Mercurial > repos > mcharles > rapsosnp

comparison rapsodyn/Galaxy-Workflow-rapsosnp_v1.17-2x.ga @ 3:9332b9da7491 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author mcharles
date Thu, 11 Sep 2014 07:31:20 -0400
parents
children
comparison
equal deleted inserted replaced
2:761fecc07fa9 3:9332b9da7491
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "rapsosnp v1.17-2x",
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": 200,
21 "top": 814
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": 200,
44 "top": 899
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": 2916,
67 "top": 906
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": 2679,
90 "top": 1493
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": "SplitFile2x",
110 "outputs": [
111 {
112 "name": "output_file1",
113 "type": "txt"
114 },
115 {
116 "name": "output_file2",
117 "type": "txt"
118 }
119 ],
120 "position": {
121 "left": 475,
122 "top": 1049.5
123 },
124 "post_job_actions": {},
125 "tool_errors": null,
126 "tool_id": "SplitFile2x",
127 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
128 "tool_version": "0.01",
129 "type": "tool",
130 "user_outputs": []
131 },
132 "5": {
133 "annotation": "",
134 "id": 5,
135 "input_connections": {
136 "input_file": {
137 "id": 1,
138 "output_name": "output"
139 }
140 },
141 "inputs": [],
142 "name": "SplitFile2x",
143 "outputs": [
144 {
145 "name": "output_file1",
146 "type": "txt"
147 },
148 {
149 "name": "output_file2",
150 "type": "txt"
151 }
152 ],
153 "position": {
154 "left": 476,
155 "top": 1240.5
156 },
157 "post_job_actions": {},
158 "tool_errors": null,
159 "tool_id": "SplitFile2x",
160 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
161 "tool_version": "0.01",
162 "type": "tool",
163 "user_outputs": []
164 },
165 "6": {
166 "annotation": "",
167 "id": 6,
168 "input_connections": {
169 "input_fasta": {
170 "id": 2,
171 "output_name": "output"
172 }
173 },
174 "inputs": [],
175 "name": "fastaGroomerForMakeBlastdb",
176 "outputs": [
177 {
178 "name": "output_fasta",
179 "type": "fasta"
180 }
181 ],
182 "position": {
183 "left": 3163,
184 "top": 638
185 },
186 "post_job_actions": {},
187 "tool_errors": null,
188 "tool_id": "fastaGroomerForMakeBlastdb",
189 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
190 "tool_version": "0.01",
191 "type": "tool",
192 "user_outputs": []
193 },
194 "7": {
195 "annotation": "",
196 "id": 7,
197 "input_connections": {
198 "input_read1_file": {
199 "id": 4,
200 "output_name": "output_file1"
201 },
202 "input_read2_file": {
203 "id": 5,
204 "output_name": "output_file1"
205 }
206 },
207 "inputs": [],
208 "name": "PrepareFastqLight",
209 "outputs": [
210 {
211 "name": "output_read1_file",
212 "type": "fastqsanger"
213 },
214 {
215 "name": "output_read2_file",
216 "type": "fastqsanger"
217 }
218 ],
219 "position": {
220 "left": 791,
221 "top": 1053
222 },
223 "post_job_actions": {},
224 "tool_errors": null,
225 "tool_id": "PrepareFastqLight",
226 "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\"}",
227 "tool_version": "0.01",
228 "type": "tool",
229 "user_outputs": []
230 },
231 "8": {
232 "annotation": "",
233 "id": 8,
234 "input_connections": {
235 "input_read1_file": {
236 "id": 4,
237 "output_name": "output_file2"
238 },
239 "input_read2_file": {
240 "id": 5,
241 "output_name": "output_file2"
242 }
243 },
244 "inputs": [],
245 "name": "PrepareFastqLight",
246 "outputs": [
247 {
248 "name": "output_read1_file",
249 "type": "fastqsanger"
250 },
251 {
252 "name": "output_read2_file",
253 "type": "fastqsanger"
254 }
255 ],
256 "position": {
257 "left": 792,
258 "top": 1244.5
259 },
260 "post_job_actions": {},
261 "tool_errors": null,
262 "tool_id": "PrepareFastqLight",
263 "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\"}",
264 "tool_version": "0.01",
265 "type": "tool",
266 "user_outputs": []
267 },
268 "9": {
269 "annotation": "",
270 "id": 9,
271 "input_connections": {
272 "input_file": {
273 "id": 6,
274 "output_name": "output_fasta"
275 }
276 },
277 "inputs": [],
278 "name": "NCBI BLAST+ makeblastdb",
279 "outputs": [
280 {
281 "name": "outfile",
282 "type": "data"
283 }
284 ],
285 "position": {
286 "left": 3561,
287 "top": 595
288 },
289 "post_job_actions": {},
290 "tool_errors": null,
291 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
292 "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\\\"\"}",
293 "tool_version": "0.1.00",
294 "type": "tool",
295 "user_outputs": []
296 },
297 "10": {
298 "annotation": "",
299 "id": 10,
300 "input_connections": {
301 "genomeSource|ownFile": {
302 "id": 2,
303 "output_name": "output"
304 },
305 "paired|input1": {
306 "id": 7,
307 "output_name": "output_read1_file"
308 },
309 "paired|input2": {
310 "id": 7,
311 "output_name": "output_read2_file"
312 }
313 },
314 "inputs": [],
315 "name": "Map with BWA for Illumina",
316 "outputs": [
317 {
318 "name": "output",
319 "type": "sam"
320 }
321 ],
322 "position": {
323 "left": 1197,
324 "top": 998
325 },
326 "post_job_actions": {},
327 "tool_errors": null,
328 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
329 "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\\\"\"}",
330 "tool_version": "1.2.3",
331 "type": "tool",
332 "user_outputs": []
333 },
334 "11": {
335 "annotation": "",
336 "id": 11,
337 "input_connections": {
338 "genomeSource|ownFile": {
339 "id": 2,
340 "output_name": "output"
341 },
342 "paired|input1": {
343 "id": 8,
344 "output_name": "output_read1_file"
345 },
346 "paired|input2": {
347 "id": 8,
348 "output_name": "output_read2_file"
349 }
350 },
351 "inputs": [],
352 "name": "Map with BWA for Illumina",
353 "outputs": [
354 {
355 "name": "output",
356 "type": "sam"
357 }
358 ],
359 "position": {
360 "left": 1197.5,
361 "top": 1226.5
362 },
363 "post_job_actions": {},
364 "tool_errors": null,
365 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
366 "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\\\"\"}",
367 "tool_version": "1.2.3",
368 "type": "tool",
369 "user_outputs": []
370 },
371 "12": {
372 "annotation": "",
373 "id": 12,
374 "input_connections": {
375 "input_sam_file": {
376 "id": 10,
377 "output_name": "output"
378 }
379 },
380 "inputs": [],
381 "name": "filtersam_mapped_and_unique",
382 "outputs": [
383 {
384 "name": "output_file",
385 "type": "sam"
386 }
387 ],
388 "position": {
389 "left": 1571,
390 "top": 1033
391 },
392 "post_job_actions": {},
393 "tool_errors": null,
394 "tool_id": "filtersam_mapped_and_unique",
395 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
396 "tool_version": "0.01",
397 "type": "tool",
398 "user_outputs": []
399 },
400 "13": {
401 "annotation": "",
402 "id": 13,
403 "input_connections": {
404 "input_sam_file": {
405 "id": 11,
406 "output_name": "output"
407 }
408 },
409 "inputs": [],
410 "name": "filtersam_mapped_and_unique",
411 "outputs": [
412 {
413 "name": "output_file",
414 "type": "sam"
415 }
416 ],
417 "position": {
418 "left": 1549,
419 "top": 1215.5
420 },
421 "post_job_actions": {},
422 "tool_errors": null,
423 "tool_id": "filtersam_mapped_and_unique",
424 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_sam_file\": \"null\"}",
425 "tool_version": "0.01",
426 "type": "tool",
427 "user_outputs": []
428 },
429 "14": {
430 "annotation": "",
431 "id": 14,
432 "input_connections": {
433 "source|input1": {
434 "id": 12,
435 "output_name": "output_file"
436 },
437 "source|ref_file": {
438 "id": 2,
439 "output_name": "output"
440 }
441 },
442 "inputs": [],
443 "name": "SAM-to-BAM",
444 "outputs": [
445 {
446 "name": "output1",
447 "type": "bam"
448 }
449 ],
450 "position": {
451 "left": 1920,
452 "top": 1033
453 },
454 "post_job_actions": {},
455 "tool_errors": null,
456 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
457 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
458 "tool_version": "1.1.4",
459 "type": "tool",
460 "user_outputs": []
461 },
462 "15": {
463 "annotation": "",
464 "id": 15,
465 "input_connections": {
466 "source|input1": {
467 "id": 13,
468 "output_name": "output_file"
469 },
470 "source|ref_file": {
471 "id": 2,
472 "output_name": "output"
473 }
474 },
475 "inputs": [],
476 "name": "SAM-to-BAM",
477 "outputs": [
478 {
479 "name": "output1",
480 "type": "bam"
481 }
482 ],
483 "position": {
484 "left": 1919,
485 "top": 1214.5
486 },
487 "post_job_actions": {},
488 "tool_errors": null,
489 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
490 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
491 "tool_version": "1.1.4",
492 "type": "tool",
493 "user_outputs": []
494 },
495 "16": {
496 "annotation": "",
497 "id": 16,
498 "input_connections": {
499 "input1": {
500 "id": 14,
501 "output_name": "output1"
502 },
503 "input2": {
504 "id": 15,
505 "output_name": "output1"
506 }
507 },
508 "inputs": [],
509 "name": "Merge BAM Files",
510 "outputs": [
511 {
512 "name": "output1",
513 "type": "bam"
514 },
515 {
516 "name": "outlog",
517 "type": "txt"
518 }
519 ],
520 "position": {
521 "left": 2163,
522 "top": 1158.5
523 },
524 "post_job_actions": {},
525 "tool_errors": null,
526 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2",
527 "tool_state": "{\"input2\": \"null\", \"inputs\": \"[]\", \"input1\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"title\": \"\\\"None\\\"\", \"mergeSD\": \"\\\"True\\\"\"}",
528 "tool_version": "1.1.2",
529 "type": "tool",
530 "user_outputs": []
531 },
532 "17": {
533 "annotation": "",
534 "id": 17,
535 "input_connections": {
536 "reference_source|input_bams_0|input_bam": {
537 "id": 16,
538 "output_name": "output1"
539 },
540 "reference_source|ref_file": {
541 "id": 2,
542 "output_name": "output"
543 }
544 },
545 "inputs": [],
546 "name": "MPileup",
547 "outputs": [
548 {
549 "name": "output_mpileup",
550 "type": "pileup"
551 },
552 {
553 "name": "output_log",
554 "type": "txt"
555 }
556 ],
557 "position": {
558 "left": 2374,
559 "top": 1170
560 },
561 "post_job_actions": {},
562 "tool_errors": null,
563 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
564 "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\\\": \\\"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\\\"}\", \"__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}\"}",
565 "tool_version": "0.0.3",
566 "type": "tool",
567 "user_outputs": []
568 },
569 "18": {
570 "annotation": "",
571 "id": 18,
572 "input_connections": {
573 "input_file": {
574 "id": 17,
575 "output_name": "output_mpileup"
576 }
577 },
578 "inputs": [],
579 "name": "PileupVariant",
580 "outputs": [
581 {
582 "name": "output_file",
583 "type": "pileup"
584 }
585 ],
586 "position": {
587 "left": 2545,
588 "top": 998
589 },
590 "post_job_actions": {},
591 "tool_errors": null,
592 "tool_id": "PileupVariant",
593 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
594 "tool_version": "0.01",
595 "type": "tool",
596 "user_outputs": []
597 },
598 "19": {
599 "annotation": "",
600 "id": 19,
601 "input_connections": {
602 "input_listA": {
603 "id": 18,
604 "output_name": "output_file"
605 },
606 "input_listB": {
607 "id": 3,
608 "output_name": "output"
609 }
610 },
611 "inputs": [],
612 "name": "listfiltering",
613 "outputs": [
614 {
615 "name": "output_file",
616 "type": "pileup"
617 }
618 ],
619 "position": {
620 "left": 2939,
621 "top": 1078
622 },
623 "post_job_actions": {},
624 "tool_errors": null,
625 "tool_id": "listfiltering",
626 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}",
627 "tool_version": "0.01",
628 "type": "tool",
629 "user_outputs": []
630 },
631 "20": {
632 "annotation": "",
633 "id": 20,
634 "input_connections": {
635 "input_file": {
636 "id": 19,
637 "output_name": "output_file"
638 }
639 },
640 "inputs": [],
641 "name": "SplitFile2x",
642 "outputs": [
643 {
644 "name": "output_file1",
645 "type": "txt"
646 },
647 {
648 "name": "output_file2",
649 "type": "txt"
650 }
651 ],
652 "position": {
653 "left": 3292,
654 "top": 1066.5
655 },
656 "post_job_actions": {},
657 "tool_errors": null,
658 "tool_id": "SplitFile2x",
659 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
660 "tool_version": "0.01",
661 "type": "tool",
662 "user_outputs": []
663 },
664 "21": {
665 "annotation": "",
666 "id": 21,
667 "input_connections": {
668 "input_assembly_file": {
669 "id": 2,
670 "output_name": "output"
671 },
672 "input_variant_file": {
673 "id": 20,
674 "output_name": "output_file1"
675 }
676 },
677 "inputs": [],
678 "name": "extractseq",
679 "outputs": [
680 {
681 "name": "output_file",
682 "type": "fasta"
683 }
684 ],
685 "position": {
686 "left": 3662,
687 "top": 979
688 },
689 "post_job_actions": {},
690 "tool_errors": null,
691 "tool_id": "extractseq",
692 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
693 "tool_version": "0.03",
694 "type": "tool",
695 "user_outputs": []
696 },
697 "22": {
698 "annotation": "",
699 "id": 22,
700 "input_connections": {
701 "input_assembly_file": {
702 "id": 2,
703 "output_name": "output"
704 },
705 "input_variant_file": {
706 "id": 20,
707 "output_name": "output_file2"
708 }
709 },
710 "inputs": [],
711 "name": "extractseq",
712 "outputs": [
713 {
714 "name": "output_file",
715 "type": "fasta"
716 }
717 ],
718 "position": {
719 "left": 3656,
720 "top": 1161.5
721 },
722 "post_job_actions": {},
723 "tool_errors": null,
724 "tool_id": "extractseq",
725 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
726 "tool_version": "0.03",
727 "type": "tool",
728 "user_outputs": []
729 },
730 "23": {
731 "annotation": "",
732 "id": 23,
733 "input_connections": {
734 "db_opts|histdb": {
735 "id": 9,
736 "output_name": "outfile"
737 },
738 "query": {
739 "id": 21,
740 "output_name": "output_file"
741 }
742 },
743 "inputs": [],
744 "name": "NCBI BLAST+ blastn",
745 "outputs": [
746 {
747 "name": "output1",
748 "type": "tabular"
749 }
750 ],
751 "position": {
752 "left": 4008,
753 "top": 956
754 },
755 "post_job_actions": {},
756 "tool_errors": null,
757 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
758 "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\"}",
759 "tool_version": "0.1.00",
760 "type": "tool",
761 "user_outputs": []
762 },
763 "24": {
764 "annotation": "",
765 "id": 24,
766 "input_connections": {
767 "db_opts|histdb": {
768 "id": 9,
769 "output_name": "outfile"
770 },
771 "query": {
772 "id": 22,
773 "output_name": "output_file"
774 }
775 },
776 "inputs": [],
777 "name": "NCBI BLAST+ blastn",
778 "outputs": [
779 {
780 "name": "output1",
781 "type": "tabular"
782 }
783 ],
784 "position": {
785 "left": 4011,
786 "top": 1117.5
787 },
788 "post_job_actions": {},
789 "tool_errors": null,
790 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
791 "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\"}",
792 "tool_version": "0.1.00",
793 "type": "tool",
794 "user_outputs": []
795 },
796 "25": {
797 "annotation": "",
798 "id": 25,
799 "input_connections": {
800 "input_blast_file": {
801 "id": 23,
802 "output_name": "output1"
803 },
804 "input_variant_file": {
805 "id": 20,
806 "output_name": "output_file1"
807 }
808 },
809 "inputs": [],
810 "name": "ParseBlastForUniqueMatch",
811 "outputs": [
812 {
813 "name": "output_file",
814 "type": "pileup"
815 }
816 ],
817 "position": {
818 "left": 4304,
819 "top": 824
820 },
821 "post_job_actions": {},
822 "tool_errors": null,
823 "tool_id": "ParseBlastForUniqueMatch",
824 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
825 "tool_version": "0.01",
826 "type": "tool",
827 "user_outputs": []
828 },
829 "26": {
830 "annotation": "",
831 "id": 26,
832 "input_connections": {
833 "input_blast_file": {
834 "id": 24,
835 "output_name": "output1"
836 },
837 "input_variant_file": {
838 "id": 20,
839 "output_name": "output_file2"
840 }
841 },
842 "inputs": [],
843 "name": "ParseBlastForUniqueMatch",
844 "outputs": [
845 {
846 "name": "output_file",
847 "type": "pileup"
848 }
849 ],
850 "position": {
851 "left": 4303.5,
852 "top": 1037.5
853 },
854 "post_job_actions": {},
855 "tool_errors": null,
856 "tool_id": "ParseBlastForUniqueMatch",
857 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
858 "tool_version": "0.01",
859 "type": "tool",
860 "user_outputs": []
861 },
862 "27": {
863 "annotation": "",
864 "id": 27,
865 "input_connections": {
866 "input_file1": {
867 "id": 25,
868 "output_name": "output_file"
869 },
870 "input_file2": {
871 "id": 26,
872 "output_name": "output_file"
873 }
874 },
875 "inputs": [],
876 "name": "MergeFile2x",
877 "outputs": [
878 {
879 "name": "output_file",
880 "type": "txt"
881 }
882 ],
883 "position": {
884 "left": 4707,
885 "top": 957.5
886 },
887 "post_job_actions": {},
888 "tool_errors": null,
889 "tool_id": "MergeFile2x",
890 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file1\": \"null\", \"input_file2\": \"null\"}",
891 "tool_version": "0.01",
892 "type": "tool",
893 "user_outputs": []
894 },
895 "28": {
896 "annotation": "",
897 "id": 28,
898 "input_connections": {
899 "input_file": {
900 "id": 27,
901 "output_name": "output_file"
902 }
903 },
904 "inputs": [],
905 "name": "mpileupfilterandstat",
906 "outputs": [
907 {
908 "name": "output_file",
909 "type": "pileup"
910 },
911 {
912 "name": "log_file",
913 "type": "txt"
914 }
915 ],
916 "position": {
917 "left": 5067,
918 "top": 1011.5
919 },
920 "post_job_actions": {},
921 "tool_errors": null,
922 "tool_id": "mpileupfilterandstat",
923 "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\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
924 "tool_version": "0.08",
925 "type": "tool",
926 "user_outputs": []
927 },
928 "29": {
929 "annotation": "",
930 "id": 29,
931 "input_connections": {
932 "input_blast_filtered_part1_file": {
933 "id": 25,
934 "output_name": "output_file"
935 },
936 "input_blast_filtered_part2_file": {
937 "id": 26,
938 "output_name": "output_file"
939 },
940 "input_list_filtered_file": {
941 "id": 19,
942 "output_name": "output_file"
943 },
944 "input_mpileup_variant_file": {
945 "id": 18,
946 "output_name": "output_file"
947 },
948 "input_read1_part1_trimmed_file": {
949 "id": 7,
950 "output_name": "output_read1_file"
951 },
952 "input_read1_part2_trimmed_file": {
953 "id": 8,
954 "output_name": "output_read1_file"
955 },
956 "input_read1_row_file": {
957 "id": 0,
958 "output_name": "output"
959 },
960 "input_read2_part1_trimmed_file": {
961 "id": 7,
962 "output_name": "output_read2_file"
963 },
964 "input_read2_part2_trimmed_file": {
965 "id": 8,
966 "output_name": "output_read2_file"
967 },
968 "input_read2_row_file": {
969 "id": 1,
970 "output_name": "output"
971 },
972 "input_sam_filtered_part1_file": {
973 "id": 12,
974 "output_name": "output_file"
975 },
976 "input_sam_filtered_part2_file": {
977 "id": 13,
978 "output_name": "output_file"
979 },
980 "input_sam_row_part1_file": {
981 "id": 10,
982 "output_name": "output"
983 },
984 "input_sam_row_part2_file": {
985 "id": 11,
986 "output_name": "output"
987 },
988 "input_snp_selected_file": {
989 "id": 28,
990 "output_name": "output_file"
991 }
992 },
993 "inputs": [],
994 "name": "rapsosnp_stats2x",
995 "outputs": [
996 {
997 "name": "output_file",
998 "type": "txt"
999 }
1000 ],
1001 "position": {
1002 "left": 2133.5,
1003 "top": 165.5
1004 },
1005 "post_job_actions": {},
1006 "tool_errors": null,
1007 "tool_id": "rapsosnp_stats2x",
1008 "tool_state": "{\"input_blast_filtered_part1_file\": \"null\", \"input_blast_filtered_part2_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"__page__\": 0, \"input_list_filtered_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_read2_row_file\": \"null\", \"input_mpileup_variant_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\"}",
1009 "tool_version": "0.01",
1010 "type": "tool",
1011 "user_outputs": []
1012 }
1013 }
1014 }