|
3
|
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": [],
|
|
|
45 "position": {
|
|
|
46 "left": 163.83331298828125,
|
|
|
47 "top": 263.8333282470703
|
|
|
48 },
|
|
|
49 "tool_errors": null,
|
|
|
50 "tool_id": null,
|
|
|
51 "tool_state": "{\"name\": \"Input Dataset\"}",
|
|
|
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 }
|
|
|
117 ],
|
|
|
118 "position": {
|
|
|
119 "left": 563.8333129882812,
|
|
|
120 "top": 364.83331298828125
|
|
|
121 },
|
|
|
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"
|
|
|
130 }
|
|
|
131 },
|
|
|
132 "uuid": "5b7bf29e-1272-4211-b345-37695989c6fa"
|
|
|
133 } |
