annotate ngsap-vc/SAMTools.ga @ 3:0d10255b5434 draft default tip

Uploaded
author scisjnu123
date Thu, 03 Oct 2019 10:42:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
1 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
2 "a_galaxy_workflow": "true",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
3 "annotation": "SAMTools workflow",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
4 "format-version": "0.1",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
5 "name": "SAMTools",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
6 "steps": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
7 "0": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
8 "annotation": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
9 "id": 0,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
10 "input_connections": {},
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
11 "inputs": [
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
12 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
13 "description": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
14 "name": "Input Dataset"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
15 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
16 ],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
17 "label": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
18 "name": "Input dataset",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
19 "outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
20 "position": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
21 "left": 162,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
22 "top": 169
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
23 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
24 "tool_errors": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
25 "tool_id": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
26 "tool_state": "{\"name\": \"Input Dataset\"}",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
27 "tool_version": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
28 "type": "data_input",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
29 "user_outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
30 "uuid": "1eec712c-2fe0-43a8-b033-f027a74c6a48"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
31 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
32 "1": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
33 "annotation": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
34 "id": 1,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
35 "input_connections": {},
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
36 "inputs": [
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
37 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
38 "description": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
39 "name": "Input Dataset"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
40 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
41 ],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
42 "label": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
43 "name": "Input dataset",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
44 "outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
45 "position": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
46 "left": 273.83331298828125,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
47 "top": 341.83331298828125
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
48 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
49 "tool_errors": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
50 "tool_id": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
51 "tool_state": "{\"name\": \"Input Dataset\"}",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
52 "tool_version": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
53 "type": "data_input",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
54 "user_outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
55 "uuid": "98d5e3bf-4715-48a2-9b2b-29b21179c425"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
56 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
57 "2": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
58 "annotation": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
59 "id": 2,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
60 "input_connections": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
61 "input1": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
62 "id": 0,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
63 "output_name": "output"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
64 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
65 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
66 "inputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
67 "label": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
68 "name": "Sort",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
69 "outputs": [
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
70 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
71 "name": "output1",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
72 "type": "bam"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
73 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
74 ],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
75 "position": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
76 "left": 330,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
77 "top": 222
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
78 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
79 "post_job_actions": {},
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
80 "tool_errors": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
81 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
82 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
83 "tool_version": "2.0",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
84 "type": "tool",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
85 "user_outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
86 "uuid": "5e9aef3e-c2ad-43d1-b248-7d94d6a974bc"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
87 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
88 "3": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
89 "annotation": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
90 "id": 3,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
91 "input_connections": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
92 "reference_source|input_bams_0|input_bam": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
93 "id": 2,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
94 "output_name": "output1"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
95 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
96 "reference_source|ref_file": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
97 "id": 1,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
98 "output_name": "output"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
99 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
100 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
101 "inputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
102 "label": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
103 "name": "MPileup",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
104 "outputs": [
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
105 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
106 "name": "output_mpileup",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
107 "type": "pileup"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
108 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
109 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
110 "name": "output_log",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
111 "type": "txt"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
112 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
113 ],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
114 "position": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
115 "left": 484.83331298828125,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
116 "top": 313.83331298828125
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
117 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
118 "post_job_actions": {},
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
119 "tool_errors": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
120 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
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}\"}",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
122 "tool_version": "2.0",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
123 "type": "tool",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
124 "user_outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
125 "uuid": "84c6d18e-1930-4eef-b58a-46c88a35339e"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
126 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
127 "4": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
128 "annotation": "",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
129 "id": 4,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
130 "input_connections": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
131 "input_file": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
132 "id": 3,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
133 "output_name": "output_mpileup"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
134 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
135 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
136 "inputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
137 "label": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
138 "name": "Pileup to VCF",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
139 "outputs": [
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
140 {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
141 "name": "output_file",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
142 "type": "vcf"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
143 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
144 ],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
145 "position": {
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
146 "left": 562.8333129882812,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
147 "top": 469.83331298828125
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
148 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
149 "post_job_actions": {},
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
150 "tool_errors": null,
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
151 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.2",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
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\\\"\"}",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
153 "tool_version": "2.2",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
154 "type": "tool",
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
155 "user_outputs": [],
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
156 "uuid": "335581bc-838e-431d-8247-1e1580260275"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
157 }
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
158 },
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
159 "uuid": "0c40a63d-b349-49b8-90b0-c927a05253ef"
0d10255b5434 Uploaded
scisjnu123
parents:
diff changeset
160 }