Mercurial > repos > jjohnson > mmuff

comparison Galaxy-Workflow-MMuFF_v1.2.ga @ 6:2aa99b7f90f4 draft default tip

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Deleted selected files
author jjohnson
date Thu, 30 May 2013 11:27:21 -0400
parents 60a6f2d92058
children
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5:60a6f2d92058 6:2aa99b7f90f4
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "MMuFF_Human_v1.2",
6 "steps": {
7 "0": {
8 "annotation": "Human RNA-seq paired reads left mates",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "Human RNA-seq paired reads left mates",
14 "name": "Forward reads fastq"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 240,
21 "top": 314
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": {
31 "annotation": "Human RNA-seq paired reads right mates",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "Human RNA-seq paired reads right mates",
37 "name": "Reverse reads fastq"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 249,
44 "top": 410
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": {
54 "annotation": "Known SNPs - dbSNP.vcf",
55 "id": 2,
56 "input_connections": {},
57 "inputs": [
58 {
59 "description": "Known SNPs - dbSNP.vcf",
60 "name": "VCF file of known variants (dbSNP)"
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
65 "position": {
66 "left": 2327,
67 "top": 785
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": {
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)",
78 "id": 3,
79 "input_connections": {},
80 "inputs": [
81 {
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)",
83 "name": "VCF file of additional known variants "
84 }
85 ],
86 "name": "Input dataset",
87 "outputs": [],
88 "position": {
89 "left": 4388,
90 "top": 576
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": {
100 "annotation": "Convert quality scores to sanger scale",
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,
123 "top": 291
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": {
134 "annotation": "Convert quality scores to sanger scale",
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,
157 "top": 431
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": {
168 "annotation": "Map paired reads to reference genome",
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 },
180 "inputs": [],
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,
202 "top": 332
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",
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\\\"}\"}",
224 "tool_version": "1.5.0",
225 "type": "tool",
226 "user_outputs": []
227 },
228 "7": {
229 "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)",
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,
247 "top": 366
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,
282 "top": 323
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": {
293 "annotation": "Add Read Group info required by GATK tools",
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,
311 "top": 503
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": {
322 "annotation": "Synchronize paired reads",
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,
340 "top": 375
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",
351 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}",
352 "tool_version": "1.56.0",
353 "type": "tool",
354 "user_outputs": []
355 },
356 "11": {
357 "annotation": "Remove duplicate reads",
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,
379 "top": 360
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": {
390 "annotation": "Reorder BAM for GATK tools",
391 "id": 12,
392 "input_connections": {
393 "inputFile": {
394 "id": 11,
395 "output_name": "out_file"
396 }
397 },
398 "inputs": [],
399 "name": "Reorder SAM/BAM",
400 "outputs": [
401 {
402 "name": "outFile",
403 "type": "bam"
404 }
405 ],
406 "position": {
407 "left": 2401,
408 "top": 332
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",
413 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}",
414 "tool_version": "1.56.0",
415 "type": "tool",
416 "user_outputs": []
417 },
418 "13": {
419 "annotation": "",
420 "id": 13,
421 "input_connections": {
422 "reference_source|input_bam": {
423 "id": 12,
424 "output_name": "outFile"
425 },
426 "rod_bind_0|rod_bind_type|input_rod": {
427 "id": 2,
428 "output_name": "output"
429 }
430 },
431 "inputs": [],
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,
445 "top": 518
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",
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}}]\"}",
457 "tool_version": "0.0.4",
458 "type": "tool",
459 "user_outputs": []
460 },
461 "14": {
462 "annotation": "Perform local realignments for indels",
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 },
474 "inputs": [],
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": {
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488 "top": 351
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",
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\": \"[]\"}",
500 "tool_version": "0.0.6",
501 "type": "tool",
502 "user_outputs": []
503 },
504 "15": {
505 "annotation": "Check again for duplicate reads and eliminate",
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,
527 "top": 318
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": {
549 "annotation": "Determine base calls at each position",
550 "id": 16,
551 "input_connections": {
552 "reference_source|input_bams_0|input_bam": {
553 "id": 15,
554 "output_name": "out_file"
555 }
556 },
557 "inputs": [],
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,
571 "top": 292
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",
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}\"}",
588 "tool_version": "0.0.1",
589 "type": "tool",
590 "user_outputs": []
591 },
592 "17": {
593 "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nLeave VCF_ID blank for tumor sample",
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