Mercurial > repos > scisjnu123 > ngsap_vc
comparison ngsap-vc/VARSCAN.ga @ 3:0d10255b5434 draft default tip
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author | scisjnu123 |
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date | Thu, 03 Oct 2019 10:42:15 -0400 |
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2:2c7824a8d764 | 3:0d10255b5434 |
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1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "VARSCAN workflow.", | |
4 "format-version": "0.1", | |
5 "name": "VARSCAN", | |
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", | |
19 "outputs": [], | |
20 "position": { | |
21 "left": 161, | |
22 "top": 187 | |
23 }, | |
24 "tool_errors": null, | |
25 "tool_id": null, | |
26 "tool_state": "{\"name\": \"Input Dataset\"}", | |
27 "tool_version": null, | |
28 "type": "data_input", | |
29 "user_outputs": [], | |
30 "uuid": "72a1326a-cd57-4567-8c41-cc66411642be" | |
31 }, | |
32 "1": { | |
33 "annotation": "", | |
34 "id": 1, | |
35 "input_connections": {}, | |
36 "inputs": [ | |
37 { | |
38 "description": "", | |
39 "name": "Input Dataset" | |
40 } | |
41 ], | |
42 "label": null, | |
43 "name": "Input dataset", | |
44 "outputs": [], | |
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52 "tool_version": null, | |
53 "type": "data_input", | |
54 "user_outputs": [], | |
55 "uuid": "d8444634-af6c-44c5-9b55-8c3284da2823" | |
56 }, | |
57 "2": { | |
58 "annotation": "", | |
59 "id": 2, | |
60 "input_connections": { | |
61 "reference_source|input_bams_0|input_bam": { | |
62 "id": 0, | |
63 "output_name": "output" | |
64 }, | |
65 "reference_source|ref_file": { | |
66 "id": 1, | |
67 "output_name": "output" | |
68 } | |
69 }, | |
70 "inputs": [], | |
71 "label": null, | |
72 "name": "MPileup", | |
73 "outputs": [ | |
74 { | |
75 "name": "output_mpileup", | |
76 "type": "pileup" | |
77 }, | |
78 { | |
79 "name": "output_log", | |
80 "type": "txt" | |
81 } | |
82 ], | |
83 "position": { | |
84 "left": 370, | |
85 "top": 187 | |
86 }, | |
87 "post_job_actions": {}, | |
88 "tool_errors": null, | |
89 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0", | |
90 "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}\"}", | |
91 "tool_version": "2.0", | |
92 "type": "tool", | |
93 "user_outputs": [], | |
94 "uuid": "26d34295-7783-40e1-950f-a485ff569f5b" | |
95 }, | |
96 "3": { | |
97 "annotation": "", | |
98 "id": 3, | |
99 "input_connections": { | |
100 "in_file": { | |
101 "id": 2, | |
102 "output_name": "output_mpileup" | |
103 } | |
104 }, | |
105 "inputs": [], | |
106 "label": null, | |
107 "name": "VarScan mpileup", | |
108 "outputs": [ | |
109 { | |
110 "name": "output", | |
111 "type": "vcf" | |
112 }, | |
113 { | |
114 "name": "log", | |
115 "type": "txt" | |
116 } | |
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122 "post_job_actions": {}, | |
123 "tool_errors": null, | |
124 "tool_id": "toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_mpileup/2.3.5", | |
125 "tool_state": "{\"strand_filter\": \"\\\"1\\\"\", \"min_avg_qual\": \"\\\"15\\\"\", \"min_coverage\": \"\\\"8\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"min_freq_for_hom\": \"\\\"0.75\\\"\", \"min_var_freq\": \"\\\"0.01\\\"\", \"exe_command\": \"\\\"mpileup2snp\\\"\", \"min_reads2\": \"\\\"2\\\"\", \"p_value\": \"\\\"0.99\\\"\", \"variants\": \"\\\"1\\\"\", \"vcf_sample_list\": \"null\", \"in_file\": \"null\"}", | |
126 "tool_version": "2.3.5", | |
127 "type": "tool", | |
128 "user_outputs": [], | |
129 "uuid": "5ff6cf71-5d74-42ad-bcdc-7c75891dc10e" | |
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132 "uuid": "5b7bf29e-1272-4211-b345-37695989c6fa" | |
133 } |