Mercurial > repos > ulfschaefer > phephenix
comparison Galaxy-Workflow-Phenix_workflow.ga @ 16:55bfe9d1888e draft
Uploaded
author | ulfschaefer |
---|---|
date | Tue, 12 Jul 2016 09:56:33 -0400 |
parents | 2e5a83c0f78f |
children |
comparison
equal
deleted
inserted
replaced
15:48c41c6ad84e | 16:55bfe9d1888e |
---|---|
18 "label": null, | 18 "label": null, |
19 "name": "Input dataset", | 19 "name": "Input dataset", |
20 "outputs": [], | 20 "outputs": [], |
21 "position": { | 21 "position": { |
22 "left": 200, | 22 "left": 200, |
23 "top": 128 | 23 "top": 141 |
24 }, | 24 }, |
25 "tool_errors": null, | 25 "tool_errors": null, |
26 "tool_id": null, | 26 "tool_id": null, |
27 "tool_state": "{\"name\": \"Reference fasta\"}", | 27 "tool_state": "{\"name\": \"Reference fasta\"}", |
28 "tool_version": null, | 28 "tool_version": null, |
29 "type": "data_input", | 29 "type": "data_input", |
30 "uuid": "2f18889e-5448-460b-8167-e04125fd51cf", | 30 "uuid": "108478ac-5f4a-4244-b9db-f6c0ae9674fb", |
31 "workflow_outputs": [] | 31 "workflow_outputs": [] |
32 }, | 32 }, |
33 "1": { | 33 "1": { |
34 "annotation": "", | 34 "annotation": "", |
35 "content_id": null, | 35 "content_id": null, |
44 "label": null, | 44 "label": null, |
45 "name": "Input dataset", | 45 "name": "Input dataset", |
46 "outputs": [], | 46 "outputs": [], |
47 "position": { | 47 "position": { |
48 "left": 189, | 48 "left": 189, |
49 "top": 296 | 49 "top": 309 |
50 }, | 50 }, |
51 "tool_errors": null, | 51 "tool_errors": null, |
52 "tool_id": null, | 52 "tool_id": null, |
53 "tool_state": "{\"name\": \"R1 fastq\"}", | 53 "tool_state": "{\"name\": \"R1 fastq\"}", |
54 "tool_version": null, | 54 "tool_version": null, |
55 "type": "data_input", | 55 "type": "data_input", |
56 "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c", | 56 "uuid": "b00e3b0f-c7b6-4704-840b-76ec70d1cb75", |
57 "workflow_outputs": [] | 57 "workflow_outputs": [] |
58 }, | 58 }, |
59 "2": { | 59 "2": { |
60 "annotation": "", | 60 "annotation": "", |
61 "content_id": null, | 61 "content_id": null, |
70 "label": null, | 70 "label": null, |
71 "name": "Input dataset", | 71 "name": "Input dataset", |
72 "outputs": [], | 72 "outputs": [], |
73 "position": { | 73 "position": { |
74 "left": 211, | 74 "left": 211, |
75 "top": 474 | 75 "top": 487 |
76 }, | 76 }, |
77 "tool_errors": null, | 77 "tool_errors": null, |
78 "tool_id": null, | 78 "tool_id": null, |
79 "tool_state": "{\"name\": \"R2 fastqs\"}", | 79 "tool_state": "{\"name\": \"R2 fastqs\"}", |
80 "tool_version": null, | 80 "tool_version": null, |
81 "type": "data_input", | 81 "type": "data_input", |
82 "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25", | 82 "uuid": "5e82d35b-0ce9-4295-a9af-0a5e35283404", |
83 "workflow_outputs": [] | 83 "workflow_outputs": [] |
84 }, | 84 }, |
85 "3": { | 85 "3": { |
86 "annotation": "", | 86 "annotation": "", |
87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", | 87 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", |
98 "reference_source|ref_file": { | 98 "reference_source|ref_file": { |
99 "id": 0, | 99 "id": 0, |
100 "output_name": "output" | 100 "output_name": "output" |
101 } | 101 } |
102 }, | 102 }, |
103 "inputs": [], | 103 "inputs": [ |
104 { | |
105 "description": "runtime parameter for tool Map with BWA-MEM", | |
106 "name": "reference_source" | |
107 }, | |
108 { | |
109 "description": "runtime parameter for tool Map with BWA-MEM", | |
110 "name": "fastq_input" | |
111 }, | |
112 { | |
113 "description": "runtime parameter for tool Map with BWA-MEM", | |
114 "name": "fastq_input" | |
115 } | |
116 ], | |
104 "label": null, | 117 "label": null, |
105 "name": "Map with BWA-MEM", | 118 "name": "Map with BWA-MEM", |
106 "outputs": [ | 119 "outputs": [ |
107 { | 120 { |
108 "name": "bam_output", | 121 "name": "bam_output", |
109 "type": "bam" | 122 "type": "bam" |
110 } | 123 } |
111 ], | 124 ], |
112 "position": { | 125 "position": { |
113 "left": 423.5, | 126 "left": 423.5, |
114 "top": 300 | 127 "top": 313 |
115 }, | 128 }, |
116 "post_job_actions": { | 129 "post_job_actions": { |
117 "RenameDatasetActionbam_output": { | 130 "RenameDatasetActionbam_output": { |
118 "action_arguments": { | 131 "action_arguments": { |
119 "newname": "#{fastq_input1 | basename}.bam" | 132 "newname": "#{fastq_input1 | basename}.bam" |
122 "output_name": "bam_output" | 135 "output_name": "bam_output" |
123 } | 136 } |
124 }, | 137 }, |
125 "tool_errors": null, | 138 "tool_errors": null, |
126 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", | 139 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", |
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\\\"}\"}", | 140 "tool_shed_repository": { |
141 "changeset_revision": "546ada4a9f43", | |
142 "name": "bwa", | |
143 "owner": "devteam", | |
144 "tool_shed": "toolshed.g2.bx.psu.edu" | |
145 }, | |
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\\\"}\"}", | |
128 "tool_version": "0.7.12.1", | 147 "tool_version": "0.7.12.1", |
129 "type": "tool", | 148 "type": "tool", |
130 "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d", | 149 "uuid": "f74219f9-2d53-4eca-9bb7-079a2a8aa65e", |
131 "workflow_outputs": [] | 150 "workflow_outputs": [] |
132 }, | 151 }, |
133 "4": { | 152 "4": { |
134 "annotation": "", | 153 "annotation": "", |
135 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", | 154 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", |
142 "ref_file": { | 161 "ref_file": { |
143 "id": 0, | 162 "id": 0, |
144 "output_name": "output" | 163 "output_name": "output" |
145 } | 164 } |
146 }, | 165 }, |
147 "inputs": [], | 166 "inputs": [ |
167 { | |
168 "description": "runtime parameter for tool PHE MPileup", | |
169 "name": "ref_file" | |
170 }, | |
171 { | |
172 "description": "runtime parameter for tool PHE MPileup", | |
173 "name": "input_bam" | |
174 } | |
175 ], | |
148 "label": null, | 176 "label": null, |
149 "name": "PHE MPileup", | 177 "name": "PHE MPileup", |
150 "outputs": [ | 178 "outputs": [ |
151 { | 179 { |
152 "name": "outvcf", | 180 "name": "outvcf", |
153 "type": "vcf" | 181 "type": "vcf" |
154 } | 182 } |
155 ], | 183 ], |
156 "position": { | 184 "position": { |
157 "left": 634, | 185 "left": 634, |
158 "top": 138 | 186 "top": 151 |
159 }, | 187 }, |
160 "post_job_actions": { | 188 "post_job_actions": { |
161 "RenameDatasetActionoutvcf": { | 189 "RenameDatasetActionoutvcf": { |
162 "action_arguments": { | 190 "action_arguments": { |
163 "newname": "#{input_bam | basename}.vcf" | 191 "newname": "#{input_bam | basename}.vcf" |
166 "output_name": "outvcf" | 194 "output_name": "outvcf" |
167 } | 195 } |
168 }, | 196 }, |
169 "tool_errors": null, | 197 "tool_errors": null, |
170 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", | 198 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", |
171 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", | 199 "tool_shed_repository": { |
200 "changeset_revision": "b13db9e677b4", | |
201 "name": "phe_samtools_mpileup", | |
202 "owner": "ulfschaefer", | |
203 "tool_shed": "toolshed.g2.bx.psu.edu" | |
204 }, | |
205 "tool_state": "{\"ref_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", | |
172 "tool_version": "1.0", | 206 "tool_version": "1.0", |
173 "type": "tool", | 207 "type": "tool", |
174 "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca", | 208 "uuid": "83294062-5c05-4a09-938a-96a409216477", |
175 "workflow_outputs": [] | 209 "workflow_outputs": [] |
176 }, | 210 }, |
177 "5": { | 211 "5": { |
178 "annotation": "", | 212 "annotation": "", |
179 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", | 213 "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", |
186 "ref_fa": { | 220 "ref_fa": { |
187 "id": 0, | 221 "id": 0, |
188 "output_name": "output" | 222 "output_name": "output" |
189 } | 223 } |
190 }, | 224 }, |
191 "inputs": [], | 225 "inputs": [ |
226 { | |
227 "description": "runtime parameter for tool Filter VCF", | |
228 "name": "input" | |
229 }, | |
230 { | |
231 "description": "runtime parameter for tool Filter VCF", | |
232 "name": "ref_fa" | |
233 } | |
234 ], | |
192 "label": null, | 235 "label": null, |
193 "name": "Filter VCF", | 236 "name": "Filter VCF", |
194 "outputs": [ | 237 "outputs": [ |
195 { | 238 { |
196 "name": "output", | 239 "name": "output", |
197 "type": "vcf" | 240 "type": "vcf" |
198 } | 241 } |
199 ], | 242 ], |
200 "position": { | 243 "position": { |
201 "left": 747, | 244 "left": 747, |
202 "top": 326 | 245 "top": 339 |
203 }, | 246 }, |
204 "post_job_actions": { | 247 "post_job_actions": { |
205 "RenameDatasetActionoutput": { | 248 "RenameDatasetActionoutput": { |
206 "action_arguments": { | 249 "action_arguments": { |
207 "newname": "#{input | basename}.filtered.vcf" | 250 "newname": "#{input | basename}.filtered.vcf" |
210 "output_name": "output" | 253 "output_name": "output" |
211 } | 254 } |
212 }, | 255 }, |
213 "tool_errors": null, | 256 "tool_errors": null, |
214 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", | 257 "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", |
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\\\"}}]\"}", | 258 "tool_shed_repository": { |
259 "changeset_revision": "48c41c6ad84e", | |
260 "name": "phephenix", | |
261 "owner": "ulfschaefer", | |
262 "tool_shed": "toolshed.g2.bx.psu.edu" | |
263 }, | |
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\\\"}}]\"}", | |
216 "tool_version": "1.0", | 265 "tool_version": "1.0", |
217 "type": "tool", | 266 "type": "tool", |
218 "uuid": "51251f05-75d4-4d89-b757-2248b934d630", | 267 "uuid": "9e3a724f-63e2-45c8-9d61-19643583f4bb", |
219 "workflow_outputs": [] | 268 "workflow_outputs": [] |
220 } | 269 } |
221 }, | 270 }, |
222 "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf" | 271 "uuid": "3392477d-d5ec-402e-b4a9-d25f79403fe9" |
223 } | 272 } |