annotate Galaxy-Workflow-Phenix_workflow.ga @ 16:55bfe9d1888e draft

Uploaded
author ulfschaefer
date Tue, 12 Jul 2016 09:56:33 -0400
parents 2e5a83c0f78f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
1 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
2 "a_galaxy_workflow": "true",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
3 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
4 "format-version": "0.1",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
5 "name": "Phenix workflow",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
6 "steps": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
7 "0": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
8 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
9 "content_id": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
10 "id": 0,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
11 "input_connections": {},
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
12 "inputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
13 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
14 "description": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
15 "name": "Reference fasta"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
16 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
17 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
18 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
19 "name": "Input dataset",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
20 "outputs": [],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
21 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
22 "left": 200,
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
23 "top": 141
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
24 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
25 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
26 "tool_id": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
27 "tool_state": "{\"name\": \"Reference fasta\"}",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
28 "tool_version": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
29 "type": "data_input",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
30 "uuid": "108478ac-5f4a-4244-b9db-f6c0ae9674fb",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
31 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
32 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
33 "1": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
34 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
35 "content_id": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
36 "id": 1,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
37 "input_connections": {},
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
38 "inputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
39 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
40 "description": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
41 "name": "R1 fastq"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
42 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
43 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
44 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
45 "name": "Input dataset",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
46 "outputs": [],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
47 "position": {
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
48 "left": 189,
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
49 "top": 309
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
50 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
51 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
52 "tool_id": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
53 "tool_state": "{\"name\": \"R1 fastq\"}",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
54 "tool_version": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
55 "type": "data_input",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
56 "uuid": "b00e3b0f-c7b6-4704-840b-76ec70d1cb75",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
57 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
58 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
59 "2": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
60 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
61 "content_id": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
62 "id": 2,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
63 "input_connections": {},
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
64 "inputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
65 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
66 "description": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
67 "name": "R2 fastqs"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
68 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
69 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
70 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
71 "name": "Input dataset",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
72 "outputs": [],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
73 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
74 "left": 211,
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
75 "top": 487
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
76 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
77 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
78 "tool_id": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
79 "tool_state": "{\"name\": \"R2 fastqs\"}",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
80 "tool_version": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
81 "type": "data_input",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
82 "uuid": "5e82d35b-0ce9-4295-a9af-0a5e35283404",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
83 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
84 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
85 "3": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
86 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
88 "id": 3,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
89 "input_connections": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
90 "fastq_input|fastq_input1": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
91 "id": 1,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
92 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
93 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
94 "fastq_input|fastq_input2": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
95 "id": 2,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
96 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
97 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
98 "reference_source|ref_file": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
99 "id": 0,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
100 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
101 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
102 },
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
103 "inputs": [
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
104 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
105 "description": "runtime parameter for tool Map with BWA-MEM",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
106 "name": "reference_source"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
107 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
108 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
109 "description": "runtime parameter for tool Map with BWA-MEM",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
110 "name": "fastq_input"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
111 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
112 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
113 "description": "runtime parameter for tool Map with BWA-MEM",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
114 "name": "fastq_input"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
115 }
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
116 ],
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
117 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
118 "name": "Map with BWA-MEM",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
119 "outputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
120 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
121 "name": "bam_output",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
122 "type": "bam"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
123 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
124 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
125 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
126 "left": 423.5,
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
127 "top": 313
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
128 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
129 "post_job_actions": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
130 "RenameDatasetActionbam_output": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
131 "action_arguments": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
132 "newname": "#{fastq_input1 | basename}.bam"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
133 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
134 "action_type": "RenameDatasetAction",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
135 "output_name": "bam_output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
136 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
137 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
138 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
139 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
140 "tool_shed_repository": {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
141 "changeset_revision": "546ada4a9f43",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
142 "name": "bwa",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
143 "owner": "devteam",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
144 "tool_shed": "toolshed.g2.bx.psu.edu"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
145 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
146 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"true\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"true\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"true\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
147 "tool_version": "0.7.12.1",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
148 "type": "tool",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
149 "uuid": "f74219f9-2d53-4eca-9bb7-079a2a8aa65e",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
150 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
151 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
152 "4": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
153 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
154 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
155 "id": 4,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
156 "input_connections": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
157 "input_bam": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
158 "id": 3,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
159 "output_name": "bam_output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
160 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
161 "ref_file": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
162 "id": 0,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
163 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
164 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
165 },
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
166 "inputs": [
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
167 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
168 "description": "runtime parameter for tool PHE MPileup",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
169 "name": "ref_file"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
170 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
171 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
172 "description": "runtime parameter for tool PHE MPileup",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
173 "name": "input_bam"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
174 }
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
175 ],
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
176 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
177 "name": "PHE MPileup",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
178 "outputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
179 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
180 "name": "outvcf",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
181 "type": "vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
182 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
183 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
184 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
185 "left": 634,
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
186 "top": 151
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
187 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
188 "post_job_actions": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
189 "RenameDatasetActionoutvcf": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
190 "action_arguments": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
191 "newname": "#{input_bam | basename}.vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
192 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
193 "action_type": "RenameDatasetAction",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
194 "output_name": "outvcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
195 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
196 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
197 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
198 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
199 "tool_shed_repository": {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
200 "changeset_revision": "b13db9e677b4",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
201 "name": "phe_samtools_mpileup",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
202 "owner": "ulfschaefer",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
203 "tool_shed": "toolshed.g2.bx.psu.edu"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
204 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
205 "tool_state": "{\"ref_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
206 "tool_version": "1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
207 "type": "tool",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
208 "uuid": "83294062-5c05-4a09-938a-96a409216477",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
209 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
210 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
211 "5": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
212 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
213 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
214 "id": 5,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
215 "input_connections": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
216 "input": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
217 "id": 4,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
218 "output_name": "outvcf"
11
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
219 },
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
220 "ref_fa": {
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
221 "id": 0,
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
222 "output_name": "output"
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
223 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
224 },
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
225 "inputs": [
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
226 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
227 "description": "runtime parameter for tool Filter VCF",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
228 "name": "input"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
229 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
230 {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
231 "description": "runtime parameter for tool Filter VCF",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
232 "name": "ref_fa"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
233 }
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
234 ],
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
235 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
236 "name": "Filter VCF",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
237 "outputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
238 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
239 "name": "output",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
240 "type": "vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
241 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
242 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
243 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
244 "left": 747,
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
245 "top": 339
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
246 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
247 "post_job_actions": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
248 "RenameDatasetActionoutput": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
249 "action_arguments": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
250 "newname": "#{input | basename}.filtered.vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
251 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
252 "action_type": "RenameDatasetAction",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
253 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
254 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
255 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
256 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
257 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
258 "tool_shed_repository": {
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
259 "changeset_revision": "48c41c6ad84e",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
260 "name": "phephenix",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
261 "owner": "ulfschaefer",
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
262 "tool_shed": "toolshed.g2.bx.psu.edu"
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
263 },
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
264 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"5\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 4, \\\"snp_filter_type\\\": {\\\"mq0f_ratio\\\": \\\"0.05\\\", \\\"__current_case__\\\": 8, \\\"snp_filter_type_selector\\\": \\\"mq0f_ratio_option\\\"}}]\"}",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
265 "tool_version": "1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
266 "type": "tool",
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
267 "uuid": "9e3a724f-63e2-45c8-9d61-19643583f4bb",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
268 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
269 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
270 },
16
55bfe9d1888e Uploaded
ulfschaefer
parents: 14
diff changeset
271 "uuid": "3392477d-d5ec-402e-b4a9-d25f79403fe9"
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
272 }