Mercurial > repos > jjohnson > mmuff

comparison Galaxy-Workflow-MMuFF_Human_germline_v1.2.ga @ 2:04e170c09922

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add a workflow for noraml tissue samples.
author Jim Johnson <jj@umn.edu>
date Fri, 12 Apr 2013 07:51:45 -0500
parents
children
comparison
equal deleted inserted replaced
1:6e49aa2461bd 2:04e170c09922
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "MMuFF_Human_germline_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": 287
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": 383
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": 758
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": "Convert quality scores to sanger scale",
78 "id": 3,
79 "input_connections": {
80 "input_file": {
81 "id": 0,
82 "output_name": "output"
83 }
84 },
85 "inputs": [
86 {
87 "description": "runtime parameter for tool FASTQ Groomer",
88 "name": "input_type"
89 }
90 ],
91 "name": "FASTQ Groomer",
92 "outputs": [
93 {
94 "name": "output_file",
95 "type": "fastqsanger"
96 }
97 ],
98 "position": {
99 "left": 510,
100 "top": 264
101 },
102 "post_job_actions": {},
103 "tool_errors": null,
104 "tool_id": "fastq_groomer",
105 "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\"}",
106 "tool_version": "1.0.4",
107 "type": "tool",
108 "user_outputs": []
109 },
110 "4": {
111 "annotation": "Convert quality scores to sanger scale",
112 "id": 4,
113 "input_connections": {
114 "input_file": {
115 "id": 1,
116 "output_name": "output"
117 }
118 },
119 "inputs": [
120 {
121 "description": "runtime parameter for tool FASTQ Groomer",
122 "name": "input_type"
123 }
124 ],
125 "name": "FASTQ Groomer",
126 "outputs": [
127 {
128 "name": "output_file",
129 "type": "fastqsanger"
130 }
131 ],
132 "position": {
133 "left": 505,
134 "top": 404
135 },
136 "post_job_actions": {},
137 "tool_errors": null,
138 "tool_id": "fastq_groomer",
139 "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\"}",
140 "tool_version": "1.0.4",
141 "type": "tool",
142 "user_outputs": []
143 },
144 "5": {
145 "annotation": "Map paired reads to reference genome",
146 "id": 5,
147 "input_connections": {
148 "input1": {
149 "id": 3,
150 "output_name": "output_file"
151 },
152 "singlePaired|input2": {
153 "id": 4,
154 "output_name": "output_file"
155 }
156 },
157 "inputs": [],
158 "name": "Tophat for Illumina",
159 "outputs": [
160 {
161 "name": "insertions",
162 "type": "bed"
163 },
164 {
165 "name": "deletions",
166 "type": "bed"
167 },
168 {
169 "name": "junctions",
170 "type": "bed"
171 },
172 {
173 "name": "accepted_hits",
174 "type": "bam"
175 }
176 ],
177 "position": {
178 "left": 884,
179 "top": 305
180 },
181 "post_job_actions": {
182 "HideDatasetActiondeletions": {
183 "action_arguments": {},
184 "action_type": "HideDatasetAction",
185 "output_name": "deletions"
186 },
187 "HideDatasetActioninsertions": {
188 "action_arguments": {},
189 "action_type": "HideDatasetAction",
190 "output_name": "insertions"
191 },
192 "HideDatasetActionjunctions": {
193 "action_arguments": {},
194 "action_type": "HideDatasetAction",
195 "output_name": "junctions"
196 }
197 },
198 "tool_errors": null,
199 "tool_id": "tophat",
200 "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\\\"}\"}",
201 "tool_version": "1.5.0",
202 "type": "tool",
203 "user_outputs": []
204 },
205 "6": {
206 "annotation": "Keep only mappings with MAPQ of 255",
207 "id": 6,
208 "input_connections": {
209 "input1": {
210 "id": 5,
211 "output_name": "accepted_hits"
212 }
213 },
214 "inputs": [],
215 "name": "Filter SAM or BAM",
216 "outputs": [
217 {
218 "name": "output1",
219 "type": "sam"
220 }
221 ],
222 "position": {
223 "left": 1154,
224 "top": 339
225 },
226 "post_job_actions": {
227 "HideDatasetActionoutput1": {
228 "action_arguments": {},
229 "action_type": "HideDatasetAction",
230 "output_name": "output1"
231 }
232 },
233 "tool_errors": null,
234 "tool_id": "samtools_filter",
235 "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}",
236 "tool_version": "1.1.0",
237 "type": "tool",
238 "user_outputs": []
239 },
240 "7": {
241 "annotation": "",
242 "id": 7,
243 "input_connections": {
244 "input1": {
245 "id": 6,
246 "output_name": "output1"
247 }
248 },
249 "inputs": [],
250 "name": "flagstat",
251 "outputs": [
252 {
253 "name": "output1",
254 "type": "txt"
255 }
256 ],
257 "position": {
258 "left": 1505,
259 "top": 296
260 },
261 "post_job_actions": {},
262 "tool_errors": null,
263 "tool_id": "samtools_flagstat",
264 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}",
265 "tool_version": "1.0.0",
266 "type": "tool",
267 "user_outputs": []
268 },
269 "8": {
270 "annotation": "Add Read Group info required by GATK tools",
271 "id": 8,
272 "input_connections": {
273 "inputFile": {
274 "id": 6,
275 "output_name": "output1"
276 }
277 },
278 "inputs": [],
279 "name": "Add or Replace Groups",
280 "outputs": [
281 {
282 "name": "outFile",
283 "type": "bam"
284 }
285 ],
286 "position": {
287 "left": 1506,
288 "top": 476
289 },
290 "post_job_actions": {},
291 "tool_errors": null,
292 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0",
293 "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\"}",
294 "tool_version": "1.56.0",
295 "type": "tool",
296 "user_outputs": []
297 },
298 "9": {
299 "annotation": "Synchronize paired reads",
300 "id": 9,
301 "input_connections": {
302 "input_file": {
303 "id": 8,
304 "output_name": "outFile"
305 }
306 },
307 "inputs": [],
308 "name": "Paired Read Mate Fixer",
309 "outputs": [
310 {
311 "name": "out_file",
312 "type": "bam"
313 }
314 ],
315 "position": {
316 "left": 1841,
317 "top": 348
318 },
319 "post_job_actions": {
320 "HideDatasetActionout_file": {
321 "action_arguments": {},
322 "action_type": "HideDatasetAction",
323 "output_name": "out_file"
324 }
325 },
326 "tool_errors": null,
327 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0",
328 "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\\\"\"}",
329 "tool_version": "1.56.0",
330 "type": "tool",
331 "user_outputs": []
332 },
333 "10": {
334 "annotation": "Remove duplicate reads",
335 "id": 10,
336 "input_connections": {
337 "input_file": {
338 "id": 9,
339 "output_name": "out_file"
340 }
341 },
342 "inputs": [],
343 "name": "Mark Duplicate reads",
344 "outputs": [
345 {
346 "name": "out_file",
347 "type": "bam"
348 },
349 {
350 "name": "html_file",
351 "type": "html"
352 }
353 ],
354 "position": {
355 "left": 2086,
356 "top": 333
357 },
358 "post_job_actions": {},
359 "tool_errors": null,
360 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
361 "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\\\"\"}",
362 "tool_version": "1.56.0",
363 "type": "tool",
364 "user_outputs": []
365 },
366 "11": {
367 "annotation": "Reorder BAM for GATK tools",
368 "id": 11,
369 "input_connections": {
370 "inputFile": {
371 "id": 10,
372 "output_name": "out_file"
373 }
374 },
375 "inputs": [],
376 "name": "Reorder SAM/BAM",
377 "outputs": [
378 {
379 "name": "outFile",
380 "type": "bam"
381 }
382 ],
383 "position": {
384 "left": 2401,
385 "top": 305
386 },
387 "post_job_actions": {},
388 "tool_errors": null,
389 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0",
390 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}",
391 "tool_version": "1.56.0",
392 "type": "tool",
393 "user_outputs": []
394 },
395 "12": {
396 "annotation": "",
397 "id": 12,
398 "input_connections": {
399 "reference_source|input_bam": {
400 "id": 11,
401 "output_name": "outFile"
402 },
403 "rod_bind_0|rod_bind_type|input_rod": {
404 "id": 2,
405 "output_name": "output"
406 }
407 },
408 "inputs": [],
409 "name": "Realigner Target Creator",
410 "outputs": [
411 {
412 "name": "output_interval",
413 "type": "gatk_interval"
414 },
415 {
416 "name": "output_log",
417 "type": "txt"
418 }
419 ],
420 "position": {
421 "left": 2565,
422 "top": 491
423 },
424 "post_job_actions": {
425 "HideDatasetActionoutput_log": {
426 "action_arguments": {},
427 "action_type": "HideDatasetAction",
428 "output_name": "output_log"
429 }
430 },
431 "tool_errors": null,
432 "tool_id": "gatk_realigner_target_creator",
433 "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}}]\"}",
434 "tool_version": "0.0.4",
435 "type": "tool",
436 "user_outputs": []
437 },
438 "13": {
439 "annotation": "Perform local realignments for indels",
440 "id": 13,
441 "input_connections": {
442 "reference_source|input_bam": {
443 "id": 11,
444 "output_name": "outFile"
445 },
446 "target_intervals": {
447 "id": 12,
448 "output_name": "output_interval"
449 }
450 },
451 "inputs": [],
452 "name": "Indel Realigner",
453 "outputs": [
454 {
455 "name": "output_bam",
456 "type": "bam"
457 },
458 {
459 "name": "output_log",
460 "type": "txt"
461 }
462 ],
463 "position": {
464 "left": 2811,
465 "top": 324
466 },
467 "post_job_actions": {
468 "HideDatasetActionoutput_log": {
469 "action_arguments": {},
470 "action_type": "HideDatasetAction",
471 "output_name": "output_log"
472 }
473 },
474 "tool_errors": null,
475 "tool_id": "gatk_indel_realigner",
476 "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\": \"[]\"}",
477 "tool_version": "0.0.6",
478 "type": "tool",
479 "user_outputs": []
480 },
481 "14": {
482 "annotation": "Check again for duplicate reads and eliminate",
483 "id": 14,
484 "input_connections": {
485 "input_file": {
486 "id": 13,
487 "output_name": "output_bam"
488 }
489 },
490 "inputs": [],
491 "name": "Mark Duplicate reads",
492 "outputs": [
493 {
494 "name": "out_file",
495 "type": "bam"
496 },
497 {
498 "name": "html_file",
499 "type": "html"
500 }
501 ],
502 "position": {
503 "left": 3174,
504 "top": 291
505 },
506 "post_job_actions": {
507 "HideDatasetActionhtml_file": {
508 "action_arguments": {},
509 "action_type": "HideDatasetAction",
510 "output_name": "html_file"
511 },
512 "HideDatasetActionout_file": {
513 "action_arguments": {},
514 "action_type": "HideDatasetAction",
515 "output_name": "out_file"
516 }
517 },
518 "tool_errors": null,
519 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
520 "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\\\"\"}",
521 "tool_version": "1.56.0",
522 "type": "tool",
523 "user_outputs": []
524 },
525 "15": {
526 "annotation": "Determine base calls at each position",
527 "id": 15,
528 "input_connections": {
529 "reference_source|input_bams_0|input_bam": {
530 "id": 14,
531 "output_name": "out_file"
532 }
533 },
534 "inputs": [],
535 "name": "MPileup",
536 "outputs": [
537 {
538 "name": "output_mpileup",
539 "type": "pileup"
540 },
541 {
542 "name": "output_log",
543 "type": "txt"
544 }
545 ],
546 "position": {
547 "left": 3554,
548 "top": 265
549 },
550 "post_job_actions": {
551 "HideDatasetActionoutput_log": {
552 "action_arguments": {},
553 "action_type": "HideDatasetAction",
554 "output_name": "output_log"
555 },
556 "HideDatasetActionoutput_mpileup": {
557 "action_arguments": {},
558 "action_type": "HideDatasetAction",
559 "output_name": "output_mpileup"
560 }
561 },
562 "tool_errors": null,
563 "tool_id": "samtools_mpileup",
564 "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}\"}",
565 "tool_version": "0.0.1",
566 "type": "tool",
567 "user_outputs": []
568 },
569 "16": {
570 "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nVCF_ID = germline",
571 "id": 16,
572 "input_connections": {
573 "input_file": {
574 "id": 15,
575 "output_name": "output_mpileup"
576 }
577 },
578 "inputs": [
579 {
580 "description": "runtime parameter for tool Pileup to VCF",
581 "name": "min_base_qual"
582 }
583 ],
584 "name": "Pileup to VCF",
585 "outputs": [
586 {
587 "name": "output_file",
588 "type": "vcf"
589 }
590 ],
591 "position": {
592 "left": 3937,
593 "top": 258
594 },
595 "post_job_actions": {},
596 "tool_errors": null,
597 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0",
598 "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"germline\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}",
599 "tool_version": "2.2",
600 "type": "tool",
601 "user_outputs": []
602 }
603 }
604 }