Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/Galaxy-Workflow-rapsosnp_v1.16_-_2x.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 - 2x", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "ASSEMBLY" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 200.000244140625, | |
21 "top": 211 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"ASSEMBLY\"}", | |
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": "READ1" | |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
41 "outputs": [], | |
42 "position": { | |
43 "left": 200.000244140625, | |
44 "top": 296 | |
45 }, | |
46 "tool_errors": null, | |
47 "tool_id": null, | |
48 "tool_state": "{\"name\": \"READ1\"}", | |
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": "READ2" | |
61 } | |
62 ], | |
63 "name": "Input dataset", | |
64 "outputs": [], | |
65 "position": { | |
66 "left": 200.000244140625, | |
67 "top": 381 | |
68 }, | |
69 "tool_errors": null, | |
70 "tool_id": null, | |
71 "tool_state": "{\"name\": \"READ2\"}", | |
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": 200.000244140625, | |
90 "top": 466 | |
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_fasta": { | |
104 "id": 0, | |
105 "output_name": "output" | |
106 } | |
107 }, | |
108 "inputs": [], | |
109 "name": "fastaGroomerForMakeBlastdb", | |
110 "outputs": [ | |
111 { | |
112 "name": "output_fasta", | |
113 "type": "fasta" | |
114 } | |
115 ], | |
116 "position": { | |
117 "left": 428.000244140625, | |
118 "top": 211 | |
119 }, | |
120 "post_job_actions": {}, | |
121 "tool_errors": null, | |
122 "tool_id": "fastaGroomerForMakeBlastdb", | |
123 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
124 "tool_version": "0.01", | |
125 "type": "tool", | |
126 "user_outputs": [] | |
127 }, | |
128 "5": { | |
129 "annotation": "", | |
130 "id": 5, | |
131 "input_connections": { | |
132 "input_file": { | |
133 "id": 1, | |
134 "output_name": "output" | |
135 } | |
136 }, | |
137 "inputs": [], | |
138 "name": "SplitFile2x", | |
139 "outputs": [ | |
140 { | |
141 "name": "output_file1", | |
142 "type": "txt" | |
143 }, | |
144 { | |
145 "name": "output_file2", | |
146 "type": "txt" | |
147 } | |
148 ], | |
149 "position": { | |
150 "left": 428.000244140625, | |
151 "top": 342 | |
152 }, | |
153 "post_job_actions": {}, | |
154 "tool_errors": null, | |
155 "tool_id": "SplitFile2x", | |
156 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", | |
157 "tool_version": "0.01", | |
158 "type": "tool", | |
159 "user_outputs": [] | |
160 }, | |
161 "6": { | |
162 "annotation": "", | |
163 "id": 6, | |
164 "input_connections": { | |
165 "input_file": { | |
166 "id": 2, | |
167 "output_name": "output" | |
168 } | |
169 }, | |
170 "inputs": [], | |
171 "name": "SplitFile2x", | |
172 "outputs": [ | |
173 { | |
174 "name": "output_file1", | |
175 "type": "txt" | |
176 }, | |
177 { | |
178 "name": "output_file2", | |
179 "type": "txt" | |
180 } | |
181 ], | |
182 "position": { | |
183 "left": 428.000244140625, | |
184 "top": 534 | |
185 }, | |
186 "post_job_actions": {}, | |
187 "tool_errors": null, | |
188 "tool_id": "SplitFile2x", | |
189 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}", | |
190 "tool_version": "0.01", | |
191 "type": "tool", | |
192 "user_outputs": [] | |
193 }, | |
194 "7": { | |
195 "annotation": "", | |
196 "id": 7, | |
197 "input_connections": { | |
198 "input_file": { | |
199 "id": 4, | |
200 "output_name": "output_fasta" | |
201 } | |
202 }, | |
203 "inputs": [], | |
204 "name": "NCBI BLAST+ makeblastdb", | |
205 "outputs": [ | |
206 { | |
207 "name": "outfile", | |
208 "type": "data" | |
209 } | |
210 ], | |
211 "position": { | |
212 "left": 756.000244140625, | |
213 "top": 615.0000305175781 | |
214 }, | |
215 "post_job_actions": {}, | |
216 "tool_errors": null, | |
217 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00", | |
218 "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\\\"\"}", | |
219 "tool_version": "0.1.00", | |
220 "type": "tool", | |
221 "user_outputs": [] | |
222 }, | |
223 "8": { | |
224 "annotation": "", | |
225 "id": 8, | |
226 "input_connections": { | |
227 "input_read1_file": { | |
228 "id": 5, | |
229 "output_name": "output_file1" | |
230 }, | |
231 "input_read2_file": { | |
232 "id": 6, | |
233 "output_name": "output_file1" | |
234 } | |
235 }, | |
236 "inputs": [], | |
237 "name": "PrepareFastqLight", | |
238 "outputs": [ | |
239 { | |
240 "name": "output_read1_file", | |
241 "type": "fastqsanger" | |
242 }, | |
243 { | |
244 "name": "output_read2_file", | |
245 "type": "fastqsanger" | |
246 } | |
247 ], | |
248 "position": { | |
249 "left": 756.000244140625, | |
250 "top": 211 | |
251 }, | |
252 "post_job_actions": {}, | |
253 "tool_errors": null, | |
254 "tool_id": "PrepareFastqLight", | |
255 "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\"}", | |
256 "tool_version": "0.01", | |
257 "type": "tool", | |
258 "user_outputs": [] | |
259 }, | |
260 "9": { | |
261 "annotation": "", | |
262 "id": 9, | |
263 "input_connections": { | |
264 "input_read1_file": { | |
265 "id": 5, | |
266 "output_name": "output_file2" | |
267 }, | |
268 "input_read2_file": { | |
269 "id": 6, | |
270 "output_name": "output_file2" | |
271 } | |
272 }, | |
273 "inputs": [], | |
274 "name": "PrepareFastqLight", | |
275 "outputs": [ | |
276 { | |
277 "name": "output_read1_file", | |
278 "type": "fastqsanger" | |
279 }, | |
280 { | |
281 "name": "output_read2_file", | |
282 "type": "fastqsanger" | |
283 } | |
284 ], | |
285 "position": { | |
286 "left": 756.000244140625, | |
287 "top": 413 | |
288 }, | |
289 "post_job_actions": {}, | |
290 "tool_errors": null, | |
291 "tool_id": "PrepareFastqLight", | |
292 "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\"}", | |
293 "tool_version": "0.01", | |
294 "type": "tool", | |
295 "user_outputs": [] | |
296 }, | |
297 "10": { | |
298 "annotation": "", | |
299 "id": 10, | |
300 "input_connections": { | |
301 "genomeSource|ownFile": { | |
302 "id": 0, | |
303 "output_name": "output" | |
304 }, | |
305 "paired|input1": { | |
306 "id": 8, | |
307 "output_name": "output_read1_file" | |
308 }, | |
309 "paired|input2": { | |
310 "id": 8, | |
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": 1084.000244140625, | |
324 "top": 211 | |
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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
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": 0, | |
340 "output_name": "output" | |
341 }, | |
342 "paired|input1": { | |
343 "id": 9, | |
344 "output_name": "output_read1_file" | |
345 }, | |
346 "paired|input2": { | |
347 "id": 9, | |
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": 1084.000244140625, | |
361 "top": 396 | |
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\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
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": 1348.000244140625, | |
390 "top": 211 | |
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, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"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": 1348.000244140625, | |
419 "top": 342 | |
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, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"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": 0, | |
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": 1676.000244140625, | |
452 "top": 211 | |
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, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__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": 0, | |
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": 1676.000244140625, | |
485 "top": 352 | |
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, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__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": 1904.000244140625, | |
522 "top": 211 | |
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\", \"title\": \"\\\"merge bam\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mergeSD\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
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": 0, | |
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": 2132.000244140625, | |
559 "top": 211 | |
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, \"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\\\"\"}", | |
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": 2458.000244140625, | |
588 "top": 211 | |
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": 2786.000244140625, | |
621 "top": 211 | |
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": 3114.000244140625, | |
654 "top": 211 | |
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": 0, | |
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": 3442.000244140625, | |
687 "top": 211 | |
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": 0, | |
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": 3442.000244140625, | |
720 "top": 386 | |
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": 7, | |
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": 3770.000244140625, | |
753 "top": 211 | |
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": 7, | |
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": 3770.000244140625, | |
786 "top": 352 | |
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\\\": \\\"0\\\"}\", \"__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": 4072.000228881836, | |
819 "top": 211 | |
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": 4072.000228881836, | |
852 "top": 420 | |
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": 4400.000228881836, | |
885 "top": 211 | |
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": 4728.000244140625, | |
918 "top": 211 | |
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\\\"\", \"do_stat\": \"\\\"YES\\\"\", \"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": 8, | |
950 "output_name": "output_read1_file" | |
951 }, | |
952 "input_read1_part2_trimmed_file": { | |
953 "id": 9, | |
954 "output_name": "output_read1_file" | |
955 }, | |
956 "input_read1_row_file": { | |
957 "id": 1, | |
958 "output_name": "output" | |
959 }, | |
960 "input_read2_part1_trimmed_file": { | |
961 "id": 8, | |
962 "output_name": "output_read2_file" | |
963 }, | |
964 "input_read2_part2_trimmed_file": { | |
965 "id": 9, | |
966 "output_name": "output_read2_file" | |
967 }, | |
968 "input_read2_row_file": { | |
969 "id": 2, | |
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": 5056.000244140625, | |
1003 "top": 211 | |
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 } |