Mercurial > repos > scisjnu123 > ngsap_vc
comparison ngsap-vc/SAMTools.ga @ 3:0d10255b5434 draft default tip
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| author | scisjnu123 |
|---|---|
| date | Thu, 03 Oct 2019 10:42:15 -0400 |
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| children |
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| 2:2c7824a8d764 | 3:0d10255b5434 |
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| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "SAMTools workflow", | |
| 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": "Input Dataset" | |
| 15 } | |
| 16 ], | |
| 17 "label": null, | |
| 18 "name": "Input dataset", | |
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| 26 "tool_state": "{\"name\": \"Input Dataset\"}", | |
| 27 "tool_version": null, | |
| 28 "type": "data_input", | |
| 29 "user_outputs": [], | |
| 30 "uuid": "1eec712c-2fe0-43a8-b033-f027a74c6a48" | |
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| 33 "annotation": "", | |
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| 35 "input_connections": {}, | |
| 36 "inputs": [ | |
| 37 { | |
| 38 "description": "", | |
| 39 "name": "Input Dataset" | |
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| 42 "label": null, | |
| 43 "name": "Input dataset", | |
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| 53 "type": "data_input", | |
| 54 "user_outputs": [], | |
| 55 "uuid": "98d5e3bf-4715-48a2-9b2b-29b21179c425" | |
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| 57 "2": { | |
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| 60 "input_connections": { | |
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| 63 "output_name": "output" | |
| 64 } | |
| 65 }, | |
| 66 "inputs": [], | |
| 67 "label": null, | |
| 68 "name": "Sort", | |
| 69 "outputs": [ | |
| 70 { | |
| 71 "name": "output1", | |
| 72 "type": "bam" | |
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| 74 ], | |
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| 79 "post_job_actions": {}, | |
| 80 "tool_errors": null, | |
| 81 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", | |
| 82 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}", | |
| 83 "tool_version": "2.0", | |
| 84 "type": "tool", | |
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| 94 "output_name": "output1" | |
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| 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" | |
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| 120 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0", | |
| 121 "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}\"}", | |
| 122 "tool_version": "2.0", | |
| 123 "type": "tool", | |
| 124 "user_outputs": [], | |
| 125 "uuid": "84c6d18e-1930-4eef-b58a-46c88a35339e" | |
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| 127 "4": { | |
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| 129 "id": 4, | |
| 130 "input_connections": { | |
| 131 "input_file": { | |
| 132 "id": 3, | |
| 133 "output_name": "output_mpileup" | |
| 134 } | |
| 135 }, | |
| 136 "inputs": [], | |
| 137 "label": null, | |
| 138 "name": "Pileup to VCF", | |
| 139 "outputs": [ | |
| 140 { | |
| 141 "name": "output_file", | |
| 142 "type": "vcf" | |
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| 145 "position": { | |
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| 149 "post_job_actions": {}, | |
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| 151 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.2", | |
| 152 "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\\\"\"}", | |
| 153 "tool_version": "2.2", | |
| 154 "type": "tool", | |
| 155 "user_outputs": [], | |
| 156 "uuid": "335581bc-838e-431d-8247-1e1580260275" | |
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| 159 "uuid": "0c40a63d-b349-49b8-90b0-c927a05253ef" | |
| 160 } |
