comparison rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga @ 7:3f7b0788a1c4 draft

Uploaded
author mcharles
date Tue, 07 Oct 2014 10:34:34 -0400
parents
children d857538d9fea
comparison
equal deleted inserted replaced
6:1776b8ddd87e 7:3f7b0788a1c4
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "rapsosnp v1.20 - 1x - sam",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "READ1"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 279,
21 "top": 617
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"READ1\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "",
37 "name": "READ2"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 276,
44 "top": 713
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"READ2\"}",
49 "tool_version": null,
50 "type": "data_input",
51 "user_outputs": []
52 },
53 "2": {
54 "annotation": "",
55 "id": 2,
56 "input_connections": {},
57 "inputs": [
58 {
59 "description": "",
60 "name": "ASSEMBLY"
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
65 "position": {
66 "left": 3921,
67 "top": 392
68 },
69 "tool_errors": null,
70 "tool_id": null,
71 "tool_state": "{\"name\": \"ASSEMBLY\"}",
72 "tool_version": null,
73 "type": "data_input",
74 "user_outputs": []
75 },
76 "3": {
77 "annotation": "",
78 "id": 3,
79 "input_connections": {},
80 "inputs": [
81 {
82 "description": "",
83 "name": "DUBIOUS"
84 }
85 ],
86 "name": "Input dataset",
87 "outputs": [],
88 "position": {
89 "left": 3415,
90 "top": 1131
91 },
92 "tool_errors": null,
93 "tool_id": null,
94 "tool_state": "{\"name\": \"DUBIOUS\"}",
95 "tool_version": null,
96 "type": "data_input",
97 "user_outputs": []
98 },
99 "4": {
100 "annotation": "",
101 "id": 4,
102 "input_connections": {
103 "input_file": {
104 "id": 0,
105 "output_name": "output"
106 }
107 },
108 "inputs": [],
109 "name": "SplitFile10x",
110 "outputs": [
111 {
112 "name": "output_file1",
113 "type": "txt"
114 },
115 {
116 "name": "output_file2",
117 "type": "txt"
118 },
119 {
120 "name": "output_file3",
121 "type": "txt"
122 },
123 {
124 "name": "output_file4",
125 "type": "txt"
126 },
127 {
128 "name": "output_file5",
129 "type": "txt"
130 },
131 {
132 "name": "output_file6",
133 "type": "txt"
134 },
135 {
136 "name": "output_file7",
137 "type": "txt"
138 },
139 {
140 "name": "output_file8",
141 "type": "txt"
142 },
143 {
144 "name": "output_file9",
145 "type": "txt"
146 },
147 {
148 "name": "output_file10",
149 "type": "txt"
150 }
151 ],
152 "position": {
153 "left": 590,
154 "top": 338
155 },
156 "post_job_actions": {},
157 "tool_errors": null,
158 "tool_id": "SplitFile10x",
159 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
160 "tool_version": "1.00",
161 "type": "tool",
162 "user_outputs": []
163 },
164 "5": {
165 "annotation": "",
166 "id": 5,
167 "input_connections": {
168 "input_file": {
169 "id": 1,
170 "output_name": "output"
171 }
172 },
173 "inputs": [],
174 "name": "SplitFile10x",
175 "outputs": [
176 {
177 "name": "output_file1",
178 "type": "txt"
179 },
180 {
181 "name": "output_file2",
182 "type": "txt"
183 },
184 {
185 "name": "output_file3",
186 "type": "txt"
187 },
188 {
189 "name": "output_file4",
190 "type": "txt"
191 },
192 {
193 "name": "output_file5",
194 "type": "txt"
195 },
196 {
197 "name": "output_file6",
198 "type": "txt"
199 },
200 {
201 "name": "output_file7",
202 "type": "txt"
203 },
204 {
205 "name": "output_file8",
206 "type": "txt"
207 },
208 {
209 "name": "output_file9",
210 "type": "txt"
211 },
212 {
213 "name": "output_file10",
214 "type": "txt"
215 }
216 ],
217 "position": {
218 "left": 581,
219 "top": 871
220 },
221 "post_job_actions": {},
222 "tool_errors": null,
223 "tool_id": "SplitFile10x",
224 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
225 "tool_version": "1.00",
226 "type": "tool",
227 "user_outputs": []
228 },
229 "6": {
230 "annotation": "",
231 "id": 6,
232 "input_connections": {
233 "input_fasta": {
234 "id": 2,
235 "output_name": "output"
236 }
237 },
238 "inputs": [],
239 "name": "fastaGroomerForMakeBlastdb",
240 "outputs": [
241 {
242 "name": "output_fasta",
243 "type": "fasta"
244 }
245 ],
246 "position": {
247 "left": 4471.25,
248 "top": 231.75
249 },
250 "post_job_actions": {},
251 "tool_errors": null,
252 "tool_id": "fastaGroomerForMakeBlastdb",
253 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
254 "tool_version": "1.00",
255 "type": "tool",
256 "user_outputs": []
257 },
258 "7": {
259 "annotation": "",
260 "id": 7,
261 "input_connections": {
262 "input_read1_file": {
263 "id": 4,
264 "output_name": "output_file1"
265 },
266 "input_read2_file": {
267 "id": 5,
268 "output_name": "output_file1"
269 }
270 },
271 "inputs": [],
272 "name": "PrepareFastqLight",
273 "outputs": [
274 {
275 "name": "output_read1_file",
276 "type": "fastqsanger"
277 },
278 {
279 "name": "output_read2_file",
280 "type": "fastqsanger"
281 },
282 {
283 "name": "log_file",
284 "type": "txt"
285 }
286 ],
287 "position": {
288 "left": 936.93310546875,
289 "top": 338.43333435058594
290 },
291 "post_job_actions": {},
292 "tool_errors": null,
293 "tool_id": "PrepareFastqLight",
294 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
295 "tool_version": "1.01",
296 "type": "tool",
297 "user_outputs": []
298 },
299 "8": {
300 "annotation": "",
301 "id": 8,
302 "input_connections": {
303 "input_read1_file": {
304 "id": 4,
305 "output_name": "output_file2"
306 },
307 "input_read2_file": {
308 "id": 5,
309 "output_name": "output_file2"
310 }
311 },
312 "inputs": [],
313 "name": "PrepareFastqLight",
314 "outputs": [
315 {
316 "name": "output_read1_file",
317 "type": "fastqsanger"
318 },
319 {
320 "name": "output_read2_file",
321 "type": "fastqsanger"
322 },
323 {
324 "name": "log_file",
325 "type": "txt"
326 }
327 ],
328 "position": {
329 "left": 943.93310546875,
330 "top": 585.4333343505859
331 },
332 "post_job_actions": {},
333 "tool_errors": null,
334 "tool_id": "PrepareFastqLight",
335 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
336 "tool_version": "1.01",
337 "type": "tool",
338 "user_outputs": []
339 },
340 "9": {
341 "annotation": "",
342 "id": 9,
343 "input_connections": {
344 "input_read1_file": {
345 "id": 4,
346 "output_name": "output_file3"
347 },
348 "input_read2_file": {
349 "id": 5,
350 "output_name": "output_file3"
351 }
352 },
353 "inputs": [],
354 "name": "PrepareFastqLight",
355 "outputs": [
356 {
357 "name": "output_read1_file",
358 "type": "fastqsanger"
359 },
360 {
361 "name": "output_read2_file",
362 "type": "fastqsanger"
363 },
364 {
365 "name": "log_file",
366 "type": "txt"
367 }
368 ],
369 "position": {
370 "left": 947.93310546875,
371 "top": 812.433349609375
372 },
373 "post_job_actions": {},
374 "tool_errors": null,
375 "tool_id": "PrepareFastqLight",
376 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
377 "tool_version": "1.01",
378 "type": "tool",
379 "user_outputs": []
380 },
381 "10": {
382 "annotation": "",
383 "id": 10,
384 "input_connections": {
385 "input_read1_file": {
386 "id": 4,
387 "output_name": "output_file6"
388 },
389 "input_read2_file": {
390 "id": 5,
391 "output_name": "output_file6"
392 }
393 },
394 "inputs": [],
395 "name": "PrepareFastqLight",
396 "outputs": [
397 {
398 "name": "output_read1_file",
399 "type": "fastqsanger"
400 },
401 {
402 "name": "output_read2_file",
403 "type": "fastqsanger"
404 },
405 {
406 "name": "log_file",
407 "type": "txt"
408 }
409 ],
410 "position": {
411 "left": 1267.93310546875,
412 "top": 343.43333435058594
413 },
414 "post_job_actions": {},
415 "tool_errors": null,
416 "tool_id": "PrepareFastqLight",
417 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
418 "tool_version": "1.01",
419 "type": "tool",
420 "user_outputs": []
421 },
422 "11": {
423 "annotation": "",
424 "id": 11,
425 "input_connections": {
426 "input_read1_file": {
427 "id": 4,
428 "output_name": "output_file7"
429 },
430 "input_read2_file": {
431 "id": 5,
432 "output_name": "output_file7"
433 }
434 },
435 "inputs": [],
436 "name": "PrepareFastqLight",
437 "outputs": [
438 {
439 "name": "output_read1_file",
440 "type": "fastqsanger"
441 },
442 {
443 "name": "output_read2_file",
444 "type": "fastqsanger"
445 },
446 {
447 "name": "log_file",
448 "type": "txt"
449 }
450 ],
451 "position": {
452 "left": 1261.93310546875,
453 "top": 587.4333343505859
454 },
455 "post_job_actions": {},
456 "tool_errors": null,
457 "tool_id": "PrepareFastqLight",
458 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
459 "tool_version": "1.01",
460 "type": "tool",
461 "user_outputs": []
462 },
463 "12": {
464 "annotation": "",
465 "id": 12,
466 "input_connections": {
467 "input_read1_file": {
468 "id": 4,
469 "output_name": "output_file4"
470 },
471 "input_read2_file": {
472 "id": 5,
473 "output_name": "output_file4"
474 }
475 },
476 "inputs": [],
477 "name": "PrepareFastqLight",
478 "outputs": [
479 {
480 "name": "output_read1_file",
481 "type": "fastqsanger"
482 },
483 {
484 "name": "output_read2_file",
485 "type": "fastqsanger"
486 },
487 {
488 "name": "log_file",
489 "type": "txt"
490 }
491 ],
492 "position": {
493 "left": 954.93310546875,
494 "top": 1044.433349609375
495 },
496 "post_job_actions": {},
497 "tool_errors": null,
498 "tool_id": "PrepareFastqLight",
499 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
500 "tool_version": "1.01",
501 "type": "tool",
502 "user_outputs": []
503 },
504 "13": {
505 "annotation": "",
506 "id": 13,
507 "input_connections": {
508 "input_read1_file": {
509 "id": 4,
510 "output_name": "output_file8"
511 },
512 "input_read2_file": {
513 "id": 5,
514 "output_name": "output_file8"
515 }
516 },
517 "inputs": [],
518 "name": "PrepareFastqLight",
519 "outputs": [
520 {
521 "name": "output_read1_file",
522 "type": "fastqsanger"
523 },
524 {
525 "name": "output_read2_file",
526 "type": "fastqsanger"
527 },
528 {
529 "name": "log_file",
530 "type": "txt"
531 }
532 ],
533 "position": {
534 "left": 1265.93310546875,
535 "top": 815.433349609375
536 },
537 "post_job_actions": {},
538 "tool_errors": null,
539 "tool_id": "PrepareFastqLight",
540 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
541 "tool_version": "1.01",
542 "type": "tool",
543 "user_outputs": []
544 },
545 "14": {
546 "annotation": "",
547 "id": 14,
548 "input_connections": {
549 "input_read1_file": {
550 "id": 4,
551 "output_name": "output_file5"
552 },
553 "input_read2_file": {
554 "id": 5,
555 "output_name": "output_file5"
556 }
557 },
558 "inputs": [],
559 "name": "PrepareFastqLight",
560 "outputs": [
561 {
562 "name": "output_read1_file",
563 "type": "fastqsanger"
564 },
565 {
566 "name": "output_read2_file",
567 "type": "fastqsanger"
568 },
569 {
570 "name": "log_file",
571 "type": "txt"
572 }
573 ],
574 "position": {
575 "left": 953.93310546875,
576 "top": 1282.433349609375
577 },
578 "post_job_actions": {},
579 "tool_errors": null,
580 "tool_id": "PrepareFastqLight",
581 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
582 "tool_version": "1.01",
583 "type": "tool",
584 "user_outputs": []
585 },
586 "15": {
587 "annotation": "",
588 "id": 15,
589 "input_connections": {
590 "input_read1_file": {
591 "id": 4,
592 "output_name": "output_file9"
593 },
594 "input_read2_file": {
595 "id": 5,
596 "output_name": "output_file9"
597 }
598 },
599 "inputs": [],
600 "name": "PrepareFastqLight",
601 "outputs": [
602 {
603 "name": "output_read1_file",
604 "type": "fastqsanger"
605 },
606 {
607 "name": "output_read2_file",
608 "type": "fastqsanger"
609 },
610 {
611 "name": "log_file",
612 "type": "txt"
613 }
614 ],
615 "position": {
616 "left": 1265.93310546875,
617 "top": 1043.433349609375
618 },
619 "post_job_actions": {},
620 "tool_errors": null,
621 "tool_id": "PrepareFastqLight",
622 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
623 "tool_version": "1.01",
624 "type": "tool",
625 "user_outputs": []
626 },
627 "16": {
628 "annotation": "",
629 "id": 16,
630 "input_connections": {
631 "input_read1_file": {
632 "id": 4,
633 "output_name": "output_file10"
634 },
635 "input_read2_file": {
636 "id": 5,
637 "output_name": "output_file10"
638 }
639 },
640 "inputs": [],
641 "name": "PrepareFastqLight",
642 "outputs": [
643 {
644 "name": "output_read1_file",
645 "type": "fastqsanger"
646 },
647 {
648 "name": "output_read2_file",
649 "type": "fastqsanger"
650 },
651 {
652 "name": "log_file",
653 "type": "txt"
654 }
655 ],
656 "position": {
657 "left": 1270.93310546875,
658 "top": 1281.433349609375
659 },
660 "post_job_actions": {},
661 "tool_errors": null,
662 "tool_id": "PrepareFastqLight",
663 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
664 "tool_version": "1.01",
665 "type": "tool",
666 "user_outputs": []
667 },
668 "17": {
669 "annotation": "",
670 "id": 17,
671 "input_connections": {
672 "input_file": {
673 "id": 6,
674 "output_name": "output_fasta"
675 }
676 },
677 "inputs": [],
678 "name": "NCBI BLAST+ makeblastdb",
679 "outputs": [
680 {
681 "name": "outfile",
682 "type": "data"
683 }
684 ],
685 "position": {
686 "left": 5062.25,
687 "top": 221.75
688 },
689 "post_job_actions": {},
690 "tool_errors": null,
691 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
692 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}",
693 "tool_version": "0.1.00",
694 "type": "tool",
695 "user_outputs": []
696 },
697 "18": {
698 "annotation": "",
699 "id": 18,
700 "input_connections": {
701 "genomeSource|ownFile": {
702 "id": 2,
703 "output_name": "output"
704 },
705 "paired|input1": {
706 "id": 7,
707 "output_name": "output_read1_file"
708 },
709 "paired|input2": {
710 "id": 7,
711 "output_name": "output_read2_file"
712 }
713 },
714 "inputs": [],
715 "name": "Map with BWA for Illumina",
716 "outputs": [
717 {
718 "name": "output",
719 "type": "sam"
720 }
721 ],
722 "position": {
723 "left": 1576.25,
724 "top": 346.75
725 },
726 "post_job_actions": {},
727 "tool_errors": null,
728 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
729 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
730 "tool_version": "1.2.3",
731 "type": "tool",
732 "user_outputs": []
733 },
734 "19": {
735 "annotation": "",
736 "id": 19,
737 "input_connections": {
738 "genomeSource|ownFile": {
739 "id": 2,
740 "output_name": "output"
741 },
742 "paired|input1": {
743 "id": 8,
744 "output_name": "output_read1_file"
745 },
746 "paired|input2": {
747 "id": 8,
748 "output_name": "output_read2_file"
749 }
750 },
751 "inputs": [],
752 "name": "Map with BWA for Illumina",
753 "outputs": [
754 {
755 "name": "output",
756 "type": "sam"
757 }
758 ],
759 "position": {
760 "left": 1571.25,
761 "top": 589.75
762 },
763 "post_job_actions": {},
764 "tool_errors": null,
765 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
766 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
767 "tool_version": "1.2.3",
768 "type": "tool",
769 "user_outputs": []
770 },
771 "20": {
772 "annotation": "",
773 "id": 20,
774 "input_connections": {
775 "genomeSource|ownFile": {
776 "id": 2,
777 "output_name": "output"
778 },
779 "paired|input1": {
780 "id": 9,
781 "output_name": "output_read1_file"
782 },
783 "paired|input2": {
784 "id": 9,
785 "output_name": "output_read2_file"
786 }
787 },
788 "inputs": [],
789 "name": "Map with BWA for Illumina",
790 "outputs": [
791 {
792 "name": "output",
793 "type": "sam"
794 }
795 ],
796 "position": {
797 "left": 1562.25,
798 "top": 819.75
799 },
800 "post_job_actions": {},
801 "tool_errors": null,
802 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
803 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
804 "tool_version": "1.2.3",
805 "type": "tool",
806 "user_outputs": []
807 },
808 "21": {
809 "annotation": "",
810 "id": 21,
811 "input_connections": {
812 "genomeSource|ownFile": {
813 "id": 2,
814 "output_name": "output"
815 },
816 "paired|input1": {
817 "id": 10,
818 "output_name": "output_read1_file"
819 },
820 "paired|input2": {
821 "id": 10,
822 "output_name": "output_read2_file"
823 }
824 },
825 "inputs": [],
826 "name": "Map with BWA for Illumina",
827 "outputs": [
828 {
829 "name": "output",
830 "type": "sam"
831 }
832 ],
833 "position": {
834 "left": 1826.25,
835 "top": 350.75
836 },
837 "post_job_actions": {},
838 "tool_errors": null,
839 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
840 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
841 "tool_version": "1.2.3",
842 "type": "tool",
843 "user_outputs": []
844 },
845 "22": {
846 "annotation": "",
847 "id": 22,
848 "input_connections": {
849 "genomeSource|ownFile": {
850 "id": 2,
851 "output_name": "output"
852 },
853 "paired|input1": {
854 "id": 11,
855 "output_name": "output_read1_file"
856 },
857 "paired|input2": {
858 "id": 11,
859 "output_name": "output_read2_file"
860 }
861 },
862 "inputs": [],
863 "name": "Map with BWA for Illumina",
864 "outputs": [
865 {
866 "name": "output",
867 "type": "sam"
868 }
869 ],
870 "position": {
871 "left": 1824.25,
872 "top": 592.75
873 },
874 "post_job_actions": {},
875 "tool_errors": null,
876 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
877 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
878 "tool_version": "1.2.3",
879 "type": "tool",
880 "user_outputs": []
881 },
882 "23": {
883 "annotation": "",
884 "id": 23,
885 "input_connections": {
886 "genomeSource|ownFile": {
887 "id": 2,
888 "output_name": "output"
889 },
890 "paired|input1": {
891 "id": 12,
892 "output_name": "output_read1_file"
893 },
894 "paired|input2": {
895 "id": 12,
896 "output_name": "output_read2_file"
897 }
898 },
899 "inputs": [],
900 "name": "Map with BWA for Illumina",
901 "outputs": [
902 {
903 "name": "output",
904 "type": "sam"
905 }
906 ],
907 "position": {
908 "left": 1562.25,
909 "top": 1045.75
910 },
911 "post_job_actions": {},
912 "tool_errors": null,
913 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
914 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
915 "tool_version": "1.2.3",
916 "type": "tool",
917 "user_outputs": []
918 },
919 "24": {
920 "annotation": "",
921 "id": 24,
922 "input_connections": {
923 "genomeSource|ownFile": {
924 "id": 2,
925 "output_name": "output"
926 },
927 "paired|input1": {
928 "id": 13,
929 "output_name": "output_read1_file"
930 },
931 "paired|input2": {
932 "id": 13,
933 "output_name": "output_read2_file"
934 }
935 },
936 "inputs": [],
937 "name": "Map with BWA for Illumina",
938 "outputs": [
939 {
940 "name": "output",
941 "type": "sam"
942 }
943 ],
944 "position": {
945 "left": 1818.25,
946 "top": 821.75
947 },
948 "post_job_actions": {},
949 "tool_errors": null,
950 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
951 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
952 "tool_version": "1.2.3",
953 "type": "tool",
954 "user_outputs": []
955 },
956 "25": {
957 "annotation": "",
958 "id": 25,
959 "input_connections": {
960 "genomeSource|ownFile": {
961 "id": 2,
962 "output_name": "output"
963 },
964 "paired|input1": {
965 "id": 14,
966 "output_name": "output_read1_file"
967 },
968 "paired|input2": {
969 "id": 14,
970 "output_name": "output_read2_file"
971 }
972 },
973 "inputs": [],
974 "name": "Map with BWA for Illumina",
975 "outputs": [
976 {
977 "name": "output",
978 "type": "sam"
979 }
980 ],
981 "position": {
982 "left": 1563.25,
983 "top": 1284.75
984 },
985 "post_job_actions": {},
986 "tool_errors": null,
987 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
988 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
989 "tool_version": "1.2.3",
990 "type": "tool",
991 "user_outputs": []
992 },
993 "26": {
994 "annotation": "",
995 "id": 26,
996 "input_connections": {
997 "genomeSource|ownFile": {
998 "id": 2,
999 "output_name": "output"
1000 },
1001 "paired|input1": {
1002 "id": 15,
1003 "output_name": "output_read1_file"
1004 },
1005 "paired|input2": {
1006 "id": 15,
1007 "output_name": "output_read2_file"
1008 }
1009 },
1010 "inputs": [],
1011 "name": "Map with BWA for Illumina",
1012 "outputs": [
1013 {
1014 "name": "output",
1015 "type": "sam"
1016 }
1017 ],
1018 "position": {
1019 "left": 1813.25,
1020 "top": 1044.75
1021 },
1022 "post_job_actions": {},
1023 "tool_errors": null,
1024 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
1025 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
1026 "tool_version": "1.2.3",
1027 "type": "tool",
1028 "user_outputs": []
1029 },
1030 "27": {
1031 "annotation": "",
1032 "id": 27,
1033 "input_connections": {
1034 "genomeSource|ownFile": {
1035 "id": 2,
1036 "output_name": "output"
1037 },
1038 "paired|input1": {
1039 "id": 16,
1040 "output_name": "output_read1_file"
1041 },
1042 "paired|input2": {
1043 "id": 16,
1044 "output_name": "output_read2_file"
1045 }
1046 },
1047 "inputs": [],
1048 "name": "Map with BWA for Illumina",
1049 "outputs": [
1050 {
1051 "name": "output",
1052 "type": "sam"
1053 }
1054 ],
1055 "position": {
1056 "left": 1807.25,
1057 "top": 1286.75
1058 },
1059 "post_job_actions": {},
1060 "tool_errors": null,
1061 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
1062 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
1063 "tool_version": "1.2.3",
1064 "type": "tool",
1065 "user_outputs": []
1066 },
1067 "28": {
1068 "annotation": "",
1069 "id": 28,
1070 "input_connections": {
1071 "input_sam_file": {
1072 "id": 18,
1073 "output_name": "output"
1074 }
1075 },
1076 "inputs": [],
1077 "name": "filtersam_mapped_and_unique",
1078 "outputs": [
1079 {
1080 "name": "output_sam_file",
1081 "type": "sam"
1082 },
1083 {
1084 "name": "log_file",
1085 "type": "txt"
1086 }
1087 ],
1088 "position": {
1089 "left": 2096.75,
1090 "top": 353.75
1091 },
1092 "post_job_actions": {},
1093 "tool_errors": null,
1094 "tool_id": "filtersam_mapped_and_unique",
1095 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1096 "tool_version": "1.01",
1097 "type": "tool",
1098 "user_outputs": []
1099 },
1100 "29": {
1101 "annotation": "",
1102 "id": 29,
1103 "input_connections": {
1104 "input_sam_file": {
1105 "id": 19,
1106 "output_name": "output"
1107 }
1108 },
1109 "inputs": [],
1110 "name": "filtersam_mapped_and_unique",
1111 "outputs": [
1112 {
1113 "name": "output_sam_file",
1114 "type": "sam"
1115 },
1116 {
1117 "name": "log_file",
1118 "type": "txt"
1119 }
1120 ],
1121 "position": {
1122 "left": 2093.75,
1123 "top": 596.75
1124 },
1125 "post_job_actions": {},
1126 "tool_errors": null,
1127 "tool_id": "filtersam_mapped_and_unique",
1128 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1129 "tool_version": "1.01",
1130 "type": "tool",
1131 "user_outputs": []
1132 },
1133 "30": {
1134 "annotation": "",
1135 "id": 30,
1136 "input_connections": {
1137 "input_sam_file": {
1138 "id": 20,
1139 "output_name": "output"
1140 }
1141 },
1142 "inputs": [],
1143 "name": "filtersam_mapped_and_unique",
1144 "outputs": [
1145 {
1146 "name": "output_sam_file",
1147 "type": "sam"
1148 },
1149 {
1150 "name": "log_file",
1151 "type": "txt"
1152 }
1153 ],
1154 "position": {
1155 "left": 2091.75,
1156 "top": 827.75
1157 },
1158 "post_job_actions": {},
1159 "tool_errors": null,
1160 "tool_id": "filtersam_mapped_and_unique",
1161 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1162 "tool_version": "1.01",
1163 "type": "tool",
1164 "user_outputs": []
1165 },
1166 "31": {
1167 "annotation": "",
1168 "id": 31,
1169 "input_connections": {
1170 "input_sam_file": {
1171 "id": 21,
1172 "output_name": "output"
1173 }
1174 },
1175 "inputs": [],
1176 "name": "filtersam_mapped_and_unique",
1177 "outputs": [
1178 {
1179 "name": "output_sam_file",
1180 "type": "sam"
1181 },
1182 {
1183 "name": "log_file",
1184 "type": "txt"
1185 }
1186 ],
1187 "position": {
1188 "left": 2443.75,
1189 "top": 356.75
1190 },
1191 "post_job_actions": {},
1192 "tool_errors": null,
1193 "tool_id": "filtersam_mapped_and_unique",
1194 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1195 "tool_version": "1.01",
1196 "type": "tool",
1197 "user_outputs": []
1198 },
1199 "32": {
1200 "annotation": "",
1201 "id": 32,
1202 "input_connections": {
1203 "input_sam_file": {
1204 "id": 22,
1205 "output_name": "output"
1206 }
1207 },
1208 "inputs": [],
1209 "name": "filtersam_mapped_and_unique",
1210 "outputs": [
1211 {
1212 "name": "output_sam_file",
1213 "type": "sam"
1214 },
1215 {
1216 "name": "log_file",
1217 "type": "txt"
1218 }
1219 ],
1220 "position": {
1221 "left": 2438.75,
1222 "top": 596.75
1223 },
1224 "post_job_actions": {},
1225 "tool_errors": null,
1226 "tool_id": "filtersam_mapped_and_unique",
1227 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1228 "tool_version": "1.01",
1229 "type": "tool",
1230 "user_outputs": []
1231 },
1232 "33": {
1233 "annotation": "",
1234 "id": 33,
1235 "input_connections": {
1236 "input_sam_file": {
1237 "id": 23,
1238 "output_name": "output"
1239 }
1240 },
1241 "inputs": [],
1242 "name": "filtersam_mapped_and_unique",
1243 "outputs": [
1244 {
1245 "name": "output_sam_file",
1246 "type": "sam"
1247 },
1248 {
1249 "name": "log_file",
1250 "type": "txt"
1251 }
1252 ],
1253 "position": {
1254 "left": 2087.75,
1255 "top": 1046.75
1256 },
1257 "post_job_actions": {},
1258 "tool_errors": null,
1259 "tool_id": "filtersam_mapped_and_unique",
1260 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1261 "tool_version": "1.01",
1262 "type": "tool",
1263 "user_outputs": []
1264 },
1265 "34": {
1266 "annotation": "",
1267 "id": 34,
1268 "input_connections": {
1269 "input_sam_file": {
1270 "id": 24,
1271 "output_name": "output"
1272 }
1273 },
1274 "inputs": [],
1275 "name": "filtersam_mapped_and_unique",
1276 "outputs": [
1277 {
1278 "name": "output_sam_file",
1279 "type": "sam"
1280 },
1281 {
1282 "name": "log_file",
1283 "type": "txt"
1284 }
1285 ],
1286 "position": {
1287 "left": 2432.75,
1288 "top": 826.75
1289 },
1290 "post_job_actions": {},
1291 "tool_errors": null,
1292 "tool_id": "filtersam_mapped_and_unique",
1293 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1294 "tool_version": "1.01",
1295 "type": "tool",
1296 "user_outputs": []
1297 },
1298 "35": {
1299 "annotation": "",
1300 "id": 35,
1301 "input_connections": {
1302 "input_sam_file": {
1303 "id": 25,
1304 "output_name": "output"
1305 }
1306 },
1307 "inputs": [],
1308 "name": "filtersam_mapped_and_unique",
1309 "outputs": [
1310 {
1311 "name": "output_sam_file",
1312 "type": "sam"
1313 },
1314 {
1315 "name": "log_file",
1316 "type": "txt"
1317 }
1318 ],
1319 "position": {
1320 "left": 2089.75,
1321 "top": 1289.75
1322 },
1323 "post_job_actions": {},
1324 "tool_errors": null,
1325 "tool_id": "filtersam_mapped_and_unique",
1326 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1327 "tool_version": "1.01",
1328 "type": "tool",
1329 "user_outputs": []
1330 },
1331 "36": {
1332 "annotation": "",
1333 "id": 36,
1334 "input_connections": {
1335 "input_sam_file": {
1336 "id": 26,
1337 "output_name": "output"
1338 }
1339 },
1340 "inputs": [],
1341 "name": "filtersam_mapped_and_unique",
1342 "outputs": [
1343 {
1344 "name": "output_sam_file",
1345 "type": "sam"
1346 },
1347 {
1348 "name": "log_file",
1349 "type": "txt"
1350 }
1351 ],
1352 "position": {
1353 "left": 2436.75,
1354 "top": 1048.75
1355 },
1356 "post_job_actions": {},
1357 "tool_errors": null,
1358 "tool_id": "filtersam_mapped_and_unique",
1359 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1360 "tool_version": "1.01",
1361 "type": "tool",
1362 "user_outputs": []
1363 },
1364 "37": {
1365 "annotation": "",
1366 "id": 37,
1367 "input_connections": {
1368 "input_sam_file": {
1369 "id": 27,
1370 "output_name": "output"
1371 }
1372 },
1373 "inputs": [],
1374 "name": "filtersam_mapped_and_unique",
1375 "outputs": [
1376 {
1377 "name": "output_sam_file",
1378 "type": "sam"
1379 },
1380 {
1381 "name": "log_file",
1382 "type": "txt"
1383 }
1384 ],
1385 "position": {
1386 "left": 2437.75,
1387 "top": 1289.75
1388 },
1389 "post_job_actions": {},
1390 "tool_errors": null,
1391 "tool_id": "filtersam_mapped_and_unique",
1392 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
1393 "tool_version": "1.01",
1394 "type": "tool",
1395 "user_outputs": []
1396 },
1397 "38": {
1398 "annotation": "",
1399 "id": 38,
1400 "input_connections": {
1401 "input_files": [
1402 {
1403 "id": 37,
1404 "output_name": "output_sam_file"
1405 },
1406 {
1407 "id": 36,
1408 "output_name": "output_sam_file"
1409 },
1410 {
1411 "id": 35,
1412 "output_name": "output_sam_file"
1413 },
1414 {
1415 "id": 34,
1416 "output_name": "output_sam_file"
1417 },
1418 {
1419 "id": 33,
1420 "output_name": "output_sam_file"
1421 },
1422 {
1423 "id": 32,
1424 "output_name": "output_sam_file"
1425 },
1426 {
1427 "id": 31,
1428 "output_name": "output_sam_file"
1429 },
1430 {
1431 "id": 30,
1432 "output_name": "output_sam_file"
1433 },
1434 {
1435 "id": 29,
1436 "output_name": "output_sam_file"
1437 },
1438 {
1439 "id": 28,
1440 "output_name": "output_sam_file"
1441 }
1442 ]
1443 },
1444 "inputs": [],
1445 "name": "MergeSamFiles",
1446 "outputs": [
1447 {
1448 "name": "output_file",
1449 "type": "sam"
1450 }
1451 ],
1452 "position": {
1453 "left": 2900.25,
1454 "top": 806.75
1455 },
1456 "post_job_actions": {},
1457 "tool_errors": null,
1458 "tool_id": "MergeSamFiles",
1459 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}",
1460 "tool_version": "1.00",
1461 "type": "tool",
1462 "user_outputs": []
1463 },
1464 "39": {
1465 "annotation": "",
1466 "id": 39,
1467 "input_connections": {
1468 "source|input1": {
1469 "id": 38,
1470 "output_name": "output_file"
1471 },
1472 "source|ref_file": {
1473 "id": 2,
1474 "output_name": "output"
1475 }
1476 },
1477 "inputs": [],
1478 "name": "SAM-to-BAM",
1479 "outputs": [
1480 {
1481 "name": "output1",
1482 "type": "bam"
1483 }
1484 ],
1485 "position": {
1486 "left": 3233.25,
1487 "top": 807.75
1488 },
1489 "post_job_actions": {},
1490 "tool_errors": null,
1491 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
1492 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
1493 "tool_version": "1.1.4",
1494 "type": "tool",
1495 "user_outputs": []
1496 },
1497 "40": {
1498 "annotation": "",
1499 "id": 40,
1500 "input_connections": {
1501 "reference_source|input_bams_0|input_bam": {
1502 "id": 39,
1503 "output_name": "output1"
1504 },
1505 "reference_source|ref_file": {
1506 "id": 2,
1507 "output_name": "output"
1508 }
1509 },
1510 "inputs": [],
1511 "name": "MPileup",
1512 "outputs": [
1513 {
1514 "name": "output_mpileup",
1515 "type": "pileup"
1516 },
1517 {
1518 "name": "output_log",
1519 "type": "txt"
1520 }
1521 ],
1522 "position": {
1523 "left": 3462.25,
1524 "top": 809.75
1525 },
1526 "post_job_actions": {},
1527 "tool_errors": null,
1528 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
1529 "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"0\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\"}",
1530 "tool_version": "0.0.3",
1531 "type": "tool",
1532 "user_outputs": []
1533 },
1534 "41": {
1535 "annotation": "",
1536 "id": 41,
1537 "input_connections": {
1538 "input_pileup_file": {
1539 "id": 40,
1540 "output_name": "output_mpileup"
1541 }
1542 },
1543 "inputs": [],
1544 "name": "PileupVariant",
1545 "outputs": [
1546 {
1547 "name": "output_pileup_file",
1548 "type": "pileup"
1549 },
1550 {
1551 "name": "log_file",
1552 "type": "txt"
1553 }
1554 ],
1555 "position": {
1556 "left": 3743.25,
1557 "top": 901.75
1558 },
1559 "post_job_actions": {},
1560 "tool_errors": null,
1561 "tool_id": "PileupVariant",
1562 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_pileup_file\": \"null\"}",
1563 "tool_version": "1.01",
1564 "type": "tool",
1565 "user_outputs": []
1566 },
1567 "42": {
1568 "annotation": "",
1569 "id": 42,
1570 "input_connections": {
1571 "input_list1": {
1572 "id": 41,
1573 "output_name": "output_pileup_file"
1574 },
1575 "input_list2": {
1576 "id": 3,
1577 "output_name": "output"
1578 }
1579 },
1580 "inputs": [],
1581 "name": "listfiltering",
1582 "outputs": [
1583 {
1584 "name": "output_file",
1585 "type": "pileup"
1586 },
1587 {
1588 "name": "log_file",
1589 "type": "txt"
1590 }
1591 ],
1592 "position": {
1593 "left": 4107.25,
1594 "top": 905.75
1595 },
1596 "post_job_actions": {},
1597 "tool_errors": null,
1598 "tool_id": "listfiltering",
1599 "tool_state": "{\"__page__\": 0, \"input_list2\": \"null\", \"input_list1\": \"null\", \"__rerun_remap_job_id__\": null, \"nb_col\": \"\\\"2\\\"\", \"type\": \"\\\"specific\\\"\"}",
1600 "tool_version": "1.01",
1601 "type": "tool",
1602 "user_outputs": []
1603 },
1604 "43": {
1605 "annotation": "",
1606 "id": 43,
1607 "input_connections": {
1608 "input_file": {
1609 "id": 42,
1610 "output_name": "output_file"
1611 }
1612 },
1613 "inputs": [],
1614 "name": "SplitFile10x",
1615 "outputs": [
1616 {
1617 "name": "output_file1",
1618 "type": "txt"
1619 },
1620 {
1621 "name": "output_file2",
1622 "type": "txt"
1623 },
1624 {
1625 "name": "output_file3",
1626 "type": "txt"
1627 },
1628 {
1629 "name": "output_file4",
1630 "type": "txt"
1631 },
1632 {
1633 "name": "output_file5",
1634 "type": "txt"
1635 },
1636 {
1637 "name": "output_file6",
1638 "type": "txt"
1639 },
1640 {
1641 "name": "output_file7",
1642 "type": "txt"
1643 },
1644 {
1645 "name": "output_file8",
1646 "type": "txt"
1647 },
1648 {
1649 "name": "output_file9",
1650 "type": "txt"
1651 },
1652 {
1653 "name": "output_file10",
1654 "type": "txt"
1655 }
1656 ],
1657 "position": {
1658 "left": 4405.25,
1659 "top": 635.75
1660 },
1661 "post_job_actions": {},
1662 "tool_errors": null,
1663 "tool_id": "SplitFile10x",
1664 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
1665 "tool_version": "1.00",
1666 "type": "tool",
1667 "user_outputs": []
1668 },
1669 "44": {
1670 "annotation": "",
1671 "id": 44,
1672 "input_connections": {
1673 "input_assembly_file": {
1674 "id": 2,
1675 "output_name": "output"
1676 },
1677 "input_variant_file": {
1678 "id": 43,
1679 "output_name": "output_file1"
1680 }
1681 },
1682 "inputs": [],
1683 "name": "extractseq",
1684 "outputs": [
1685 {
1686 "name": "output_file",
1687 "type": "fasta"
1688 }
1689 ],
1690 "position": {
1691 "left": 4738.25,
1692 "top": 471.75
1693 },
1694 "post_job_actions": {},
1695 "tool_errors": null,
1696 "tool_id": "extractseq",
1697 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1698 "tool_version": "1.01",
1699 "type": "tool",
1700 "user_outputs": []
1701 },
1702 "45": {
1703 "annotation": "",
1704 "id": 45,
1705 "input_connections": {
1706 "input_assembly_file": {
1707 "id": 2,
1708 "output_name": "output"
1709 },
1710 "input_variant_file": {
1711 "id": 43,
1712 "output_name": "output_file2"
1713 }
1714 },
1715 "inputs": [],
1716 "name": "extractseq",
1717 "outputs": [
1718 {
1719 "name": "output_file",
1720 "type": "fasta"
1721 }
1722 ],
1723 "position": {
1724 "left": 4739.25,
1725 "top": 655.75
1726 },
1727 "post_job_actions": {},
1728 "tool_errors": null,
1729 "tool_id": "extractseq",
1730 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1731 "tool_version": "1.01",
1732 "type": "tool",
1733 "user_outputs": []
1734 },
1735 "46": {
1736 "annotation": "",
1737 "id": 46,
1738 "input_connections": {
1739 "input_assembly_file": {
1740 "id": 2,
1741 "output_name": "output"
1742 },
1743 "input_variant_file": {
1744 "id": 43,
1745 "output_name": "output_file3"
1746 }
1747 },
1748 "inputs": [],
1749 "name": "extractseq",
1750 "outputs": [
1751 {
1752 "name": "output_file",
1753 "type": "fasta"
1754 }
1755 ],
1756 "position": {
1757 "left": 4733.25,
1758 "top": 855.75
1759 },
1760 "post_job_actions": {},
1761 "tool_errors": null,
1762 "tool_id": "extractseq",
1763 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1764 "tool_version": "1.01",
1765 "type": "tool",
1766 "user_outputs": []
1767 },
1768 "47": {
1769 "annotation": "",
1770 "id": 47,
1771 "input_connections": {
1772 "input_assembly_file": {
1773 "id": 2,
1774 "output_name": "output"
1775 },
1776 "input_variant_file": {
1777 "id": 43,
1778 "output_name": "output_file4"
1779 }
1780 },
1781 "inputs": [],
1782 "name": "extractseq",
1783 "outputs": [
1784 {
1785 "name": "output_file",
1786 "type": "fasta"
1787 }
1788 ],
1789 "position": {
1790 "left": 4737.25,
1791 "top": 1051.75
1792 },
1793 "post_job_actions": {},
1794 "tool_errors": null,
1795 "tool_id": "extractseq",
1796 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1797 "tool_version": "1.01",
1798 "type": "tool",
1799 "user_outputs": []
1800 },
1801 "48": {
1802 "annotation": "",
1803 "id": 48,
1804 "input_connections": {
1805 "input_assembly_file": {
1806 "id": 2,
1807 "output_name": "output"
1808 },
1809 "input_variant_file": {
1810 "id": 43,
1811 "output_name": "output_file5"
1812 }
1813 },
1814 "inputs": [],
1815 "name": "extractseq",
1816 "outputs": [
1817 {
1818 "name": "output_file",
1819 "type": "fasta"
1820 }
1821 ],
1822 "position": {
1823 "left": 4742.25,
1824 "top": 1228.75
1825 },
1826 "post_job_actions": {},
1827 "tool_errors": null,
1828 "tool_id": "extractseq",
1829 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1830 "tool_version": "1.01",
1831 "type": "tool",
1832 "user_outputs": []
1833 },
1834 "49": {
1835 "annotation": "",
1836 "id": 49,
1837 "input_connections": {
1838 "input_assembly_file": {
1839 "id": 2,
1840 "output_name": "output"
1841 },
1842 "input_variant_file": {
1843 "id": 43,
1844 "output_name": "output_file6"
1845 }
1846 },
1847 "inputs": [],
1848 "name": "extractseq",
1849 "outputs": [
1850 {
1851 "name": "output_file",
1852 "type": "fasta"
1853 }
1854 ],
1855 "position": {
1856 "left": 5066.25,
1857 "top": 474.75
1858 },
1859 "post_job_actions": {},
1860 "tool_errors": null,
1861 "tool_id": "extractseq",
1862 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1863 "tool_version": "1.01",
1864 "type": "tool",
1865 "user_outputs": []
1866 },
1867 "50": {
1868 "annotation": "",
1869 "id": 50,
1870 "input_connections": {
1871 "input_assembly_file": {
1872 "id": 2,
1873 "output_name": "output"
1874 },
1875 "input_variant_file": {
1876 "id": 43,
1877 "output_name": "output_file7"
1878 }
1879 },
1880 "inputs": [],
1881 "name": "extractseq",
1882 "outputs": [
1883 {
1884 "name": "output_file",
1885 "type": "fasta"
1886 }
1887 ],
1888 "position": {
1889 "left": 5069.25,
1890 "top": 656.75
1891 },
1892 "post_job_actions": {},
1893 "tool_errors": null,
1894 "tool_id": "extractseq",
1895 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1896 "tool_version": "1.01",
1897 "type": "tool",
1898 "user_outputs": []
1899 },
1900 "51": {
1901 "annotation": "",
1902 "id": 51,
1903 "input_connections": {
1904 "input_assembly_file": {
1905 "id": 2,
1906 "output_name": "output"
1907 },
1908 "input_variant_file": {
1909 "id": 43,
1910 "output_name": "output_file8"
1911 }
1912 },
1913 "inputs": [],
1914 "name": "extractseq",
1915 "outputs": [
1916 {
1917 "name": "output_file",
1918 "type": "fasta"
1919 }
1920 ],
1921 "position": {
1922 "left": 5073.25,
1923 "top": 858.75
1924 },
1925 "post_job_actions": {},
1926 "tool_errors": null,
1927 "tool_id": "extractseq",
1928 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1929 "tool_version": "1.01",
1930 "type": "tool",
1931 "user_outputs": []
1932 },
1933 "52": {
1934 "annotation": "",
1935 "id": 52,
1936 "input_connections": {
1937 "input_assembly_file": {
1938 "id": 2,
1939 "output_name": "output"
1940 },
1941 "input_variant_file": {
1942 "id": 43,
1943 "output_name": "output_file9"
1944 }
1945 },
1946 "inputs": [],
1947 "name": "extractseq",
1948 "outputs": [
1949 {
1950 "name": "output_file",
1951 "type": "fasta"
1952 }
1953 ],
1954 "position": {
1955 "left": 5071.25,
1956 "top": 1046.75
1957 },
1958 "post_job_actions": {},
1959 "tool_errors": null,
1960 "tool_id": "extractseq",
1961 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1962 "tool_version": "1.01",
1963 "type": "tool",
1964 "user_outputs": []
1965 },
1966 "53": {
1967 "annotation": "",
1968 "id": 53,
1969 "input_connections": {
1970 "input_assembly_file": {
1971 "id": 2,
1972 "output_name": "output"
1973 },
1974 "input_variant_file": {
1975 "id": 43,
1976 "output_name": "output_file10"
1977 }
1978 },
1979 "inputs": [],
1980 "name": "extractseq",
1981 "outputs": [
1982 {
1983 "name": "output_file",
1984 "type": "fasta"
1985 }
1986 ],
1987 "position": {
1988 "left": 5078.25,
1989 "top": 1229.75
1990 },
1991 "post_job_actions": {},
1992 "tool_errors": null,
1993 "tool_id": "extractseq",
1994 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1995 "tool_version": "1.01",
1996 "type": "tool",
1997 "user_outputs": []
1998 },
1999 "54": {
2000 "annotation": "",
2001 "id": 54,
2002 "input_connections": {
2003 "db_opts|histdb": {
2004 "id": 17,
2005 "output_name": "outfile"
2006 },
2007 "query": {
2008 "id": 44,
2009 "output_name": "output_file"
2010 }
2011 },
2012 "inputs": [],
2013 "name": "NCBI BLAST+ blastn",
2014 "outputs": [
2015 {
2016 "name": "output1",
2017 "type": "tabular"
2018 }
2019 ],
2020 "position": {
2021 "left": 5398.75,
2022 "top": 475.75
2023 },
2024 "post_job_actions": {},
2025 "tool_errors": null,
2026 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2027 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2028 "tool_version": "0.1.00",
2029 "type": "tool",
2030 "user_outputs": []
2031 },
2032 "55": {
2033 "annotation": "",
2034 "id": 55,
2035 "input_connections": {
2036 "db_opts|histdb": {
2037 "id": 17,
2038 "output_name": "outfile"
2039 },
2040 "query": {
2041 "id": 45,
2042 "output_name": "output_file"
2043 }
2044 },
2045 "inputs": [],
2046 "name": "NCBI BLAST+ blastn",
2047 "outputs": [
2048 {
2049 "name": "output1",
2050 "type": "tabular"
2051 }
2052 ],
2053 "position": {
2054 "left": 5395.75,
2055 "top": 656.75
2056 },
2057 "post_job_actions": {},
2058 "tool_errors": null,
2059 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2060 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2061 "tool_version": "0.1.00",
2062 "type": "tool",
2063 "user_outputs": []
2064 },
2065 "56": {
2066 "annotation": "",
2067 "id": 56,
2068 "input_connections": {
2069 "db_opts|histdb": {
2070 "id": 17,
2071 "output_name": "outfile"
2072 },
2073 "query": {
2074 "id": 46,
2075 "output_name": "output_file"
2076 }
2077 },
2078 "inputs": [],
2079 "name": "NCBI BLAST+ blastn",
2080 "outputs": [
2081 {
2082 "name": "output1",
2083 "type": "tabular"
2084 }
2085 ],
2086 "position": {
2087 "left": 5391.75,
2088 "top": 860.75
2089 },
2090 "post_job_actions": {},
2091 "tool_errors": null,
2092 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2093 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2094 "tool_version": "0.1.00",
2095 "type": "tool",
2096 "user_outputs": []
2097 },
2098 "57": {
2099 "annotation": "",
2100 "id": 57,
2101 "input_connections": {
2102 "db_opts|histdb": {
2103 "id": 17,
2104 "output_name": "outfile"
2105 },
2106 "query": {
2107 "id": 47,
2108 "output_name": "output_file"
2109 }
2110 },
2111 "inputs": [],
2112 "name": "NCBI BLAST+ blastn",
2113 "outputs": [
2114 {
2115 "name": "output1",
2116 "type": "tabular"
2117 }
2118 ],
2119 "position": {
2120 "left": 5389.75,
2121 "top": 1051.75
2122 },
2123 "post_job_actions": {},
2124 "tool_errors": null,
2125 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2126 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2127 "tool_version": "0.1.00",
2128 "type": "tool",
2129 "user_outputs": []
2130 },
2131 "58": {
2132 "annotation": "",
2133 "id": 58,
2134 "input_connections": {
2135 "db_opts|histdb": {
2136 "id": 17,
2137 "output_name": "outfile"
2138 },
2139 "query": {
2140 "id": 48,
2141 "output_name": "output_file"
2142 }
2143 },
2144 "inputs": [],
2145 "name": "NCBI BLAST+ blastn",
2146 "outputs": [
2147 {
2148 "name": "output1",
2149 "type": "tabular"
2150 }
2151 ],
2152 "position": {
2153 "left": 5397.75,
2154 "top": 1237.75
2155 },
2156 "post_job_actions": {},
2157 "tool_errors": null,
2158 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2159 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2160 "tool_version": "0.1.00",
2161 "type": "tool",
2162 "user_outputs": []
2163 },
2164 "59": {
2165 "annotation": "",
2166 "id": 59,
2167 "input_connections": {
2168 "db_opts|histdb": {
2169 "id": 17,
2170 "output_name": "outfile"
2171 },
2172 "query": {
2173 "id": 48,
2174 "output_name": "output_file"
2175 }
2176 },
2177 "inputs": [],
2178 "name": "NCBI BLAST+ blastn",
2179 "outputs": [
2180 {
2181 "name": "output1",
2182 "type": "tabular"
2183 }
2184 ],
2185 "position": {
2186 "left": 5684.75,
2187 "top": 1231.75
2188 },
2189 "post_job_actions": {},
2190 "tool_errors": null,
2191 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2192 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2193 "tool_version": "0.1.00",
2194 "type": "tool",
2195 "user_outputs": []
2196 },
2197 "60": {
2198 "annotation": "",
2199 "id": 60,
2200 "input_connections": {
2201 "db_opts|histdb": {
2202 "id": 17,
2203 "output_name": "outfile"
2204 },
2205 "query": {
2206 "id": 49,
2207 "output_name": "output_file"
2208 }
2209 },
2210 "inputs": [],
2211 "name": "NCBI BLAST+ blastn",
2212 "outputs": [
2213 {
2214 "name": "output1",
2215 "type": "tabular"
2216 }
2217 ],
2218 "position": {
2219 "left": 5676.75,
2220 "top": 476.75
2221 },
2222 "post_job_actions": {},
2223 "tool_errors": null,
2224 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2225 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2226 "tool_version": "0.1.00",
2227 "type": "tool",
2228 "user_outputs": []
2229 },
2230 "61": {
2231 "annotation": "",
2232 "id": 61,
2233 "input_connections": {
2234 "db_opts|histdb": {
2235 "id": 17,
2236 "output_name": "outfile"
2237 },
2238 "query": {
2239 "id": 50,
2240 "output_name": "output_file"
2241 }
2242 },
2243 "inputs": [],
2244 "name": "NCBI BLAST+ blastn",
2245 "outputs": [
2246 {
2247 "name": "output1",
2248 "type": "tabular"
2249 }
2250 ],
2251 "position": {
2252 "left": 5681.75,
2253 "top": 657.75
2254 },
2255 "post_job_actions": {},
2256 "tool_errors": null,
2257 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2258 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2259 "tool_version": "0.1.00",
2260 "type": "tool",
2261 "user_outputs": []
2262 },
2263 "62": {
2264 "annotation": "",
2265 "id": 62,
2266 "input_connections": {
2267 "db_opts|histdb": {
2268 "id": 17,
2269 "output_name": "outfile"
2270 },
2271 "query": {
2272 "id": 51,
2273 "output_name": "output_file"
2274 }
2275 },
2276 "inputs": [],
2277 "name": "NCBI BLAST+ blastn",
2278 "outputs": [
2279 {
2280 "name": "output1",
2281 "type": "tabular"
2282 }
2283 ],
2284 "position": {
2285 "left": 5688.75,
2286 "top": 862.75
2287 },
2288 "post_job_actions": {},
2289 "tool_errors": null,
2290 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2291 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2292 "tool_version": "0.1.00",
2293 "type": "tool",
2294 "user_outputs": []
2295 },
2296 "63": {
2297 "annotation": "",
2298 "id": 63,
2299 "input_connections": {
2300 "db_opts|histdb": {
2301 "id": 17,
2302 "output_name": "outfile"
2303 },
2304 "query": {
2305 "id": 52,
2306 "output_name": "output_file"
2307 }
2308 },
2309 "inputs": [],
2310 "name": "NCBI BLAST+ blastn",
2311 "outputs": [
2312 {
2313 "name": "output1",
2314 "type": "tabular"
2315 }
2316 ],
2317 "position": {
2318 "left": 5688.75,
2319 "top": 1056.75
2320 },
2321 "post_job_actions": {},
2322 "tool_errors": null,
2323 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
2324 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
2325 "tool_version": "0.1.00",
2326 "type": "tool",
2327 "user_outputs": []
2328 },
2329 "64": {
2330 "annotation": "",
2331 "id": 64,
2332 "input_connections": {
2333 "input_blast_file": {
2334 "id": 54,
2335 "output_name": "output1"
2336 },
2337 "input_variant_file": {
2338 "id": 43,
2339 "output_name": "output_file1"
2340 }
2341 },
2342 "inputs": [],
2343 "name": "ParseBlastForUniqueMatch",
2344 "outputs": [
2345 {
2346 "name": "output_variant_file",
2347 "type": "pileup"
2348 },
2349 {
2350 "name": "log_file",
2351 "type": "txt"
2352 }
2353 ],
2354 "position": {
2355 "left": 6013.25,
2356 "top": 432.75
2357 },
2358 "post_job_actions": {},
2359 "tool_errors": null,
2360 "tool_id": "ParseBlastForUniqueMatch",
2361 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2362 "tool_version": "1.01",
2363 "type": "tool",
2364 "user_outputs": []
2365 },
2366 "65": {
2367 "annotation": "",
2368 "id": 65,
2369 "input_connections": {
2370 "input_blast_file": {
2371 "id": 55,
2372 "output_name": "output1"
2373 },
2374 "input_variant_file": {
2375 "id": 43,
2376 "output_name": "output_file2"
2377 }
2378 },
2379 "inputs": [],
2380 "name": "ParseBlastForUniqueMatch",
2381 "outputs": [
2382 {
2383 "name": "output_variant_file",
2384 "type": "pileup"
2385 },
2386 {
2387 "name": "log_file",
2388 "type": "txt"
2389 }
2390 ],
2391 "position": {
2392 "left": 6010.25,
2393 "top": 656.75
2394 },
2395 "post_job_actions": {},
2396 "tool_errors": null,
2397 "tool_id": "ParseBlastForUniqueMatch",
2398 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2399 "tool_version": "1.01",
2400 "type": "tool",
2401 "user_outputs": []
2402 },
2403 "66": {
2404 "annotation": "",
2405 "id": 66,
2406 "input_connections": {
2407 "input_blast_file": {
2408 "id": 56,
2409 "output_name": "output1"
2410 },
2411 "input_variant_file": {
2412 "id": 43,
2413 "output_name": "output_file3"
2414 }
2415 },
2416 "inputs": [],
2417 "name": "ParseBlastForUniqueMatch",
2418 "outputs": [
2419 {
2420 "name": "output_variant_file",
2421 "type": "pileup"
2422 },
2423 {
2424 "name": "log_file",
2425 "type": "txt"
2426 }
2427 ],
2428 "position": {
2429 "left": 6014.25,
2430 "top": 891.75
2431 },
2432 "post_job_actions": {},
2433 "tool_errors": null,
2434 "tool_id": "ParseBlastForUniqueMatch",
2435 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2436 "tool_version": "1.01",
2437 "type": "tool",
2438 "user_outputs": []
2439 },
2440 "67": {
2441 "annotation": "",
2442 "id": 67,
2443 "input_connections": {
2444 "input_blast_file": {
2445 "id": 57,
2446 "output_name": "output1"
2447 },
2448 "input_variant_file": {
2449 "id": 43,
2450 "output_name": "output_file4"
2451 }
2452 },
2453 "inputs": [],
2454 "name": "ParseBlastForUniqueMatch",
2455 "outputs": [
2456 {
2457 "name": "output_variant_file",
2458 "type": "pileup"
2459 },
2460 {
2461 "name": "log_file",
2462 "type": "txt"
2463 }
2464 ],
2465 "position": {
2466 "left": 6014.25,
2467 "top": 1120.75
2468 },
2469 "post_job_actions": {},
2470 "tool_errors": null,
2471 "tool_id": "ParseBlastForUniqueMatch",
2472 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2473 "tool_version": "1.01",
2474 "type": "tool",
2475 "user_outputs": []
2476 },
2477 "68": {
2478 "annotation": "",
2479 "id": 68,
2480 "input_connections": {
2481 "input_blast_file": {
2482 "id": 58,
2483 "output_name": "output1"
2484 },
2485 "input_variant_file": {
2486 "id": 43,
2487 "output_name": "output_file5"
2488 }
2489 },
2490 "inputs": [],
2491 "name": "ParseBlastForUniqueMatch",
2492 "outputs": [
2493 {
2494 "name": "output_variant_file",
2495 "type": "pileup"
2496 },
2497 {
2498 "name": "log_file",
2499 "type": "txt"
2500 }
2501 ],
2502 "position": {
2503 "left": 6013.25,
2504 "top": 1352.75
2505 },
2506 "post_job_actions": {},
2507 "tool_errors": null,
2508 "tool_id": "ParseBlastForUniqueMatch",
2509 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2510 "tool_version": "1.01",
2511 "type": "tool",
2512 "user_outputs": []
2513 },
2514 "69": {
2515 "annotation": "",
2516 "id": 69,
2517 "input_connections": {
2518 "input_blast_file": {
2519 "id": 59,
2520 "output_name": "output1"
2521 },
2522 "input_variant_file": {
2523 "id": 43,
2524 "output_name": "output_file10"
2525 }
2526 },
2527 "inputs": [],
2528 "name": "ParseBlastForUniqueMatch",
2529 "outputs": [
2530 {
2531 "name": "output_variant_file",
2532 "type": "pileup"
2533 },
2534 {
2535 "name": "log_file",
2536 "type": "txt"
2537 }
2538 ],
2539 "position": {
2540 "left": 6313.25,
2541 "top": 1356.75
2542 },
2543 "post_job_actions": {},
2544 "tool_errors": null,
2545 "tool_id": "ParseBlastForUniqueMatch",
2546 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2547 "tool_version": "1.01",
2548 "type": "tool",
2549 "user_outputs": []
2550 },
2551 "70": {
2552 "annotation": "",
2553 "id": 70,
2554 "input_connections": {
2555 "input_blast_file": {
2556 "id": 60,
2557 "output_name": "output1"
2558 },
2559 "input_variant_file": {
2560 "id": 43,
2561 "output_name": "output_file6"
2562 }
2563 },
2564 "inputs": [],
2565 "name": "ParseBlastForUniqueMatch",
2566 "outputs": [
2567 {
2568 "name": "output_variant_file",
2569 "type": "pileup"
2570 },
2571 {
2572 "name": "log_file",
2573 "type": "txt"
2574 }
2575 ],
2576 "position": {
2577 "left": 6300.25,
2578 "top": 428.75
2579 },
2580 "post_job_actions": {},
2581 "tool_errors": null,
2582 "tool_id": "ParseBlastForUniqueMatch",
2583 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2584 "tool_version": "1.01",
2585 "type": "tool",
2586 "user_outputs": []
2587 },
2588 "71": {
2589 "annotation": "",
2590 "id": 71,
2591 "input_connections": {
2592 "input_blast_file": {
2593 "id": 61,
2594 "output_name": "output1"
2595 },
2596 "input_variant_file": {
2597 "id": 43,
2598 "output_name": "output_file7"
2599 }
2600 },
2601 "inputs": [],
2602 "name": "ParseBlastForUniqueMatch",
2603 "outputs": [
2604 {
2605 "name": "output_variant_file",
2606 "type": "pileup"
2607 },
2608 {
2609 "name": "log_file",
2610 "type": "txt"
2611 }
2612 ],
2613 "position": {
2614 "left": 6302.25,
2615 "top": 657.75
2616 },
2617 "post_job_actions": {},
2618 "tool_errors": null,
2619 "tool_id": "ParseBlastForUniqueMatch",
2620 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2621 "tool_version": "1.01",
2622 "type": "tool",
2623 "user_outputs": []
2624 },
2625 "72": {
2626 "annotation": "",
2627 "id": 72,
2628 "input_connections": {
2629 "input_blast_file": {
2630 "id": 62,
2631 "output_name": "output1"
2632 },
2633 "input_variant_file": {
2634 "id": 43,
2635 "output_name": "output_file8"
2636 }
2637 },
2638 "inputs": [],
2639 "name": "ParseBlastForUniqueMatch",
2640 "outputs": [
2641 {
2642 "name": "output_variant_file",
2643 "type": "pileup"
2644 },
2645 {
2646 "name": "log_file",
2647 "type": "txt"
2648 }
2649 ],
2650 "position": {
2651 "left": 6304.25,
2652 "top": 893.75
2653 },
2654 "post_job_actions": {},
2655 "tool_errors": null,
2656 "tool_id": "ParseBlastForUniqueMatch",
2657 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2658 "tool_version": "1.01",
2659 "type": "tool",
2660 "user_outputs": []
2661 },
2662 "73": {
2663 "annotation": "",
2664 "id": 73,
2665 "input_connections": {
2666 "input_blast_file": {
2667 "id": 63,
2668 "output_name": "output1"
2669 },
2670 "input_variant_file": {
2671 "id": 43,
2672 "output_name": "output_file9"
2673 }
2674 },
2675 "inputs": [],
2676 "name": "ParseBlastForUniqueMatch",
2677 "outputs": [
2678 {
2679 "name": "output_variant_file",
2680 "type": "pileup"
2681 },
2682 {
2683 "name": "log_file",
2684 "type": "txt"
2685 }
2686 ],
2687 "position": {
2688 "left": 6306.25,
2689 "top": 1124.75
2690 },
2691 "post_job_actions": {},
2692 "tool_errors": null,
2693 "tool_id": "ParseBlastForUniqueMatch",
2694 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
2695 "tool_version": "1.01",
2696 "type": "tool",
2697 "user_outputs": []
2698 },
2699 "74": {
2700 "annotation": "",
2701 "id": 74,
2702 "input_connections": {
2703 "input_files": [
2704 {
2705 "id": 64,
2706 "output_name": "output_variant_file"
2707 },
2708 {
2709 "id": 65,
2710 "output_name": "output_variant_file"
2711 },
2712 {
2713 "id": 66,
2714 "output_name": "output_variant_file"
2715 },
2716 {
2717 "id": 67,
2718 "output_name": "output_variant_file"
2719 },
2720 {
2721 "id": 68,
2722 "output_name": "output_variant_file"
2723 },
2724 {
2725 "id": 70,
2726 "output_name": "output_variant_file"
2727 },
2728 {
2729 "id": 71,
2730 "output_name": "output_variant_file"
2731 },
2732 {
2733 "id": 72,
2734 "output_name": "output_variant_file"
2735 },
2736 {
2737 "id": 73,
2738 "output_name": "output_variant_file"
2739 },
2740 {
2741 "id": 69,
2742 "output_name": "output_variant_file"
2743 }
2744 ]
2745 },
2746 "inputs": [],
2747 "name": "MergeMultiFile",
2748 "outputs": [
2749 {
2750 "name": "output_file",
2751 "type": "txt"
2752 }
2753 ],
2754 "position": {
2755 "left": 6737.25,
2756 "top": 872.75
2757 },
2758 "post_job_actions": {},
2759 "tool_errors": null,
2760 "tool_id": "MergeMultiFile",
2761 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}",
2762 "tool_version": "1.00",
2763 "type": "tool",
2764 "user_outputs": []
2765 },
2766 "75": {
2767 "annotation": "",
2768 "id": 75,
2769 "input_connections": {
2770 "input_file": {
2771 "id": 74,
2772 "output_name": "output_file"
2773 }
2774 },
2775 "inputs": [],
2776 "name": "mpileupfilterandstat",
2777 "outputs": [
2778 {
2779 "name": "output_file",
2780 "type": "pileup"
2781 },
2782 {
2783 "name": "log_file",
2784 "type": "txt"
2785 }
2786 ],
2787 "position": {
2788 "left": 7105.75,
2789 "top": 903.75
2790 },
2791 "post_job_actions": {},
2792 "tool_errors": null,
2793 "tool_id": "mpileupfilterandstat",
2794 "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"4\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"20\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"4\\\", \\\"stat_max_depth_min\\\": \\\"200\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.2\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.0\\\"\", \"min_depth\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"500\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
2795 "tool_version": "1.00",
2796 "type": "tool",
2797 "user_outputs": []
2798 },
2799 "76": {
2800 "annotation": "",
2801 "id": 76,
2802 "input_connections": {
2803 "input_files": [
2804 {
2805 "id": 7,
2806 "output_name": "log_file"
2807 },
2808 {
2809 "id": 8,
2810 "output_name": "log_file"
2811 },
2812 {
2813 "id": 9,
2814 "output_name": "log_file"
2815 },
2816 {
2817 "id": 12,
2818 "output_name": "log_file"
2819 },
2820 {
2821 "id": 14,
2822 "output_name": "log_file"
2823 },
2824 {
2825 "id": 10,
2826 "output_name": "log_file"
2827 },
2828 {
2829 "id": 11,
2830 "output_name": "log_file"
2831 },
2832 {
2833 "id": 13,
2834 "output_name": "log_file"
2835 },
2836 {
2837 "id": 15,
2838 "output_name": "log_file"
2839 },
2840 {
2841 "id": 16,
2842 "output_name": "log_file"
2843 },
2844 {
2845 "id": 28,
2846 "output_name": "log_file"
2847 },
2848 {
2849 "id": 29,
2850 "output_name": "log_file"
2851 },
2852 {
2853 "id": 30,
2854 "output_name": "log_file"
2855 },
2856 {
2857 "id": 33,
2858 "output_name": "log_file"
2859 },
2860 {
2861 "id": 35,
2862 "output_name": "log_file"
2863 },
2864 {
2865 "id": 31,
2866 "output_name": "log_file"
2867 },
2868 {
2869 "id": 32,
2870 "output_name": "log_file"
2871 },
2872 {
2873 "id": 34,
2874 "output_name": "log_file"
2875 },
2876 {
2877 "id": 36,
2878 "output_name": "log_file"
2879 },
2880 {
2881 "id": 37,
2882 "output_name": "log_file"
2883 },
2884 {
2885 "id": 41,
2886 "output_name": "log_file"
2887 },
2888 {
2889 "id": 42,
2890 "output_name": "log_file"
2891 },
2892 {
2893 "id": 64,
2894 "output_name": "log_file"
2895 },
2896 {
2897 "id": 65,
2898 "output_name": "log_file"
2899 },
2900 {
2901 "id": 66,
2902 "output_name": "log_file"
2903 },
2904 {
2905 "id": 67,
2906 "output_name": "log_file"
2907 },
2908 {
2909 "id": 68,
2910 "output_name": "log_file"
2911 },
2912 {
2913 "id": 70,
2914 "output_name": "log_file"
2915 },
2916 {
2917 "id": 71,
2918 "output_name": "log_file"
2919 },
2920 {
2921 "id": 72,
2922 "output_name": "log_file"
2923 },
2924 {
2925 "id": 73,
2926 "output_name": "log_file"
2927 },
2928 {
2929 "id": 69,
2930 "output_name": "log_file"
2931 },
2932 {
2933 "id": 75,
2934 "output_name": "log_file"
2935 }
2936 ]
2937 },
2938 "inputs": [],
2939 "name": "MergeMultiFile",
2940 "outputs": [
2941 {
2942 "name": "output_file",
2943 "type": "txt"
2944 }
2945 ],
2946 "position": {
2947 "left": 7458.25,
2948 "top": 1140.75
2949 },
2950 "post_job_actions": {
2951 "RenameDatasetActionoutput_file": {
2952 "action_arguments": {
2953 "newname": "LOGS"
2954 },
2955 "action_type": "RenameDatasetAction",
2956 "output_name": "output_file"
2957 }
2958 },
2959 "tool_errors": null,
2960 "tool_id": "MergeMultiFile",
2961 "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}",
2962 "tool_version": "1.00",
2963 "type": "tool",
2964 "user_outputs": []
2965 }
2966 }
2967 }