comparison CFSAN_SNP_Pipeline.ga @ 0:eefdd97a6749

planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Wed, 24 Jan 2018 14:18:21 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:eefdd97a6749
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "CFSAN SNP Pipeline",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "errors": null,
11 "id": 0,
12 "input_connections": {},
13 "inputs": [],
14 "label": "Reference FASTA",
15 "name": "Input dataset",
16 "outputs": [],
17 "position": {
18 "left": 241.5,
19 "top": 381
20 },
21 "tool_id": null,
22 "tool_state": "{}",
23 "tool_version": null,
24 "type": "data_input",
25 "uuid": "024fcab7-2daf-4b89-9730-614ee2737db8",
26 "workflow_outputs": [
27 {
28 "label": null,
29 "output_name": "output",
30 "uuid": "87db8281-092f-4f81-be41-152af355ebd6"
31 }
32 ]
33 },
34 "1": {
35 "annotation": "",
36 "content_id": null,
37 "errors": null,
38 "id": 1,
39 "input_connections": {},
40 "inputs": [],
41 "label": "Collection of Paired-End Reads",
42 "name": "Input dataset collection",
43 "outputs": [],
44 "position": {
45 "left": 222,
46 "top": 746
47 },
48 "tool_id": null,
49 "tool_state": "{\"collection_type\": \"list:paired\"}",
50 "tool_version": null,
51 "type": "data_collection_input",
52 "uuid": "66a18e16-33f7-4488-ac17-508725a58279",
53 "workflow_outputs": [
54 {
55 "label": null,
56 "output_name": "output",
57 "uuid": "1a3c2f8a-e443-44cc-8490-35ebb5a9ebc4"
58 }
59 ]
60 },
61 "2": {
62 "annotation": "",
63 "content_id": "map_reads",
64 "errors": null,
65 "id": 2,
66 "input_connections": {
67 "reads|coll": {
68 "id": 1,
69 "output_name": "output"
70 },
71 "source|reference": {
72 "id": 0,
73 "output_name": "output"
74 }
75 },
76 "inputs": [
77 {
78 "description": "runtime parameter for tool 1. Map Reads",
79 "name": "source"
80 },
81 {
82 "description": "runtime parameter for tool 1. Map Reads",
83 "name": "reads"
84 }
85 ],
86 "label": null,
87 "name": "1. Map Reads",
88 "outputs": [
89 {
90 "name": "align_from_collection",
91 "type": "sam"
92 },
93 {
94 "name": "align_from_history",
95 "type": "sam"
96 },
97 {
98 "name": "cache_log",
99 "type": "txt"
100 },
101 {
102 "name": "ref_out",
103 "type": "fasta"
104 }
105 ],
106 "position": {
107 "left": 505.5,
108 "top": 536.5
109 },
110 "post_job_actions": {},
111 "tool_id": "map_reads",
112 "tool_state": "{\"source\": \"{\\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"source_select\\\": \\\"history\\\"}\", \"reads\": \"{\\\"coll\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"reads_select\\\": \\\"collection\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
113 "tool_version": "1.0.1",
114 "type": "tool",
115 "uuid": "112e11d9-2670-4aae-9bee-3b25e0dd3398",
116 "workflow_outputs": []
117 },
118 "3": {
119 "annotation": "",
120 "content_id": "call_sites",
121 "errors": null,
122 "id": 3,
123 "input_connections": {
124 "input": {
125 "id": 0,
126 "output_name": "output"
127 },
128 "sample": {
129 "id": 2,
130 "output_name": "align_from_collection"
131 }
132 },
133 "inputs": [],
134 "label": null,
135 "name": "2. Call Sites",
136 "outputs": [
137 {
138 "name": "calls",
139 "type": "vcf"
140 },
141 {
142 "name": "pileup",
143 "type": "pileup"
144 },
145 {
146 "name": "metrics",
147 "type": "txt"
148 },
149 {
150 "name": "cache_log",
151 "type": "txt"
152 }
153 ],
154 "position": {
155 "left": 915.5,
156 "top": 536.5
157 },
158 "post_job_actions": {},
159 "tool_id": "call_sites",
160 "tool_state": "{\"sample\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 24}]}\", \"input\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
161 "tool_version": "1.0.1",
162 "type": "tool",
163 "uuid": "23b2c1b4-f213-41a2-ad71-6a2c579ac36b",
164 "workflow_outputs": []
165 },
166 "4": {
167 "annotation": "",
168 "content_id": "filter_regions",
169 "errors": null,
170 "id": 4,
171 "input_connections": {
172 "calls": {
173 "id": 3,
174 "output_name": "calls"
175 },
176 "reference": {
177 "id": 0,
178 "output_name": "output"
179 }
180 },
181 "inputs": [],
182 "label": null,
183 "name": "3. Filter SNP Regions",
184 "outputs": [
185 {
186 "name": "filcalls",
187 "type": "vcf"
188 },
189 {
190 "name": "excludes",
191 "type": "vcf"
192 }
193 ],
194 "position": {
195 "left": 1231,
196 "top": 304.5
197 },
198 "post_job_actions": {},
199 "tool_id": "filter_regions",
200 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"calls\": \"null\"}",
201 "tool_version": "1.0.1",
202 "type": "tool",
203 "uuid": "b2f3ecfe-ecdb-4014-a362-78f35426559f",
204 "workflow_outputs": []
205 },
206 "5": {
207 "annotation": "",
208 "content_id": "merge_sites",
209 "errors": null,
210 "id": 5,
211 "input_connections": {
212 "calls": {
213 "id": 3,
214 "output_name": "calls"
215 }
216 },
217 "inputs": [
218 {
219 "description": "runtime parameter for tool 4. Merge Sites",
220 "name": "calls"
221 }
222 ],
223 "label": null,
224 "name": "4. Merge Sites",
225 "outputs": [
226 {
227 "name": "snplist",
228 "type": "txt"
229 }
230 ],
231 "position": {
232 "left": 1535.5,
233 "top": 717
234 },
235 "post_job_actions": {
236 "TagDatasetActionsnplist": {
237 "action_arguments": {
238 "tags": "unfiltered"
239 },
240 "action_type": "TagDatasetAction",
241 "output_name": "snplist"
242 }
243 },
244 "tool_id": "merge_sites",
245 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"calls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
246 "tool_version": "1.0.1",
247 "type": "tool",
248 "uuid": "012268fa-41bf-4227-b812-47009b8315c3",
249 "workflow_outputs": [
250 {
251 "label": "Unfiltered SNP list",
252 "output_name": "snplist",
253 "uuid": "0dd22e5c-15b8-4772-8304-a81d3de1bee4"
254 }
255 ]
256 },
257 "6": {
258 "annotation": "",
259 "content_id": "merge_sites",
260 "errors": null,
261 "id": 6,
262 "input_connections": {
263 "calls": {
264 "id": 4,
265 "output_name": "filcalls"
266 }
267 },
268 "inputs": [
269 {
270 "description": "runtime parameter for tool 4. Merge Sites",
271 "name": "calls"
272 }
273 ],
274 "label": null,
275 "name": "4. Merge Sites",
276 "outputs": [
277 {
278 "name": "snplist",
279 "type": "txt"
280 }
281 ],
282 "position": {
283 "left": 1530.5,
284 "top": 299
285 },
286 "post_job_actions": {
287 "TagDatasetActionsnplist": {
288 "action_arguments": {
289 "tags": "filtered"
290 },
291 "action_type": "TagDatasetAction",
292 "output_name": "snplist"
293 }
294 },
295 "tool_id": "merge_sites",
296 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"calls\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
297 "tool_version": "1.0.1",
298 "type": "tool",
299 "uuid": "bb0d410f-4d22-400e-8dc2-ddf62027ca3d",
300 "workflow_outputs": [
301 {
302 "label": "Filtered SNP list",
303 "output_name": "snplist",
304 "uuid": "ab240b50-625d-4468-90fe-02363974abea"
305 }
306 ]
307 },
308 "7": {
309 "annotation": "",
310 "content_id": "call_consensus",
311 "errors": null,
312 "id": 7,
313 "input_connections": {
314 "call_pileup": {
315 "id": 3,
316 "output_name": "pileup"
317 },
318 "calls": {
319 "id": 3,
320 "output_name": "calls"
321 },
322 "snps": {
323 "id": 5,
324 "output_name": "snplist"
325 }
326 },
327 "inputs": [],
328 "label": null,
329 "name": "5. Call consensus SNPs",
330 "outputs": [
331 {
332 "name": "calls_consensus_vcf",
333 "type": "vcf"
334 },
335 {
336 "name": "calls_consensus_fa",
337 "type": "fasta"
338 },
339 {
340 "name": "cache_log",
341 "type": "txt"
342 }
343 ],
344 "position": {
345 "left": 1748.5,
346 "top": 707.5
347 },
348 "post_job_actions": {},
349 "tool_id": "call_consensus",
350 "tool_state": "{\"snps\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"call_pileup\": \"null\", \"calls\": \"null\"}",
351 "tool_version": "1.0.1",
352 "type": "tool",
353 "uuid": "8785777e-c7c0-4416-8c5c-5201d218fa71",
354 "workflow_outputs": []
355 },
356 "8": {
357 "annotation": "",
358 "content_id": "call_consensus",
359 "errors": null,
360 "id": 8,
361 "input_connections": {
362 "call_pileup": {
363 "id": 3,
364 "output_name": "pileup"
365 },
366 "calls": {
367 "id": 4,
368 "output_name": "filcalls"
369 },
370 "snps": {
371 "id": 6,
372 "output_name": "snplist"
373 }
374 },
375 "inputs": [],
376 "label": null,
377 "name": "5. Call consensus SNPs",
378 "outputs": [
379 {
380 "name": "calls_consensus_vcf",
381 "type": "vcf"
382 },
383 {
384 "name": "calls_consensus_fa",
385 "type": "fasta"
386 },
387 {
388 "name": "cache_log",
389 "type": "txt"
390 }
391 ],
392 "position": {
393 "left": 1752.5,
394 "top": 289.5
395 },
396 "post_job_actions": {},
397 "tool_id": "call_consensus",
398 "tool_state": "{\"snps\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"call_pileup\": \"null\", \"calls\": \"null\"}",
399 "tool_version": "1.0.1",
400 "type": "tool",
401 "uuid": "14dbd077-15fc-4dbe-8883-b6184d696428",
402 "workflow_outputs": []
403 },
404 "9": {
405 "annotation": "",
406 "content_id": "merge_vcfs",
407 "errors": null,
408 "id": 9,
409 "input_connections": {
410 "vcfs": {
411 "id": 7,
412 "output_name": "calls_consensus_vcf"
413 }
414 },
415 "inputs": [
416 {
417 "description": "runtime parameter for tool 6. Merge VCFs",
418 "name": "vcfs"
419 }
420 ],
421 "label": null,
422 "name": "6. Merge VCFs",
423 "outputs": [
424 {
425 "name": "snpmav",
426 "type": "vcf"
427 }
428 ],
429 "position": {
430 "left": 2050.5,
431 "top": 644
432 },
433 "post_job_actions": {
434 "TagDatasetActionsnpmav": {
435 "action_arguments": {
436 "tags": "unfiltered"
437 },
438 "action_type": "TagDatasetAction",
439 "output_name": "snpmav"
440 }
441 },
442 "tool_id": "merge_vcfs",
443 "tool_state": "{\"vcfs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
444 "tool_version": "1.0.1",
445 "type": "tool",
446 "uuid": "37131dc0-b85a-4f76-9bfc-96d1ce05f485",
447 "workflow_outputs": [
448 {
449 "label": "Unfiltered SNP matrix (VCF)",
450 "output_name": "snpmav",
451 "uuid": "4cf3ea09-55ae-4656-abc7-9e0ae6f96a3e"
452 }
453 ]
454 },
455 "10": {
456 "annotation": "",
457 "content_id": "snp_matrix",
458 "errors": null,
459 "id": 10,
460 "input_connections": {
461 "cons": {
462 "id": 7,
463 "output_name": "calls_consensus_fa"
464 },
465 "reference|reference": {
466 "id": 0,
467 "output_name": "output"
468 },
469 "snplist": {
470 "id": 5,
471 "output_name": "snplist"
472 }
473 },
474 "inputs": [
475 {
476 "description": "runtime parameter for tool 7. Create a SNP matrix",
477 "name": "snplist"
478 },
479 {
480 "description": "runtime parameter for tool 7. Create a SNP matrix",
481 "name": "cons"
482 },
483 {
484 "description": "runtime parameter for tool 7. Create a SNP matrix",
485 "name": "reference"
486 }
487 ],
488 "label": null,
489 "name": "7. Create a SNP matrix",
490 "outputs": [
491 {
492 "name": "snpma",
493 "type": "fasta"
494 },
495 {
496 "name": "pairws",
497 "type": "tsv"
498 },
499 {
500 "name": "distma",
501 "type": "tsv"
502 },
503 {
504 "name": "referenceSNP",
505 "type": "fasta"
506 },
507 {
508 "name": "metrics",
509 "type": "tsv"
510 }
511 ],
512 "position": {
513 "left": 2053,
514 "top": 784
515 },
516 "post_job_actions": {
517 "HideDatasetActionmetrics": {
518 "action_arguments": {},
519 "action_type": "HideDatasetAction",
520 "output_name": "metrics"
521 },
522 "TagDatasetActiondistma": {
523 "action_arguments": {
524 "tags": "unfiltered"
525 },
526 "action_type": "TagDatasetAction",
527 "output_name": "distma"
528 },
529 "TagDatasetActionreferenceSNP": {
530 "action_arguments": {
531 "tags": "unfiltered"
532 },
533 "action_type": "TagDatasetAction",
534 "output_name": "referenceSNP"
535 },
536 "TagDatasetActionsnpma": {
537 "action_arguments": {
538 "tags": "unfiltered"
539 },
540 "action_type": "TagDatasetAction",
541 "output_name": "snpma"
542 }
543 },
544 "tool_id": "snp_matrix",
545 "tool_state": "{\"__page__\": null, \"snplist\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"cons\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"ref\\\": \\\"history\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
546 "tool_version": "1.0.1",
547 "type": "tool",
548 "uuid": "22e52e86-ab1d-4201-9850-86d4bc0a8110",
549 "workflow_outputs": [
550 {
551 "label": "Unfiltered SNP distance matrix",
552 "output_name": "distma",
553 "uuid": "c8e44902-b18f-45d5-9aa6-81471cfcd73d"
554 },
555 {
556 "label": "Unfiltered SNP reference (FASTA)",
557 "output_name": "referenceSNP",
558 "uuid": "b60c56cf-c9df-4eef-85d0-39717232aef0"
559 },
560 {
561 "label": "Unfiltered SNP matrix (FASTA)",
562 "output_name": "snpma",
563 "uuid": "07789496-d5db-48ec-98ad-0c25f5e93fcc"
564 },
565 {
566 "label": "Unfiltered pairwise SNP distance table",
567 "output_name": "pairws",
568 "uuid": "e34a6bc0-7165-4444-ae06-e7679248b6bf"
569 }
570 ]
571 },
572 "11": {
573 "annotation": "",
574 "content_id": "merge_vcfs",
575 "errors": null,
576 "id": 11,
577 "input_connections": {
578 "vcfs": {
579 "id": 8,
580 "output_name": "calls_consensus_vcf"
581 }
582 },
583 "inputs": [
584 {
585 "description": "runtime parameter for tool 6. Merge VCFs",
586 "name": "vcfs"
587 }
588 ],
589 "label": null,
590 "name": "6. Merge VCFs",
591 "outputs": [
592 {
593 "name": "snpmav",
594 "type": "vcf"
595 }
596 ],
597 "position": {
598 "left": 2054.5,
599 "top": 227
600 },
601 "post_job_actions": {
602 "TagDatasetActionsnpmav": {
603 "action_arguments": {
604 "tags": "filtered"
605 },
606 "action_type": "TagDatasetAction",
607 "output_name": "snpmav"
608 }
609 },
610 "tool_id": "merge_vcfs",
611 "tool_state": "{\"vcfs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
612 "tool_version": "1.0.1",
613 "type": "tool",
614 "uuid": "55024e57-310a-4ab7-927b-034c78b757d9",
615 "workflow_outputs": [
616 {
617 "label": "Filtered SNP matrix (VCF)",
618 "output_name": "snpmav",
619 "uuid": "b4118679-e622-4a93-8a15-aaab125c2475"
620 }
621 ]
622 },
623 "12": {
624 "annotation": "",
625 "content_id": "snp_matrix",
626 "errors": null,
627 "id": 12,
628 "input_connections": {
629 "cons": {
630 "id": 8,
631 "output_name": "calls_consensus_fa"
632 },
633 "reference|reference": {
634 "id": 0,
635 "output_name": "output"
636 },
637 "snplist": {
638 "id": 6,
639 "output_name": "snplist"
640 }
641 },
642 "inputs": [
643 {
644 "description": "runtime parameter for tool 7. Create a SNP matrix",
645 "name": "snplist"
646 },
647 {
648 "description": "runtime parameter for tool 7. Create a SNP matrix",
649 "name": "cons"
650 },
651 {
652 "description": "runtime parameter for tool 7. Create a SNP matrix",
653 "name": "reference"
654 }
655 ],
656 "label": null,
657 "name": "7. Create a SNP matrix",
658 "outputs": [
659 {
660 "name": "snpma",
661 "type": "fasta"
662 },
663 {
664 "name": "pairws",
665 "type": "tsv"
666 },
667 {
668 "name": "distma",
669 "type": "tsv"
670 },
671 {
672 "name": "referenceSNP",
673 "type": "fasta"
674 },
675 {
676 "name": "metrics",
677 "type": "tsv"
678 }
679 ],
680 "position": {
681 "left": 2050,
682 "top": 349
683 },
684 "post_job_actions": {
685 "HideDatasetActionmetrics": {
686 "action_arguments": {},
687 "action_type": "HideDatasetAction",
688 "output_name": "metrics"
689 },
690 "TagDatasetActiondistma": {
691 "action_arguments": {
692 "tags": "filtered"
693 },
694 "action_type": "TagDatasetAction",
695 "output_name": "distma"
696 },
697 "TagDatasetActionpairws": {
698 "action_arguments": {
699 "tags": "filtered"
700 },
701 "action_type": "TagDatasetAction",
702 "output_name": "pairws"
703 },
704 "TagDatasetActionreferenceSNP": {
705 "action_arguments": {
706 "tags": "filtered"
707 },
708 "action_type": "TagDatasetAction",
709 "output_name": "referenceSNP"
710 },
711 "TagDatasetActionsnpma": {
712 "action_arguments": {
713 "tags": "filtered"
714 },
715 "action_type": "TagDatasetAction",
716 "output_name": "snpma"
717 }
718 },
719 "tool_id": "snp_matrix",
720 "tool_state": "{\"__page__\": null, \"snplist\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"cons\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"ref\\\": \\\"history\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\"}",
721 "tool_version": "1.0.1",
722 "type": "tool",
723 "uuid": "6d0adb1c-637a-436a-aa32-64cb54b414f6",
724 "workflow_outputs": [
725 {
726 "label": "Filtered SNP distance matrix",
727 "output_name": "distma",
728 "uuid": "0b3437f6-5370-415c-bd02-f85fd4527783"
729 },
730 {
731 "label": "Filtered SNP reference (FASTA)",
732 "output_name": "referenceSNP",
733 "uuid": "bca4048e-2af1-4764-a1de-cf987914fc2a"
734 },
735 {
736 "label": "Filtered SNP matrix (FASTA)",
737 "output_name": "snpma",
738 "uuid": "2ca775f1-917f-4824-b11a-1506c2e75bc6"
739 },
740 {
741 "label": "Filtered pairwise SNP distance table",
742 "output_name": "pairws",
743 "uuid": "6d385865-e585-4bc1-956f-95110edf6095"
744 }
745 ]
746 }
747 },
748 "tags": [],
749 "uuid": "304cdcb3-78a5-43bf-be17-c0824e30e02c"
750 }