Mercurial > repos > jjohnson > mmuff
annotate Galaxy-Workflow-MMuFF_v1.2.ga @ 3:0b3a14a7b5f1
Fix link from SnpEff to SnpSift
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Fri, 12 Apr 2013 09:30:08 -0500 |
parents | 04e170c09922 |
children | 6c284cb55352 |
rev | line source |
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0 | 1 { |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
2
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5 "name": "MMuFF_Human_v1.2", |
0 | 6 "steps": { |
7 "0": { | |
2
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8 "annotation": "Human RNA-seq paired reads left mates", |
0 | 9 "id": 0, |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
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13 "description": "Human RNA-seq paired reads left mates", |
0 | 14 "name": "Forward reads fastq" |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
2
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20 "left": 240, |
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21 "top": 287 |
0 | 22 }, |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"Forward reads fastq\"}", | |
26 "tool_version": null, | |
27 "type": "data_input", | |
28 "user_outputs": [] | |
29 }, | |
30 "1": { | |
2
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31 "annotation": "Human RNA-seq paired reads right mates", |
0 | 32 "id": 1, |
33 "input_connections": {}, | |
34 "inputs": [ | |
35 { | |
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36 "description": "Human RNA-seq paired reads right mates", |
0 | 37 "name": "Reverse reads fastq" |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
41 "outputs": [], | |
42 "position": { | |
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43 "left": 249, |
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44 "top": 383 |
0 | 45 }, |
46 "tool_errors": null, | |
47 "tool_id": null, | |
48 "tool_state": "{\"name\": \"Reverse reads fastq\"}", | |
49 "tool_version": null, | |
50 "type": "data_input", | |
51 "user_outputs": [] | |
52 }, | |
53 "2": { | |
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54 "annotation": "Known SNPs - dbSNP.vcf", |
0 | 55 "id": 2, |
56 "input_connections": {}, | |
57 "inputs": [ | |
58 { | |
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59 "description": "Known SNPs - dbSNP.vcf", |
0 | 60 "name": "VCF file of known variants (dbSNP)" |
61 } | |
62 ], | |
63 "name": "Input dataset", | |
64 "outputs": [], | |
65 "position": { | |
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66 "left": 2327, |
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67 "top": 758 |
0 | 68 }, |
69 "tool_errors": null, | |
70 "tool_id": null, | |
71 "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", | |
72 "tool_version": null, | |
73 "type": "data_input", | |
74 "user_outputs": [] | |
75 }, | |
76 "3": { | |
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77 "annotation": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)", |
0 | 78 "id": 3, |
79 "input_connections": {}, | |
80 "inputs": [ | |
81 { | |
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82 "description": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)", |
0 | 83 "name": "VCF file of additional known variants " |
84 } | |
85 ], | |
86 "name": "Input dataset", | |
87 "outputs": [], | |
88 "position": { | |
89 "left": 4388, | |
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90 "top": 549 |
0 | 91 }, |
92 "tool_errors": null, | |
93 "tool_id": null, | |
94 "tool_state": "{\"name\": \"VCF file of additional known variants \"}", | |
95 "tool_version": null, | |
96 "type": "data_input", | |
97 "user_outputs": [] | |
98 }, | |
99 "4": { | |
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100 "annotation": "Convert quality scores to sanger scale", |
0 | 101 "id": 4, |
102 "input_connections": { | |
103 "input_file": { | |
104 "id": 0, | |
105 "output_name": "output" | |
106 } | |
107 }, | |
108 "inputs": [ | |
109 { | |
110 "description": "runtime parameter for tool FASTQ Groomer", | |
111 "name": "input_type" | |
112 } | |
113 ], | |
114 "name": "FASTQ Groomer", | |
115 "outputs": [ | |
116 { | |
117 "name": "output_file", | |
118 "type": "fastqsanger" | |
119 } | |
120 ], | |
121 "position": { | |
122 "left": 510, | |
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123 "top": 264 |
0 | 124 }, |
125 "post_job_actions": {}, | |
126 "tool_errors": null, | |
127 "tool_id": "fastq_groomer", | |
128 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", | |
129 "tool_version": "1.0.4", | |
130 "type": "tool", | |
131 "user_outputs": [] | |
132 }, | |
133 "5": { | |
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134 "annotation": "Convert quality scores to sanger scale", |
0 | 135 "id": 5, |
136 "input_connections": { | |
137 "input_file": { | |
138 "id": 1, | |
139 "output_name": "output" | |
140 } | |
141 }, | |
142 "inputs": [ | |
143 { | |
144 "description": "runtime parameter for tool FASTQ Groomer", | |
145 "name": "input_type" | |
146 } | |
147 ], | |
148 "name": "FASTQ Groomer", | |
149 "outputs": [ | |
150 { | |
151 "name": "output_file", | |
152 "type": "fastqsanger" | |
153 } | |
154 ], | |
155 "position": { | |
156 "left": 505, | |
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157 "top": 404 |
0 | 158 }, |
159 "post_job_actions": {}, | |
160 "tool_errors": null, | |
161 "tool_id": "fastq_groomer", | |
162 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", | |
163 "tool_version": "1.0.4", | |
164 "type": "tool", | |
165 "user_outputs": [] | |
166 }, | |
167 "6": { | |
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168 "annotation": "Map paired reads to reference genome", |
0 | 169 "id": 6, |
170 "input_connections": { | |
171 "input1": { | |
172 "id": 4, | |
173 "output_name": "output_file" | |
174 }, | |
175 "singlePaired|input2": { | |
176 "id": 5, | |
177 "output_name": "output_file" | |
178 } | |
179 }, | |
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180 "inputs": [], |
0 | 181 "name": "Tophat for Illumina", |
182 "outputs": [ | |
183 { | |
184 "name": "insertions", | |
185 "type": "bed" | |
186 }, | |
187 { | |
188 "name": "deletions", | |
189 "type": "bed" | |
190 }, | |
191 { | |
192 "name": "junctions", | |
193 "type": "bed" | |
194 }, | |
195 { | |
196 "name": "accepted_hits", | |
197 "type": "bam" | |
198 } | |
199 ], | |
200 "position": { | |
201 "left": 884, | |
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202 "top": 305 |
0 | 203 }, |
204 "post_job_actions": { | |
205 "HideDatasetActiondeletions": { | |
206 "action_arguments": {}, | |
207 "action_type": "HideDatasetAction", | |
208 "output_name": "deletions" | |
209 }, | |
210 "HideDatasetActioninsertions": { | |
211 "action_arguments": {}, | |
212 "action_type": "HideDatasetAction", | |
213 "output_name": "insertions" | |
214 }, | |
215 "HideDatasetActionjunctions": { | |
216 "action_arguments": {}, | |
217 "action_type": "HideDatasetAction", | |
218 "output_name": "junctions" | |
219 } | |
220 }, | |
221 "tool_errors": null, | |
222 "tool_id": "tophat", | |
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223 "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"80\\\"}\"}", |
0 | 224 "tool_version": "1.5.0", |
225 "type": "tool", | |
226 "user_outputs": [] | |
227 }, | |
228 "7": { | |
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229 "annotation": "Keep only mappings with MAPQ of 255", |
0 | 230 "id": 7, |
231 "input_connections": { | |
232 "input1": { | |
233 "id": 6, | |
234 "output_name": "accepted_hits" | |
235 } | |
236 }, | |
237 "inputs": [], | |
238 "name": "Filter SAM or BAM", | |
239 "outputs": [ | |
240 { | |
241 "name": "output1", | |
242 "type": "sam" | |
243 } | |
244 ], | |
245 "position": { | |
246 "left": 1154, | |
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247 "top": 339 |
0 | 248 }, |
249 "post_job_actions": { | |
250 "HideDatasetActionoutput1": { | |
251 "action_arguments": {}, | |
252 "action_type": "HideDatasetAction", | |
253 "output_name": "output1" | |
254 } | |
255 }, | |
256 "tool_errors": null, | |
257 "tool_id": "samtools_filter", | |
258 "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}", | |
259 "tool_version": "1.1.0", | |
260 "type": "tool", | |
261 "user_outputs": [] | |
262 }, | |
263 "8": { | |
264 "annotation": "", | |
265 "id": 8, | |
266 "input_connections": { | |
267 "input1": { | |
268 "id": 7, | |
269 "output_name": "output1" | |
270 } | |
271 }, | |
272 "inputs": [], | |
273 "name": "flagstat", | |
274 "outputs": [ | |
275 { | |
276 "name": "output1", | |
277 "type": "txt" | |
278 } | |
279 ], | |
280 "position": { | |
281 "left": 1505, | |
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282 "top": 296 |
0 | 283 }, |
284 "post_job_actions": {}, | |
285 "tool_errors": null, | |
286 "tool_id": "samtools_flagstat", | |
287 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", | |
288 "tool_version": "1.0.0", | |
289 "type": "tool", | |
290 "user_outputs": [] | |
291 }, | |
292 "9": { | |
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293 "annotation": "Add Read Group info required by GATK tools", |
0 | 294 "id": 9, |
295 "input_connections": { | |
296 "inputFile": { | |
297 "id": 7, | |
298 "output_name": "output1" | |
299 } | |
300 }, | |
301 "inputs": [], | |
302 "name": "Add or Replace Groups", | |
303 "outputs": [ | |
304 { | |
305 "name": "outFile", | |
306 "type": "bam" | |
307 } | |
308 ], | |
309 "position": { | |
310 "left": 1506, | |
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311 "top": 476 |
0 | 312 }, |
313 "post_job_actions": {}, | |
314 "tool_errors": null, | |
315 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", | |
316 "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", | |
317 "tool_version": "1.56.0", | |
318 "type": "tool", | |
319 "user_outputs": [] | |
320 }, | |
321 "10": { | |
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322 "annotation": "Synchronize paired reads", |
0 | 323 "id": 10, |
324 "input_connections": { | |
325 "input_file": { | |
326 "id": 9, | |
327 "output_name": "outFile" | |
328 } | |
329 }, | |
330 "inputs": [], | |
331 "name": "Paired Read Mate Fixer", | |
332 "outputs": [ | |
333 { | |
334 "name": "out_file", | |
335 "type": "bam" | |
336 } | |
337 ], | |
338 "position": { | |
339 "left": 1841, | |
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340 "top": 348 |
0 | 341 }, |
342 "post_job_actions": { | |
343 "HideDatasetActionout_file": { | |
344 "action_arguments": {}, | |
345 "action_type": "HideDatasetAction", | |
346 "output_name": "out_file" | |
347 } | |
348 }, | |
349 "tool_errors": null, | |
350 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", | |
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352 "tool_version": "1.56.0", | |
353 "type": "tool", | |
354 "user_outputs": [] | |
355 }, | |
356 "11": { | |
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357 "annotation": "Remove duplicate reads", |
0 | 358 "id": 11, |
359 "input_connections": { | |
360 "input_file": { | |
361 "id": 10, | |
362 "output_name": "out_file" | |
363 } | |
364 }, | |
365 "inputs": [], | |
366 "name": "Mark Duplicate reads", | |
367 "outputs": [ | |
368 { | |
369 "name": "out_file", | |
370 "type": "bam" | |
371 }, | |
372 { | |
373 "name": "html_file", | |
374 "type": "html" | |
375 } | |
376 ], | |
377 "position": { | |
378 "left": 2086, | |
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379 "top": 333 |
0 | 380 }, |
381 "post_job_actions": {}, | |
382 "tool_errors": null, | |
383 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", | |
384 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", | |
385 "tool_version": "1.56.0", | |
386 "type": "tool", | |
387 "user_outputs": [] | |
388 }, | |
389 "12": { | |
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390 "annotation": "Reorder BAM for GATK tools", |
0 | 391 "id": 12, |
392 "input_connections": { | |
393 "inputFile": { | |
394 "id": 11, | |
395 "output_name": "out_file" | |
396 } | |
397 }, | |
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398 "inputs": [], |
0 | 399 "name": "Reorder SAM/BAM", |
400 "outputs": [ | |
401 { | |
402 "name": "outFile", | |
403 "type": "bam" | |
404 } | |
405 ], | |
406 "position": { | |
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407 "left": 2401, |
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408 "top": 305 |
0 | 409 }, |
410 "post_job_actions": {}, | |
411 "tool_errors": null, | |
412 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0", | |
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413 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", |
0 | 414 "tool_version": "1.56.0", |
415 "type": "tool", | |
416 "user_outputs": [] | |
417 }, | |
418 "13": { | |
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419 "annotation": "", |
0 | 420 "id": 13, |
421 "input_connections": { | |
422 "reference_source|input_bam": { | |
423 "id": 12, | |
424 "output_name": "outFile" | |
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425 }, |
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426 "rod_bind_0|rod_bind_type|input_rod": { |
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427 "id": 2, |
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428 "output_name": "output" |
0 | 429 } |
430 }, | |
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431 "inputs": [], |
0 | 432 "name": "Realigner Target Creator", |
433 "outputs": [ | |
434 { | |
435 "name": "output_interval", | |
436 "type": "gatk_interval" | |
437 }, | |
438 { | |
439 "name": "output_log", | |
440 "type": "txt" | |
441 } | |
442 ], | |
443 "position": { | |
444 "left": 2565, | |
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445 "top": 491 |
0 | 446 }, |
447 "post_job_actions": { | |
448 "HideDatasetActionoutput_log": { | |
449 "action_arguments": {}, | |
450 "action_type": "HideDatasetAction", | |
451 "output_name": "output_log" | |
452 } | |
453 }, | |
454 "tool_errors": null, | |
455 "tool_id": "gatk_realigner_target_creator", | |
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456 "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", |
0 | 457 "tool_version": "0.0.4", |
458 "type": "tool", | |
459 "user_outputs": [] | |
460 }, | |
461 "14": { | |
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462 "annotation": "Perform local realignments for indels", |
0 | 463 "id": 14, |
464 "input_connections": { | |
465 "reference_source|input_bam": { | |
466 "id": 12, | |
467 "output_name": "outFile" | |
468 }, | |
469 "target_intervals": { | |
470 "id": 13, | |
471 "output_name": "output_interval" | |
472 } | |
473 }, | |
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474 "inputs": [], |
0 | 475 "name": "Indel Realigner", |
476 "outputs": [ | |
477 { | |
478 "name": "output_bam", | |
479 "type": "bam" | |
480 }, | |
481 { | |
482 "name": "output_log", | |
483 "type": "txt" | |
484 } | |
485 ], | |
486 "position": { | |
487 "left": 2811, | |
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488 "top": 324 |
0 | 489 }, |
490 "post_job_actions": { | |
491 "HideDatasetActionoutput_log": { | |
492 "action_arguments": {}, | |
493 "action_type": "HideDatasetAction", | |
494 "output_name": "output_log" | |
495 } | |
496 }, | |
497 "tool_errors": null, | |
498 "tool_id": "gatk_indel_realigner", | |
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499 "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", |
0 | 500 "tool_version": "0.0.6", |
501 "type": "tool", | |
502 "user_outputs": [] | |
503 }, | |
504 "15": { | |
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505 "annotation": "Check again for duplicate reads and eliminate", |
0 | 506 "id": 15, |
507 "input_connections": { | |
508 "input_file": { | |
509 "id": 14, | |
510 "output_name": "output_bam" | |
511 } | |
512 }, | |
513 "inputs": [], | |
514 "name": "Mark Duplicate reads", | |
515 "outputs": [ | |
516 { | |
517 "name": "out_file", | |
518 "type": "bam" | |
519 }, | |
520 { | |
521 "name": "html_file", | |
522 "type": "html" | |
523 } | |
524 ], | |
525 "position": { | |
526 "left": 3174, | |
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527 "top": 291 |
0 | 528 }, |
529 "post_job_actions": { | |
530 "HideDatasetActionhtml_file": { | |
531 "action_arguments": {}, | |
532 "action_type": "HideDatasetAction", | |
533 "output_name": "html_file" | |
534 }, | |
535 "HideDatasetActionout_file": { | |
536 "action_arguments": {}, | |
537 "action_type": "HideDatasetAction", | |
538 "output_name": "out_file" | |
539 } | |
540 }, | |
541 "tool_errors": null, | |
542 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", | |
543 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", | |
544 "tool_version": "1.56.0", | |
545 "type": "tool", | |
546 "user_outputs": [] | |
547 }, | |
548 "16": { | |
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549 "annotation": "Determine base calls at each position", |
0 | 550 "id": 16, |
551 "input_connections": { | |
552 "reference_source|input_bams_0|input_bam": { | |
553 "id": 15, | |
554 "output_name": "out_file" | |
555 } | |
556 }, | |
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557 "inputs": [], |
0 | 558 "name": "MPileup", |
559 "outputs": [ | |
560 { | |
561 "name": "output_mpileup", | |
562 "type": "pileup" | |
563 }, | |
564 { | |
565 "name": "output_log", | |
566 "type": "txt" | |
567 } | |
568 ], | |
569 "position": { | |
570 "left": 3554, | |
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571 "top": 265 |
0 | 572 }, |
573 "post_job_actions": { | |
574 "HideDatasetActionoutput_log": { | |
575 "action_arguments": {}, | |
576 "action_type": "HideDatasetAction", | |
577 "output_name": "output_log" | |
578 }, | |
579 "HideDatasetActionoutput_mpileup": { | |
580 "action_arguments": {}, | |
581 "action_type": "HideDatasetAction", | |
582 "output_name": "output_mpileup" | |
583 } | |
584 }, | |
585 "tool_errors": null, | |
586 "tool_id": "samtools_mpileup", | |
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587 "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", |
0 | 588 "tool_version": "0.0.1", |
589 "type": "tool", | |
590 "user_outputs": [] | |
591 }, | |
592 "17": { | |
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593 "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nLeave VCF_ID blank for tumor sample", |
0 | 594 "id": 17, |
595 "input_connections": { | |
596 "input_file": { | |
597 "id": 16, | |
598 "output_name": "output_mpileup" | |
599 } | |
600 }, | |
601 "inputs": [ | |
602 { | |
603 "description": "runtime parameter for tool Pileup to VCF", | |
604 "name": "min_base_qual" | |
605 } | |
606 ], | |
607 "name": "Pileup to VCF", | |
608 "outputs": [ | |
609 { | |
610 "name": "output_file", | |
611 "type": "vcf" | |
612 } | |
613 ], | |
614 "position": { | |
615 "left": 4029, | |
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616 "top": 296 |
0 | 617 }, |
618 "post_job_actions": {}, | |
619 "tool_errors": null, | |
620 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0", | |
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621 "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", |
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622 "tool_version": "2.2", |
0 | 623 "type": "tool", |
624 "user_outputs": [] | |
625 }, | |
626 "18": { | |
627 "annotation": "Annotate the ID field with dbSNP IDs.", | |
628 "id": 18, | |
629 "input_connections": { | |
630 "dbSnp": { | |
631 "id": 2, | |
632 "output_name": "output" | |
633 }, | |
634 "input": { | |
635 "id": 17, | |
636 "output_name": "output_file" | |
637 } | |
638 }, | |
639 "inputs": [], | |
640 "name": "SnpSift Annotate", | |
641 "outputs": [ | |
642 { | |
643 "name": "output", | |
644 "type": "vcf" | |
645 } | |
646 ], | |
647 "position": { | |
648 "left": 4421, | |
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649 "top": 285 |
0 | 650 }, |
651 "post_job_actions": { | |
652 "HideDatasetActionoutput": { | |
653 "action_arguments": {}, | |
654 "action_type": "HideDatasetAction", | |
655 "output_name": "output" | |
656 } | |
657 }, | |
658 "tool_errors": null, | |
659 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.1", | |
660 "tool_state": "{\"input\": \"null\", \"dbSnp\": \"null\", \"__page__\": 0}", | |
661 "tool_version": "3.1", | |
662 "type": "tool", | |
663 "user_outputs": [] | |
664 }, | |
665 "19": { | |
666 "annotation": "Annotate the ID field with users known variant IDs.", | |
667 "id": 19, | |
668 "input_connections": { | |
669 "dbSnp": { | |
670 "id": 3, | |
671 "output_name": "output" | |
672 }, | |
673 "input": { | |
674 "id": 18, | |
675 "output_name": "output" | |
676 } | |
677 }, | |
678 "inputs": [], | |
679 "name": "SnpSift Annotate", | |
680 "outputs": [ | |
681 { | |
682 "name": "output", | |
683 "type": "vcf" | |
684 } | |
685 ], | |
686 "position": { | |
687 "left": 4724, | |
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688 "top": 433 |
0 | 689 }, |
690 "post_job_actions": { | |
691 "HideDatasetActionoutput": { | |
692 "action_arguments": {}, | |
693 "action_type": "HideDatasetAction", | |
694 "output_name": "output" | |
695 } | |
696 }, | |
697 "tool_errors": null, | |
698 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.1", | |
699 "tool_state": "{\"input\": \"null\", \"dbSnp\": \"null\", \"__page__\": 0}", | |
700 "tool_version": "3.1", | |
701 "type": "tool", | |
702 "user_outputs": [] | |
703 }, | |
704 "20": { | |
705 "annotation": "Filter out chrM variations and any variant with an annotated ID", | |
706 "id": 20, | |
707 "input_connections": { | |
708 "input": { | |
709 "id": 19, | |
710 "output_name": "output" | |
711 } | |
712 }, | |
713 "inputs": [], | |
714 "name": "SnpSift Filter", | |
715 "outputs": [ | |
716 { | |
717 "name": "output", | |
718 "type": "vcf" | |
719 } | |
720 ], | |
721 "position": { | |
722 "left": 5043, | |
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723 "top": 483 |
0 | 724 }, |
725 "post_job_actions": {}, | |
726 "tool_errors": null, | |
727 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.1", | |
728 "tool_state": "{\"__page__\": 0, \"expr\": \"\\\"(CHROM !~ 'chrM') & (ID = '')\\\"\", \"input\": \"null\"}", | |
729 "tool_version": "3.1", | |
730 "type": "tool", | |
731 "user_outputs": [] | |
732 }, | |
733 "21": { | |
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734 "annotation": "Use Genome from Ensembl, e.g GRCh37.68 so we get ensembl transcript name info", |
0 | 735 "id": 21, |
736 "input_connections": { | |
737 "input": { | |
738 "id": 20, | |
739 "output_name": "output" | |
740 } | |
741 }, | |
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742 "inputs": [], |
0 | 743 "name": "SnpEff", |
744 "outputs": [ | |
745 { | |
746 "name": "output", | |
747 "type": "tabular" | |
748 }, | |
749 { | |
750 "name": "statsFile", | |
751 "type": "html" | |
752 } | |
753 ], | |
754 "position": { | |
755 "left": 5277, | |
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756 "top": 442 |
0 | 757 }, |
758 "post_job_actions": { | |
759 "HideDatasetActionstatsFile": { | |
760 "action_arguments": {}, | |
761 "action_type": "HideDatasetAction", | |
762 "output_name": "statsFile" | |
763 } | |
764 }, | |
765 "tool_errors": null, | |
766 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.1", | |
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767 "tool_state": "{\"filterHomHet\": \"\\\"\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"filterOut\": \"[\\\"downstream\\\", \\\"intergenic\\\", \\\"intron\\\", \\\"upstream\\\", \\\"utr\\\"]\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"\\\"\", \"__page__\": 0, \"udLength\": \"\\\"0\\\"\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"offset\": \"\\\"\\\"\", \"input\": \"null\"}", |
0 | 768 "tool_version": "3.1", |
769 "type": "tool", | |
770 "user_outputs": [] | |
771 }, | |
772 "22": { | |
773 "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants", | |
774 "id": 22, | |
775 "input_connections": { | |
776 "input": { | |
777 "id": 21, | |
778 "output_name": "output" | |
779 } | |
780 }, | |
781 "inputs": [], | |
782 "name": "SnpSift Filter", | |
783 "outputs": [ | |
784 { | |
785 "name": "output", | |
786 "type": "vcf" | |
787 } | |
788 ], | |
789 "position": { | |
790 "left": 5595, | |
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791 "top": 405 |
0 | 792 }, |
793 "post_job_actions": {}, | |
794 "tool_errors": null, | |
795 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.1", | |
796 "tool_state": "{\"__page__\": 0, \"expr\": \"\\\"( EFF[*].EFFECT = 'FRAME_SHIFT' )\\\"\", \"input\": \"null\"}", | |
797 "tool_version": "3.1", | |
798 "type": "tool", | |
799 "user_outputs": [] | |
800 }, | |
801 "23": { | |
802 "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING \nvariants", | |
803 "id": 23, | |
804 "input_connections": { | |
805 "input": { | |
806 "id": 21, | |
3 | 807 "output_name": "output" |
0 | 808 } |
809 }, | |
810 "inputs": [], | |
811 "name": "SnpSift Filter", | |
812 "outputs": [ | |
813 { | |
814 "name": "output", | |
815 "type": "vcf" | |
816 } | |
817 ], | |
818 "position": { | |
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819 "left": 5600, |
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820 "top": 584 |
0 | 821 }, |
822 "post_job_actions": {}, | |
823 "tool_errors": null, | |
824 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.1", | |
825 "tool_state": "{\"__page__\": 0, \"expr\": \"\\\"( EFF[*].EFFECT = 'NON_SYNONYMOUS_CODING')\\\"\", \"input\": \"null\"}", | |
826 "tool_version": "3.1", | |
827 "type": "tool", | |
828 "user_outputs": [] | |
829 }, | |
830 "24": { | |
831 "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", | |
832 "id": 24, | |
833 "input_connections": { | |
834 "snp_effect_vcf": { | |
835 "id": 22, | |
836 "output_name": "output" | |
837 } | |
838 }, | |
839 "inputs": [], | |
840 "name": "SnpEff Ensembl CDS", | |
841 "outputs": [ | |
842 { | |
843 "name": "html_report", | |
844 "type": "html" | |
845 }, | |
846 { | |
847 "name": "tsv_report", | |
848 "type": "tabular" | |
849 }, | |
850 { | |
851 "name": "text_report", | |
852 "type": "text" | |
853 } | |
854 ], | |
855 "position": { | |
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856 "left": 5810, |
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857 "top": 364 |
0 | 858 }, |
859 "post_job_actions": { | |
860 "HideDatasetActionhtml_report": { | |
861 "action_arguments": {}, | |
862 "action_type": "HideDatasetAction", | |
863 "output_name": "html_report" | |
864 }, | |
865 "HideDatasetActiontext_report": { | |
866 "action_arguments": {}, | |
867 "action_type": "HideDatasetAction", | |
868 "output_name": "text_report" | |
869 }, | |
870 "HideDatasetActiontsv_report": { | |
871 "action_arguments": {}, | |
872 "action_type": "HideDatasetAction", | |
873 "output_name": "tsv_report" | |
874 } | |
875 }, | |
876 "tool_errors": null, | |
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Jim Johnson <jj@umn.edu>
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877 "tool_id": "SnpEff-cds-report", |
0 | 878 "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", |
879 "tool_version": "1.0", | |
880 "type": "tool", | |
881 "user_outputs": [] | |
882 }, | |
883 "25": { | |
884 "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence", | |
885 "id": 25, | |
886 "input_connections": { | |
887 "snp_effect_vcf": { | |
888 "id": 23, | |
889 "output_name": "output" | |
890 } | |
891 }, | |
892 "inputs": [], | |
893 "name": "SnpEff Ensembl CDS", | |
894 "outputs": [ | |
895 { | |
896 "name": "html_report", | |
897 "type": "html" | |
898 }, | |
899 { | |
900 "name": "tsv_report", | |
901 "type": "tabular" | |
902 }, | |
903 { | |
904 "name": "text_report", | |
905 "type": "text" | |
906 } | |
907 ], | |
908 "position": { | |
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Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
|
909 "left": 5820, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
910 "top": 537 |
0 | 911 }, |
912 "post_job_actions": { | |
913 "HideDatasetActionhtml_report": { | |
914 "action_arguments": {}, | |
915 "action_type": "HideDatasetAction", | |
916 "output_name": "html_report" | |
917 }, | |
918 "HideDatasetActiontext_report": { | |
919 "action_arguments": {}, | |
920 "action_type": "HideDatasetAction", | |
921 "output_name": "text_report" | |
922 }, | |
923 "HideDatasetActiontsv_report": { | |
924 "action_arguments": {}, | |
925 "action_type": "HideDatasetAction", | |
926 "output_name": "tsv_report" | |
927 } | |
928 }, | |
929 "tool_errors": null, | |
2
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
930 "tool_id": "SnpEff-cds-report", |
0 | 931 "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"all_effects\": \"\\\"False\\\"\", \"polya\": \"\\\"5\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}", |
932 "tool_version": "1.0", | |
933 "type": "tool", | |
934 "user_outputs": [] | |
935 } | |
936 } | |
2
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
937 } |