comparison rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_4x.ga @ 1:7f36bd129321 draft

Uploaded
author mcharles
date Wed, 10 Sep 2014 10:24:01 -0400
parents
children
comparison
equal deleted inserted replaced
0:442a7c88b886 1:7f36bd129321
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "rapsosnp v1.15 - 4x",
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": 214.7666015625,
21 "top": 723
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": 219.7666015625,
44 "top": 1105
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": 2639.7666015625,
67 "top": 587
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": "DUBIUS"
84 }
85 ],
86 "name": "Input dataset",
87 "outputs": [],
88 "position": {
89 "left": 2449.7666015625,
90 "top": 1405
91 },
92 "tool_errors": null,
93 "tool_id": null,
94 "tool_state": "{\"name\": \"DUBIUS\"}",
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": "SplitFile4x",
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 "position": {
129 "left": 516.7666015625,
130 "top": 602.5
131 },
132 "post_job_actions": {},
133 "tool_errors": null,
134 "tool_id": "SplitFile4x",
135 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
136 "tool_version": "0.01",
137 "type": "tool",
138 "user_outputs": []
139 },
140 "5": {
141 "annotation": "",
142 "id": 5,
143 "input_connections": {
144 "input_file": {
145 "id": 1,
146 "output_name": "output"
147 }
148 },
149 "inputs": [],
150 "name": "SplitFile4x",
151 "outputs": [
152 {
153 "name": "output_file1",
154 "type": "txt"
155 },
156 {
157 "name": "output_file2",
158 "type": "txt"
159 },
160 {
161 "name": "output_file3",
162 "type": "txt"
163 },
164 {
165 "name": "output_file4",
166 "type": "txt"
167 }
168 ],
169 "position": {
170 "left": 519.7666015625,
171 "top": 920.5
172 },
173 "post_job_actions": {},
174 "tool_errors": null,
175 "tool_id": "SplitFile4x",
176 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
177 "tool_version": "0.01",
178 "type": "tool",
179 "user_outputs": []
180 },
181 "6": {
182 "annotation": "",
183 "id": 6,
184 "input_connections": {
185 "input_fasta": {
186 "id": 2,
187 "output_name": "output"
188 }
189 },
190 "inputs": [],
191 "name": "fastaGroomerForMakeBlastdb",
192 "outputs": [
193 {
194 "name": "output_fasta",
195 "type": "fasta"
196 }
197 ],
198 "position": {
199 "left": 2796.7666015625,
200 "top": 404.5
201 },
202 "post_job_actions": {},
203 "tool_errors": null,
204 "tool_id": "fastaGroomerForMakeBlastdb",
205 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
206 "tool_version": "0.01",
207 "type": "tool",
208 "user_outputs": []
209 },
210 "7": {
211 "annotation": "",
212 "id": 7,
213 "input_connections": {
214 "input_read1_file": {
215 "id": 4,
216 "output_name": "output_file1"
217 },
218 "input_read2_file": {
219 "id": 5,
220 "output_name": "output_file1"
221 }
222 },
223 "inputs": [],
224 "name": "PrepareFastqLight",
225 "outputs": [
226 {
227 "name": "output_read1_file",
228 "type": "fastqsanger"
229 },
230 {
231 "name": "output_read2_file",
232 "type": "fastqsanger"
233 }
234 ],
235 "position": {
236 "left": 891.7666015625,
237 "top": 481.5
238 },
239 "post_job_actions": {},
240 "tool_errors": null,
241 "tool_id": "PrepareFastqLight",
242 "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\"}",
243 "tool_version": "0.01",
244 "type": "tool",
245 "user_outputs": []
246 },
247 "8": {
248 "annotation": "",
249 "id": 8,
250 "input_connections": {
251 "input_read1_file": {
252 "id": 4,
253 "output_name": "output_file2"
254 },
255 "input_read2_file": {
256 "id": 5,
257 "output_name": "output_file2"
258 }
259 },
260 "inputs": [],
261 "name": "PrepareFastqLight",
262 "outputs": [
263 {
264 "name": "output_read1_file",
265 "type": "fastqsanger"
266 },
267 {
268 "name": "output_read2_file",
269 "type": "fastqsanger"
270 }
271 ],
272 "position": {
273 "left": 900.7666015625,
274 "top": 722.5
275 },
276 "post_job_actions": {},
277 "tool_errors": null,
278 "tool_id": "PrepareFastqLight",
279 "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\"}",
280 "tool_version": "0.01",
281 "type": "tool",
282 "user_outputs": []
283 },
284 "9": {
285 "annotation": "",
286 "id": 9,
287 "input_connections": {
288 "input_read1_file": {
289 "id": 4,
290 "output_name": "output_file3"
291 },
292 "input_read2_file": {
293 "id": 5,
294 "output_name": "output_file3"
295 }
296 },
297 "inputs": [],
298 "name": "PrepareFastqLight",
299 "outputs": [
300 {
301 "name": "output_read1_file",
302 "type": "fastqsanger"
303 },
304 {
305 "name": "output_read2_file",
306 "type": "fastqsanger"
307 }
308 ],
309 "position": {
310 "left": 890.7666015625,
311 "top": 947.5
312 },
313 "post_job_actions": {},
314 "tool_errors": null,
315 "tool_id": "PrepareFastqLight",
316 "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\"}",
317 "tool_version": "0.01",
318 "type": "tool",
319 "user_outputs": []
320 },
321 "10": {
322 "annotation": "",
323 "id": 10,
324 "input_connections": {
325 "input_read1_file": {
326 "id": 4,
327 "output_name": "output_file4"
328 },
329 "input_read2_file": {
330 "id": 5,
331 "output_name": "output_file4"
332 }
333 },
334 "inputs": [],
335 "name": "PrepareFastqLight",
336 "outputs": [
337 {
338 "name": "output_read1_file",
339 "type": "fastqsanger"
340 },
341 {
342 "name": "output_read2_file",
343 "type": "fastqsanger"
344 }
345 ],
346 "position": {
347 "left": 894.7666015625,
348 "top": 1175.5
349 },
350 "post_job_actions": {},
351 "tool_errors": null,
352 "tool_id": "PrepareFastqLight",
353 "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\"}",
354 "tool_version": "0.01",
355 "type": "tool",
356 "user_outputs": []
357 },
358 "11": {
359 "annotation": "",
360 "id": 11,
361 "input_connections": {
362 "input_file": {
363 "id": 6,
364 "output_name": "output_fasta"
365 }
366 },
367 "inputs": [],
368 "name": "NCBI BLAST+ makeblastdb",
369 "outputs": [
370 {
371 "name": "outfile",
372 "type": "data"
373 }
374 ],
375 "position": {
376 "left": 3514.2666625976562,
377 "top": 427.5
378 },
379 "post_job_actions": {},
380 "tool_errors": null,
381 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
382 "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\\\"\"}",
383 "tool_version": "0.1.00",
384 "type": "tool",
385 "user_outputs": []
386 },
387 "12": {
388 "annotation": "",
389 "id": 12,
390 "input_connections": {
391 "genomeSource|ownFile": {
392 "id": 2,
393 "output_name": "output"
394 },
395 "paired|input1": {
396 "id": 7,
397 "output_name": "output_read1_file"
398 },
399 "paired|input2": {
400 "id": 7,
401 "output_name": "output_read2_file"
402 }
403 },
404 "inputs": [],
405 "name": "Map with BWA for Illumina",
406 "outputs": [
407 {
408 "name": "output",
409 "type": "sam"
410 }
411 ],
412 "position": {
413 "left": 1355.7666015625,
414 "top": 563
415 },
416 "post_job_actions": {},
417 "tool_errors": null,
418 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
419 "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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
420 "tool_version": "1.2.3",
421 "type": "tool",
422 "user_outputs": []
423 },
424 "13": {
425 "annotation": "",
426 "id": 13,
427 "input_connections": {
428 "genomeSource|ownFile": {
429 "id": 2,
430 "output_name": "output"
431 },
432 "paired|input1": {
433 "id": 8,
434 "output_name": "output_read1_file"
435 },
436 "paired|input2": {
437 "id": 8,
438 "output_name": "output_read2_file"
439 }
440 },
441 "inputs": [],
442 "name": "Map with BWA for Illumina",
443 "outputs": [
444 {
445 "name": "output",
446 "type": "sam"
447 }
448 ],
449 "position": {
450 "left": 1349.7666015625,
451 "top": 745
452 },
453 "post_job_actions": {},
454 "tool_errors": null,
455 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
456 "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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
457 "tool_version": "1.2.3",
458 "type": "tool",
459 "user_outputs": []
460 },
461 "14": {
462 "annotation": "",
463 "id": 14,
464 "input_connections": {
465 "genomeSource|ownFile": {
466 "id": 2,
467 "output_name": "output"
468 },
469 "paired|input1": {
470 "id": 9,
471 "output_name": "output_read1_file"
472 },
473 "paired|input2": {
474 "id": 9,
475 "output_name": "output_read2_file"
476 }
477 },
478 "inputs": [],
479 "name": "Map with BWA for Illumina",
480 "outputs": [
481 {
482 "name": "output",
483 "type": "sam"
484 }
485 ],
486 "position": {
487 "left": 1349.7666015625,
488 "top": 914
489 },
490 "post_job_actions": {},
491 "tool_errors": null,
492 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
493 "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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
494 "tool_version": "1.2.3",
495 "type": "tool",
496 "user_outputs": []
497 },
498 "15": {
499 "annotation": "",
500 "id": 15,
501 "input_connections": {
502 "genomeSource|ownFile": {
503 "id": 2,
504 "output_name": "output"
505 },
506 "paired|input1": {
507 "id": 10,
508 "output_name": "output_read1_file"
509 },
510 "paired|input2": {
511 "id": 10,
512 "output_name": "output_read2_file"
513 }
514 },
515 "inputs": [],
516 "name": "Map with BWA for Illumina",
517 "outputs": [
518 {
519 "name": "output",
520 "type": "sam"
521 }
522 ],
523 "position": {
524 "left": 1349.7666015625,
525 "top": 1094
526 },
527 "post_job_actions": {},
528 "tool_errors": null,
529 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
530 "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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
531 "tool_version": "1.2.3",
532 "type": "tool",
533 "user_outputs": []
534 },
535 "16": {
536 "annotation": "",
537 "id": 16,
538 "input_connections": {
539 "input_sam_file": {
540 "id": 12,
541 "output_name": "output"
542 }
543 },
544 "inputs": [],
545 "name": "filtersam_mapped_and_unique",
546 "outputs": [
547 {
548 "name": "output_file",
549 "type": "sam"
550 }
551 ],
552 "position": {
553 "left": 1628.7666015625,
554 "top": 711
555 },
556 "post_job_actions": {},
557 "tool_errors": null,
558 "tool_id": "filtersam_mapped_and_unique",
559 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}",
560 "tool_version": "0.01",
561 "type": "tool",
562 "user_outputs": []
563 },
564 "17": {
565 "annotation": "",
566 "id": 17,
567 "input_connections": {
568 "input_sam_file": {
569 "id": 13,
570 "output_name": "output"
571 }
572 },
573 "inputs": [],
574 "name": "filtersam_mapped_and_unique",
575 "outputs": [
576 {
577 "name": "output_file",
578 "type": "sam"
579 }
580 ],
581 "position": {
582 "left": 1628.7666015625,
583 "top": 856
584 },
585 "post_job_actions": {},
586 "tool_errors": null,
587 "tool_id": "filtersam_mapped_and_unique",
588 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}",
589 "tool_version": "0.01",
590 "type": "tool",
591 "user_outputs": []
592 },
593 "18": {
594 "annotation": "",
595 "id": 18,
596 "input_connections": {
597 "input_sam_file": {
598 "id": 14,
599 "output_name": "output"
600 }
601 },
602 "inputs": [],
603 "name": "filtersam_mapped_and_unique",
604 "outputs": [
605 {
606 "name": "output_file",
607 "type": "sam"
608 }
609 ],
610 "position": {
611 "left": 1633.7666015625,
612 "top": 995
613 },
614 "post_job_actions": {},
615 "tool_errors": null,
616 "tool_id": "filtersam_mapped_and_unique",
617 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}",
618 "tool_version": "0.01",
619 "type": "tool",
620 "user_outputs": []
621 },
622 "19": {
623 "annotation": "",
624 "id": 19,
625 "input_connections": {
626 "input_sam_file": {
627 "id": 15,
628 "output_name": "output"
629 }
630 },
631 "inputs": [],
632 "name": "filtersam_mapped_and_unique",
633 "outputs": [
634 {
635 "name": "output_file",
636 "type": "sam"
637 }
638 ],
639 "position": {
640 "left": 1632.7666015625,
641 "top": 1149
642 },
643 "post_job_actions": {},
644 "tool_errors": null,
645 "tool_id": "filtersam_mapped_and_unique",
646 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}",
647 "tool_version": "0.01",
648 "type": "tool",
649 "user_outputs": []
650 },
651 "20": {
652 "annotation": "",
653 "id": 20,
654 "input_connections": {
655 "source|input1": {
656 "id": 16,
657 "output_name": "output_file"
658 },
659 "source|ref_file": {
660 "id": 2,
661 "output_name": "output"
662 }
663 },
664 "inputs": [],
665 "name": "SAM-to-BAM",
666 "outputs": [
667 {
668 "name": "output1",
669 "type": "bam"
670 }
671 ],
672 "position": {
673 "left": 1952.7666015625,
674 "top": 756
675 },
676 "post_job_actions": {},
677 "tool_errors": null,
678 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
679 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
680 "tool_version": "1.1.4",
681 "type": "tool",
682 "user_outputs": []
683 },
684 "21": {
685 "annotation": "",
686 "id": 21,
687 "input_connections": {
688 "source|input1": {
689 "id": 17,
690 "output_name": "output_file"
691 },
692 "source|ref_file": {
693 "id": 2,
694 "output_name": "output"
695 }
696 },
697 "inputs": [],
698 "name": "SAM-to-BAM",
699 "outputs": [
700 {
701 "name": "output1",
702 "type": "bam"
703 }
704 ],
705 "position": {
706 "left": 1948.7666015625,
707 "top": 903
708 },
709 "post_job_actions": {},
710 "tool_errors": null,
711 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
712 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
713 "tool_version": "1.1.4",
714 "type": "tool",
715 "user_outputs": []
716 },
717 "22": {
718 "annotation": "",
719 "id": 22,
720 "input_connections": {
721 "source|input1": {
722 "id": 18,
723 "output_name": "output_file"
724 },
725 "source|ref_file": {
726 "id": 2,
727 "output_name": "output"
728 }
729 },
730 "inputs": [],
731 "name": "SAM-to-BAM",
732 "outputs": [
733 {
734 "name": "output1",
735 "type": "bam"
736 }
737 ],
738 "position": {
739 "left": 1948.7666015625,
740 "top": 1041
741 },
742 "post_job_actions": {},
743 "tool_errors": null,
744 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
745 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
746 "tool_version": "1.1.4",
747 "type": "tool",
748 "user_outputs": []
749 },
750 "23": {
751 "annotation": "",
752 "id": 23,
753 "input_connections": {
754 "source|input1": {
755 "id": 19,
756 "output_name": "output_file"
757 },
758 "source|ref_file": {
759 "id": 2,
760 "output_name": "output"
761 }
762 },
763 "inputs": [],
764 "name": "SAM-to-BAM",
765 "outputs": [
766 {
767 "name": "output1",
768 "type": "bam"
769 }
770 ],
771 "position": {
772 "left": 1948.7666015625,
773 "top": 1193
774 },
775 "post_job_actions": {},
776 "tool_errors": null,
777 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
778 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
779 "tool_version": "1.1.4",
780 "type": "tool",
781 "user_outputs": []
782 },
783 "24": {
784 "annotation": "",
785 "id": 24,
786 "input_connections": {
787 "input1": {
788 "id": 20,
789 "output_name": "output1"
790 },
791 "input2": {
792 "id": 21,
793 "output_name": "output1"
794 },
795 "inputs_0|input": {
796 "id": 22,
797 "output_name": "output1"
798 },
799 "inputs_1|input": {
800 "id": 23,
801 "output_name": "output1"
802 }
803 },
804 "inputs": [],
805 "name": "Merge BAM Files",
806 "outputs": [
807 {
808 "name": "output1",
809 "type": "bam"
810 },
811 {
812 "name": "outlog",
813 "type": "txt"
814 }
815 ],
816 "position": {
817 "left": 2265.7666015625,
818 "top": 1038
819 },
820 "post_job_actions": {},
821 "tool_errors": null,
822 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2",
823 "tool_state": "{\"input2\": \"null\", \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}, {\\\"__index__\\\": 1, \\\"input\\\": null}]\", \"input1\": \"null\", \"title\": \"\\\"merge bam\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mergeSD\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
824 "tool_version": "1.1.2",
825 "type": "tool",
826 "user_outputs": []
827 },
828 "25": {
829 "annotation": "",
830 "id": 25,
831 "input_connections": {
832 "reference_source|input_bams_0|input_bam": {
833 "id": 24,
834 "output_name": "output1"
835 },
836 "reference_source|ref_file": {
837 "id": 2,
838 "output_name": "output"
839 }
840 },
841 "inputs": [],
842 "name": "MPileup",
843 "outputs": [
844 {
845 "name": "output_mpileup",
846 "type": "pileup"
847 },
848 {
849 "name": "output_log",
850 "type": "txt"
851 }
852 ],
853 "position": {
854 "left": 2401.7666015625,
855 "top": 764
856 },
857 "post_job_actions": {},
858 "tool_errors": null,
859 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
860 "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"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\\\": \\\"30\\\", \\\"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\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
861 "tool_version": "0.0.3",
862 "type": "tool",
863 "user_outputs": []
864 },
865 "26": {
866 "annotation": "",
867 "id": 26,
868 "input_connections": {
869 "input_file": {
870 "id": 25,
871 "output_name": "output_mpileup"
872 }
873 },
874 "inputs": [],
875 "name": "PileupVariant",
876 "outputs": [
877 {
878 "name": "output_file",
879 "type": "pileup"
880 }
881 ],
882 "position": {
883 "left": 2694.7666015625,
884 "top": 1264.5
885 },
886 "post_job_actions": {},
887 "tool_errors": null,
888 "tool_id": "PileupVariant",
889 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
890 "tool_version": "0.01",
891 "type": "tool",
892 "user_outputs": []
893 },
894 "27": {
895 "annotation": "",
896 "id": 27,
897 "input_connections": {
898 "input_listA": {
899 "id": 26,
900 "output_name": "output_file"
901 },
902 "input_listB": {
903 "id": 3,
904 "output_name": "output"
905 }
906 },
907 "inputs": [],
908 "name": "listfiltering",
909 "outputs": [
910 {
911 "name": "output_file",
912 "type": "pileup"
913 }
914 ],
915 "position": {
916 "left": 2778.7666015625,
917 "top": 956.5
918 },
919 "post_job_actions": {},
920 "tool_errors": null,
921 "tool_id": "listfiltering",
922 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}",
923 "tool_version": "0.01",
924 "type": "tool",
925 "user_outputs": []
926 },
927 "28": {
928 "annotation": "",
929 "id": 28,
930 "input_connections": {
931 "input_file": {
932 "id": 27,
933 "output_name": "output_file"
934 }
935 },
936 "inputs": [],
937 "name": "SplitFile4x",
938 "outputs": [
939 {
940 "name": "output_file1",
941 "type": "txt"
942 },
943 {
944 "name": "output_file2",
945 "type": "txt"
946 },
947 {
948 "name": "output_file3",
949 "type": "txt"
950 },
951 {
952 "name": "output_file4",
953 "type": "txt"
954 }
955 ],
956 "position": {
957 "left": 3154,
958 "top": 906.88330078125
959 },
960 "post_job_actions": {},
961 "tool_errors": null,
962 "tool_id": "SplitFile4x",
963 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
964 "tool_version": "0.01",
965 "type": "tool",
966 "user_outputs": []
967 },
968 "29": {
969 "annotation": "",
970 "id": 29,
971 "input_connections": {
972 "input_assembly_file": {
973 "id": 2,
974 "output_name": "output"
975 },
976 "input_variant_file": {
977 "id": 28,
978 "output_name": "output_file1"
979 }
980 },
981 "inputs": [],
982 "name": "extractseq",
983 "outputs": [
984 {
985 "name": "output_file",
986 "type": "fasta"
987 }
988 ],
989 "position": {
990 "left": 3512,
991 "top": 711.8833312988281
992 },
993 "post_job_actions": {},
994 "tool_errors": null,
995 "tool_id": "extractseq",
996 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
997 "tool_version": "0.03",
998 "type": "tool",
999 "user_outputs": []
1000 },
1001 "30": {
1002 "annotation": "",
1003 "id": 30,
1004 "input_connections": {
1005 "input_assembly_file": {
1006 "id": 2,
1007 "output_name": "output"
1008 },
1009 "input_variant_file": {
1010 "id": 28,
1011 "output_name": "output_file2"
1012 }
1013 },
1014 "inputs": [],
1015 "name": "extractseq",
1016 "outputs": [
1017 {
1018 "name": "output_file",
1019 "type": "fasta"
1020 }
1021 ],
1022 "position": {
1023 "left": 3517,
1024 "top": 880.8833312988281
1025 },
1026 "post_job_actions": {},
1027 "tool_errors": null,
1028 "tool_id": "extractseq",
1029 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1030 "tool_version": "0.03",
1031 "type": "tool",
1032 "user_outputs": []
1033 },
1034 "31": {
1035 "annotation": "",
1036 "id": 31,
1037 "input_connections": {
1038 "input_assembly_file": {
1039 "id": 2,
1040 "output_name": "output"
1041 },
1042 "input_variant_file": {
1043 "id": 28,
1044 "output_name": "output_file3"
1045 }
1046 },
1047 "inputs": [],
1048 "name": "extractseq",
1049 "outputs": [
1050 {
1051 "name": "output_file",
1052 "type": "fasta"
1053 }
1054 ],
1055 "position": {
1056 "left": 3518,
1057 "top": 1049.88330078125
1058 },
1059 "post_job_actions": {},
1060 "tool_errors": null,
1061 "tool_id": "extractseq",
1062 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1063 "tool_version": "0.03",
1064 "type": "tool",
1065 "user_outputs": []
1066 },
1067 "32": {
1068 "annotation": "",
1069 "id": 32,
1070 "input_connections": {
1071 "input_assembly_file": {
1072 "id": 2,
1073 "output_name": "output"
1074 },
1075 "input_variant_file": {
1076 "id": 28,
1077 "output_name": "output_file4"
1078 }
1079 },
1080 "inputs": [],
1081 "name": "extractseq",
1082 "outputs": [
1083 {
1084 "name": "output_file",
1085 "type": "fasta"
1086 }
1087 ],
1088 "position": {
1089 "left": 3525,
1090 "top": 1216.88330078125
1091 },
1092 "post_job_actions": {},
1093 "tool_errors": null,
1094 "tool_id": "extractseq",
1095 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
1096 "tool_version": "0.03",
1097 "type": "tool",
1098 "user_outputs": []
1099 },
1100 "33": {
1101 "annotation": "",
1102 "id": 33,
1103 "input_connections": {
1104 "db_opts|histdb": {
1105 "id": 11,
1106 "output_name": "outfile"
1107 },
1108 "query": {
1109 "id": 29,
1110 "output_name": "output_file"
1111 }
1112 },
1113 "inputs": [],
1114 "name": "NCBI BLAST+ blastn",
1115 "outputs": [
1116 {
1117 "name": "output1",
1118 "type": "tabular"
1119 }
1120 ],
1121 "position": {
1122 "left": 3959.7666625976562,
1123 "top": 695.5
1124 },
1125 "post_job_actions": {},
1126 "tool_errors": null,
1127 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
1128 "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\"}",
1129 "tool_version": "0.1.00",
1130 "type": "tool",
1131 "user_outputs": []
1132 },
1133 "34": {
1134 "annotation": "",
1135 "id": 34,
1136 "input_connections": {
1137 "db_opts|histdb": {
1138 "id": 11,
1139 "output_name": "outfile"
1140 },
1141 "query": {
1142 "id": 30,
1143 "output_name": "output_file"
1144 }
1145 },
1146 "inputs": [],
1147 "name": "NCBI BLAST+ blastn",
1148 "outputs": [
1149 {
1150 "name": "output1",
1151 "type": "tabular"
1152 }
1153 ],
1154 "position": {
1155 "left": 3961.7666625976562,
1156 "top": 886.5
1157 },
1158 "post_job_actions": {},
1159 "tool_errors": null,
1160 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
1161 "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\"}",
1162 "tool_version": "0.1.00",
1163 "type": "tool",
1164 "user_outputs": []
1165 },
1166 "35": {
1167 "annotation": "",
1168 "id": 35,
1169 "input_connections": {
1170 "db_opts|histdb": {
1171 "id": 11,
1172 "output_name": "outfile"
1173 },
1174 "query": {
1175 "id": 31,
1176 "output_name": "output_file"
1177 }
1178 },
1179 "inputs": [],
1180 "name": "NCBI BLAST+ blastn",
1181 "outputs": [
1182 {
1183 "name": "output1",
1184 "type": "tabular"
1185 }
1186 ],
1187 "position": {
1188 "left": 3965.7666625976562,
1189 "top": 1052.5
1190 },
1191 "post_job_actions": {},
1192 "tool_errors": null,
1193 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
1194 "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\"}",
1195 "tool_version": "0.1.00",
1196 "type": "tool",
1197 "user_outputs": []
1198 },
1199 "36": {
1200 "annotation": "",
1201 "id": 36,
1202 "input_connections": {
1203 "db_opts|histdb": {
1204 "id": 11,
1205 "output_name": "outfile"
1206 },
1207 "query": {
1208 "id": 32,
1209 "output_name": "output_file"
1210 }
1211 },
1212 "inputs": [],
1213 "name": "NCBI BLAST+ blastn",
1214 "outputs": [
1215 {
1216 "name": "output1",
1217 "type": "tabular"
1218 }
1219 ],
1220 "position": {
1221 "left": 3971.7666625976562,
1222 "top": 1220.5
1223 },
1224 "post_job_actions": {},
1225 "tool_errors": null,
1226 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
1227 "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\"}",
1228 "tool_version": "0.1.00",
1229 "type": "tool",
1230 "user_outputs": []
1231 },
1232 "37": {
1233 "annotation": "",
1234 "id": 37,
1235 "input_connections": {
1236 "input_blast_file": {
1237 "id": 33,
1238 "output_name": "output1"
1239 },
1240 "input_variant_file": {
1241 "id": 28,
1242 "output_name": "output_file1"
1243 }
1244 },
1245 "inputs": [],
1246 "name": "ParseBlastForUniqueMatch",
1247 "outputs": [
1248 {
1249 "name": "output_file",
1250 "type": "pileup"
1251 }
1252 ],
1253 "position": {
1254 "left": 4286.5,
1255 "top": 705
1256 },
1257 "post_job_actions": {},
1258 "tool_errors": null,
1259 "tool_id": "ParseBlastForUniqueMatch",
1260 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
1261 "tool_version": "0.01",
1262 "type": "tool",
1263 "user_outputs": []
1264 },
1265 "38": {
1266 "annotation": "",
1267 "id": 38,
1268 "input_connections": {
1269 "input_blast_file": {
1270 "id": 34,
1271 "output_name": "output1"
1272 },
1273 "input_variant_file": {
1274 "id": 28,
1275 "output_name": "output_file2"
1276 }
1277 },
1278 "inputs": [],
1279 "name": "ParseBlastForUniqueMatch",
1280 "outputs": [
1281 {
1282 "name": "output_file",
1283 "type": "pileup"
1284 }
1285 ],
1286 "position": {
1287 "left": 4284.5,
1288 "top": 904
1289 },
1290 "post_job_actions": {},
1291 "tool_errors": null,
1292 "tool_id": "ParseBlastForUniqueMatch",
1293 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
1294 "tool_version": "0.01",
1295 "type": "tool",
1296 "user_outputs": []
1297 },
1298 "39": {
1299 "annotation": "",
1300 "id": 39,
1301 "input_connections": {
1302 "input_blast_file": {
1303 "id": 35,
1304 "output_name": "output1"
1305 },
1306 "input_variant_file": {
1307 "id": 28,
1308 "output_name": "output_file3"
1309 }
1310 },
1311 "inputs": [],
1312 "name": "ParseBlastForUniqueMatch",
1313 "outputs": [
1314 {
1315 "name": "output_file",
1316 "type": "pileup"
1317 }
1318 ],
1319 "position": {
1320 "left": 4287.5,
1321 "top": 1103
1322 },
1323 "post_job_actions": {},
1324 "tool_errors": null,
1325 "tool_id": "ParseBlastForUniqueMatch",
1326 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
1327 "tool_version": "0.01",
1328 "type": "tool",
1329 "user_outputs": []
1330 },
1331 "40": {
1332 "annotation": "",
1333 "id": 40,
1334 "input_connections": {
1335 "input_blast_file": {
1336 "id": 36,
1337 "output_name": "output1"
1338 },
1339 "input_variant_file": {
1340 "id": 28,
1341 "output_name": "output_file4"
1342 }
1343 },
1344 "inputs": [],
1345 "name": "ParseBlastForUniqueMatch",
1346 "outputs": [
1347 {
1348 "name": "output_file",
1349 "type": "pileup"
1350 }
1351 ],
1352 "position": {
1353 "left": 4281.5,
1354 "top": 1305
1355 },
1356 "post_job_actions": {},
1357 "tool_errors": null,
1358 "tool_id": "ParseBlastForUniqueMatch",
1359 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
1360 "tool_version": "0.01",
1361 "type": "tool",
1362 "user_outputs": []
1363 },
1364 "41": {
1365 "annotation": "",
1366 "id": 41,
1367 "input_connections": {
1368 "input_file1": {
1369 "id": 37,
1370 "output_name": "output_file"
1371 },
1372 "input_file2": {
1373 "id": 38,
1374 "output_name": "output_file"
1375 },
1376 "input_file3": {
1377 "id": 39,
1378 "output_name": "output_file"
1379 },
1380 "input_file4": {
1381 "id": 40,
1382 "output_name": "output_file"
1383 }
1384 },
1385 "inputs": [],
1386 "name": "MergeFile4x",
1387 "outputs": [
1388 {
1389 "name": "output_file",
1390 "type": "txt"
1391 }
1392 ],
1393 "position": {
1394 "left": 4700,
1395 "top": 841.8833312988281
1396 },
1397 "post_job_actions": {},
1398 "tool_errors": null,
1399 "tool_id": "MergeFile4x",
1400 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file4\": \"null\", \"input_file1\": \"null\", \"input_file2\": \"null\", \"input_file3\": \"null\"}",
1401 "tool_version": "0.01",
1402 "type": "tool",
1403 "user_outputs": []
1404 },
1405 "42": {
1406 "annotation": "",
1407 "id": 42,
1408 "input_connections": {
1409 "input_file": {
1410 "id": 41,
1411 "output_name": "output_file"
1412 }
1413 },
1414 "inputs": [],
1415 "name": "mpileupfilterandstat",
1416 "outputs": [
1417 {
1418 "name": "output_file",
1419 "type": "pileup"
1420 },
1421 {
1422 "name": "log_file",
1423 "type": "txt"
1424 }
1425 ],
1426 "position": {
1427 "left": 5056,
1428 "top": 886.8833312988281
1429 },
1430 "post_job_actions": {},
1431 "tool_errors": null,
1432 "tool_id": "mpileupfilterandstat",
1433 "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"2\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"10\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"2\\\", \\\"stat_max_depth_min\\\": \\\"100\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.8\\\"\", \"do_stat\": \"\\\"YES\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
1434 "tool_version": "0.08",
1435 "type": "tool",
1436 "user_outputs": []
1437 },
1438 "43": {
1439 "annotation": "",
1440 "id": 43,
1441 "input_connections": {
1442 "input_blast_filtered_part1_file": {
1443 "id": 37,
1444 "output_name": "output_file"
1445 },
1446 "input_blast_filtered_part2_file": {
1447 "id": 38,
1448 "output_name": "output_file"
1449 },
1450 "input_blast_filtered_part3_file": {
1451 "id": 39,
1452 "output_name": "output_file"
1453 },
1454 "input_blast_filtered_part4_file": {
1455 "id": 40,
1456 "output_name": "output_file"
1457 },
1458 "input_list_filtered_file": {
1459 "id": 27,
1460 "output_name": "output_file"
1461 },
1462 "input_mpileup_variant_file": {
1463 "id": 26,
1464 "output_name": "output_file"
1465 },
1466 "input_read1_part1_trimmed_file": {
1467 "id": 7,
1468 "output_name": "output_read1_file"
1469 },
1470 "input_read1_part2_trimmed_file": {
1471 "id": 8,
1472 "output_name": "output_read1_file"
1473 },
1474 "input_read1_part3_trimmed_file": {
1475 "id": 9,
1476 "output_name": "output_read1_file"
1477 },
1478 "input_read1_part4_trimmed_file": {
1479 "id": 10,
1480 "output_name": "output_read1_file"
1481 },
1482 "input_read1_row_file": {
1483 "id": 0,
1484 "output_name": "output"
1485 },
1486 "input_read2_part1_trimmed_file": {
1487 "id": 7,
1488 "output_name": "output_read2_file"
1489 },
1490 "input_read2_part2_trimmed_file": {
1491 "id": 8,
1492 "output_name": "output_read2_file"
1493 },
1494 "input_read2_part3_trimmed_file": {
1495 "id": 9,
1496 "output_name": "output_read2_file"
1497 },
1498 "input_read2_part4_trimmed_file": {
1499 "id": 10,
1500 "output_name": "output_read2_file"
1501 },
1502 "input_read2_row_file": {
1503 "id": 1,
1504 "output_name": "output"
1505 },
1506 "input_sam_filtered_part1_file": {
1507 "id": 16,
1508 "output_name": "output_file"
1509 },
1510 "input_sam_filtered_part2_file": {
1511 "id": 17,
1512 "output_name": "output_file"
1513 },
1514 "input_sam_filtered_part3_file": {
1515 "id": 18,
1516 "output_name": "output_file"
1517 },
1518 "input_sam_filtered_part4_file": {
1519 "id": 19,
1520 "output_name": "output_file"
1521 },
1522 "input_sam_row_part1_file": {
1523 "id": 12,
1524 "output_name": "output"
1525 },
1526 "input_sam_row_part2_file": {
1527 "id": 13,
1528 "output_name": "output"
1529 },
1530 "input_sam_row_part3_file": {
1531 "id": 14,
1532 "output_name": "output"
1533 },
1534 "input_sam_row_part4_file": {
1535 "id": 15,
1536 "output_name": "output"
1537 },
1538 "input_snp_selected_file": {
1539 "id": 42,
1540 "output_name": "output_file"
1541 }
1542 },
1543 "inputs": [],
1544 "name": "rapsosnp_stats4x",
1545 "outputs": [
1546 {
1547 "name": "output_file",
1548 "type": "txt"
1549 }
1550 ],
1551 "position": {
1552 "left": 5447.5,
1553 "top": 211
1554 },
1555 "post_job_actions": {},
1556 "tool_errors": null,
1557 "tool_id": "rapsosnp_stats4x",
1558 "tool_state": "{\"input_blast_filtered_part2_file\": \"null\", \"input_blast_filtered_part3_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_read1_part4_trimmed_file\": \"null\", \"input_read1_part3_trimmed_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_mpileup_variant_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_blast_filtered_part1_file\": \"null\", \"input_sam_row_part4_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\", \"input_read2_part3_trimmed_file\": \"null\", \"input_read2_part4_trimmed_file\": \"null\", \"input_sam_filtered_part3_file\": \"null\", \"input_sam_filtered_part4_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_blast_filtered_part4_file\": \"null\", \"input_sam_row_part3_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_list_filtered_file\": \"null\"}",
1559 "tool_version": "0.01",
1560 "type": "tool",
1561 "user_outputs": []
1562 }
1563 }
1564 }