annotate Galaxy-Workflow-Phenix_workflow.ga @ 14:2e5a83c0f78f draft

Uploaded
author ulfschaefer
date Fri, 01 Jul 2016 06:09:01 -0400
parents b26e4f861e08
children 55bfe9d1888e
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,
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
23 "top": 128
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",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
30 "uuid": "2f18889e-5448-460b-8167-e04125fd51cf",
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,
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
49 "top": 296
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",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
56 "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c",
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,
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
75 "top": 474
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",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
82 "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25",
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 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
103 "inputs": [],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
104 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
105 "name": "Map with BWA-MEM",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
106 "outputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
107 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
108 "name": "bam_output",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
109 "type": "bam"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
110 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
111 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
112 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
113 "left": 423.5,
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
114 "top": 300
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
115 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
116 "post_job_actions": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
117 "RenameDatasetActionbam_output": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
118 "action_arguments": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
119 "newname": "#{fastq_input1 | basename}.bam"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
120 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
121 "action_type": "RenameDatasetAction",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
122 "output_name": "bam_output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
123 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
124 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
125 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
126 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
127 "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\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
128 "tool_version": "0.7.12.1",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
129 "type": "tool",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
130 "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
131 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
132 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
133 "4": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
134 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
135 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
136 "id": 4,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
137 "input_connections": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
138 "input_bam": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
139 "id": 3,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
140 "output_name": "bam_output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
141 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
142 "ref_file": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
143 "id": 0,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
144 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
145 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
146 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
147 "inputs": [],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
148 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
149 "name": "PHE MPileup",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
150 "outputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
151 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
152 "name": "outvcf",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
153 "type": "vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
154 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
155 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
156 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
157 "left": 634,
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
158 "top": 138
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
159 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
160 "post_job_actions": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
161 "RenameDatasetActionoutvcf": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
162 "action_arguments": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
163 "newname": "#{input_bam | basename}.vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
164 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
165 "action_type": "RenameDatasetAction",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
166 "output_name": "outvcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
167 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
168 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
169 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
170 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
171 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
172 "tool_version": "1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
173 "type": "tool",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
174 "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
175 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
176 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
177 "5": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
178 "annotation": "",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
179 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
180 "id": 5,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
181 "input_connections": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
182 "input": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
183 "id": 4,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
184 "output_name": "outvcf"
11
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
185 },
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
186 "ref_fa": {
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
187 "id": 0,
a3f15f50a4af Uploaded
ulfschaefer
parents: 1
diff changeset
188 "output_name": "output"
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
189 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
190 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
191 "inputs": [],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
192 "label": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
193 "name": "Filter VCF",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
194 "outputs": [
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
195 {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
196 "name": "output",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
197 "type": "vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
198 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
199 ],
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
200 "position": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
201 "left": 747,
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
202 "top": 326
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
203 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
204 "post_job_actions": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
205 "RenameDatasetActionoutput": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
206 "action_arguments": {
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
207 "newname": "#{input | basename}.filtered.vcf"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
208 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
209 "action_type": "RenameDatasetAction",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
210 "output_name": "output"
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
211 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
212 },
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
213 "tool_errors": null,
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
214 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
215 "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
216 "tool_version": "1.0",
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
217 "type": "tool",
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
218 "uuid": "51251f05-75d4-4d89-b757-2248b934d630",
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
219 "workflow_outputs": []
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
220 }
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
221 },
14
2e5a83c0f78f Uploaded
ulfschaefer
parents: 13
diff changeset
222 "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf"
1
162c88041ed7 Uploaded
ulfschaefer
parents:
diff changeset
223 }