |
| 128 "uuid": "6b217aca-887a-4cca-91e4-446a7cc50726" | |
| 129 } |
