Mercurial > repos > mytest > ngsap2
comparison NGSAP-Workflow-Denovo_workflow.ga @ 0:cc71440b759f draft default tip
Uploaded
author | mytest |
---|---|
date | Tue, 22 Sep 2015 01:58:00 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:cc71440b759f |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "NGSAP workflow 1", | |
4 "format-version": "0.1", | |
5 "name": "Denovo_workflow", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "R1_left" | |
15 } | |
16 ], | |
17 "label": null, | |
18 "name": "Input dataset", | |
19 "outputs": [], | |
20 "position": { | |
21 "left": 191, | |
22 "top": 195 | |
23 }, | |
24 "tool_errors": null, | |
25 "tool_id": null, | |
26 "tool_state": "{\"name\": \"R1_left\"}", | |
27 "tool_version": null, | |
28 "type": "data_input", | |
29 "user_outputs": [], | |
30 "uuid": "1c908163-a494-4e00-8463-2f3611220745" | |
31 }, | |
32 "1": { | |
33 "annotation": "", | |
34 "id": 1, | |
35 "input_connections": {}, | |
36 "inputs": [ | |
37 { | |
38 "description": "", | |
39 "name": "R1_right" | |
40 } | |
41 ], | |
42 "label": null, | |
43 "name": "Input dataset", | |
44 "outputs": [], | |
45 "position": { | |
46 "left": 200, | |
47 "top": 285 | |
48 }, | |
49 "tool_errors": null, | |
50 "tool_id": null, | |
51 "tool_state": "{\"name\": \"R1_right\"}", | |
52 "tool_version": null, | |
53 "type": "data_input", | |
54 "user_outputs": [], | |
55 "uuid": "f5d95ab6-b503-45a0-bbb4-c3c2980f4a04" | |
56 }, | |
57 "2": { | |
58 "annotation": "", | |
59 "id": 2, | |
60 "input_connections": {}, | |
61 "inputs": [ | |
62 { | |
63 "description": "", | |
64 "name": "R2_left" | |
65 } | |
66 ], | |
67 "label": null, | |
68 "name": "Input dataset", | |
69 "outputs": [], | |
70 "position": { | |
71 "left": 200, | |
72 "top": 370 | |
73 }, | |
74 "tool_errors": null, | |
75 "tool_id": null, | |
76 "tool_state": "{\"name\": \"R2_left\"}", | |
77 "tool_version": null, | |
78 "type": "data_input", | |
79 "user_outputs": [], | |
80 "uuid": "a296680e-69bd-4e43-87f3-5a19a3dfb00a" | |
81 }, | |
82 "3": { | |
83 "annotation": "", | |
84 "id": 3, | |
85 "input_connections": {}, | |
86 "inputs": [ | |
87 { | |
88 "description": "", | |
89 "name": "R4_left" | |
90 } | |
91 ], | |
92 "label": null, | |
93 "name": "Input dataset", | |
94 "outputs": [], | |
95 "position": { | |
96 "left": 200, | |
97 "top": 709.9999694824219 | |
98 }, | |
99 "tool_errors": null, | |
100 "tool_id": null, | |
101 "tool_state": "{\"name\": \"R4_left\"}", | |
102 "tool_version": null, | |
103 "type": "data_input", | |
104 "user_outputs": [], | |
105 "uuid": "da874053-bcaa-4a91-a4b6-43b722799b5a" | |
106 }, | |
107 "4": { | |
108 "annotation": "", | |
109 "id": 4, | |
110 "input_connections": {}, | |
111 "inputs": [ | |
112 { | |
113 "description": "", | |
114 "name": "R3_left" | |
115 } | |
116 ], | |
117 "label": null, | |
118 "name": "Input dataset", | |
119 "outputs": [], | |
120 "position": { | |
121 "left": 200, | |
122 "top": 539.9999694824219 | |
123 }, | |
124 "tool_errors": null, | |
125 "tool_id": null, | |
126 "tool_state": "{\"name\": \"R3_left\"}", | |
127 "tool_version": null, | |
128 "type": "data_input", | |
129 "user_outputs": [], | |
130 "uuid": "eb4256c2-b373-432b-9a27-bf15d2ff5668" | |
131 }, | |
132 "5": { | |
133 "annotation": "", | |
134 "id": 5, | |
135 "input_connections": {}, | |
136 "inputs": [ | |
137 { | |
138 "description": "", | |
139 "name": "R2_right" | |
140 } | |
141 ], | |
142 "label": null, | |
143 "name": "Input dataset", | |
144 "outputs": [], | |
145 "position": { | |
146 "left": 200, | |
147 "top": 455 | |
148 }, | |
149 "tool_errors": null, | |
150 "tool_id": null, | |
151 "tool_state": "{\"name\": \"R2_right\"}", | |
152 "tool_version": null, | |
153 "type": "data_input", | |
154 "user_outputs": [], | |
155 "uuid": "1a34e9bf-7e55-473c-813c-d2e028104a0a" | |
156 }, | |
157 "6": { | |
158 "annotation": "", | |
159 "id": 6, | |
160 "input_connections": {}, | |
161 "inputs": [ | |
162 { | |
163 "description": "", | |
164 "name": "R4_right" | |
165 } | |
166 ], | |
167 "label": null, | |
168 "name": "Input dataset", | |
169 "outputs": [], | |
170 "position": { | |
171 "left": 200, | |
172 "top": 794.9999694824219 | |
173 }, | |
174 "tool_errors": null, | |
175 "tool_id": null, | |
176 "tool_state": "{\"name\": \"R4_right\"}", | |
177 "tool_version": null, | |
178 "type": "data_input", | |
179 "user_outputs": [], | |
180 "uuid": "168365a1-1fac-446e-85c7-0066e2f5c72b" | |
181 }, | |
182 "7": { | |
183 "annotation": "", | |
184 "id": 7, | |
185 "input_connections": {}, | |
186 "inputs": [ | |
187 { | |
188 "description": "", | |
189 "name": "R3_right" | |
190 } | |
191 ], | |
192 "label": null, | |
193 "name": "Input dataset", | |
194 "outputs": [], | |
195 "position": { | |
196 "left": 200, | |
197 "top": 624.9999694824219 | |
198 }, | |
199 "tool_errors": null, | |
200 "tool_id": null, | |
201 "tool_state": "{\"name\": \"R3_right\"}", | |
202 "tool_version": null, | |
203 "type": "data_input", | |
204 "user_outputs": [], | |
205 "uuid": "31d47263-227d-4e7c-8d4f-d1cd22c4229c" | |
206 }, | |
207 "8": { | |
208 "annotation": "", | |
209 "id": 8, | |
210 "input_connections": { | |
211 "input1": { | |
212 "id": 0, | |
213 "output_name": "output" | |
214 }, | |
215 "queries_0|input2": { | |
216 "id": 2, | |
217 "output_name": "output" | |
218 }, | |
219 "queries_1|input2": { | |
220 "id": 4, | |
221 "output_name": "output" | |
222 }, | |
223 "queries_2|input2": { | |
224 "id": 3, | |
225 "output_name": "output" | |
226 } | |
227 }, | |
228 "inputs": [], | |
229 "label": null, | |
230 "name": "Concatenate datasets", | |
231 "outputs": [ | |
232 { | |
233 "name": "out_file1", | |
234 "type": "input" | |
235 } | |
236 ], | |
237 "position": { | |
238 "left": 428.0000305175781, | |
239 "top": 200 | |
240 }, | |
241 "post_job_actions": {}, | |
242 "tool_errors": null, | |
243 "tool_id": "cat1", | |
244 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}", | |
245 "tool_version": "1.0.0", | |
246 "type": "tool", | |
247 "user_outputs": [], | |
248 "uuid": "d6005191-a0e5-4092-8878-bb3ecbbada98" | |
249 }, | |
250 "9": { | |
251 "annotation": "", | |
252 "id": 9, | |
253 "input_connections": { | |
254 "input1": { | |
255 "id": 1, | |
256 "output_name": "output" | |
257 }, | |
258 "queries_0|input2": { | |
259 "id": 5, | |
260 "output_name": "output" | |
261 }, | |
262 "queries_1|input2": { | |
263 "id": 7, | |
264 "output_name": "output" | |
265 }, | |
266 "queries_2|input2": { | |
267 "id": 6, | |
268 "output_name": "output" | |
269 } | |
270 }, | |
271 "inputs": [], | |
272 "label": null, | |
273 "name": "Concatenate datasets", | |
274 "outputs": [ | |
275 { | |
276 "name": "out_file1", | |
277 "type": "input" | |
278 } | |
279 ], | |
280 "position": { | |
281 "left": 428.0000305175781, | |
282 "top": 395 | |
283 }, | |
284 "post_job_actions": {}, | |
285 "tool_errors": null, | |
286 "tool_id": "cat1", | |
287 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}", | |
288 "tool_version": "1.0.0", | |
289 "type": "tool", | |
290 "user_outputs": [], | |
291 "uuid": "506fdc53-2aa1-4a81-be5e-69b12676a6cd" | |
292 }, | |
293 "10": { | |
294 "annotation": "", | |
295 "id": 10, | |
296 "input_connections": { | |
297 "inputs|left_input": { | |
298 "id": 8, | |
299 "output_name": "out_file1" | |
300 }, | |
301 "inputs|right_input": { | |
302 "id": 9, | |
303 "output_name": "out_file1" | |
304 } | |
305 }, | |
306 "inputs": [], | |
307 "label": null, | |
308 "name": "Insilico Read Normalization", | |
309 "outputs": [ | |
310 { | |
311 "name": "insilico_read_normalization_log", | |
312 "type": "txt" | |
313 }, | |
314 { | |
315 "name": "left_normalized_read", | |
316 "type": "fastq" | |
317 }, | |
318 { | |
319 "name": "right_normalized_read", | |
320 "type": "fastq" | |
321 } | |
322 ], | |
323 "position": { | |
324 "left": 667.0000305175781, | |
325 "top": 200 | |
326 }, | |
327 "post_job_actions": {}, | |
328 "tool_errors": null, | |
329 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/insilico_read_nomalization/0.0.1", | |
330 "tool_state": "{\"__page__\": 0, \"JM\": \"\\\"1G\\\"\", \"inputs\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"left_input\\\": null, \\\"right_input\\\": null, \\\"additional_params\\\": {\\\"use_additional\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"maximum_coverage\": \"\\\"25\\\"\"}", | |
331 "tool_version": "0.0.1", | |
332 "type": "tool", | |
333 "user_outputs": [], | |
334 "uuid": "ee67cadd-54b2-4110-8046-3319c448cbbc" | |
335 }, | |
336 "11": { | |
337 "annotation": "", | |
338 "id": 11, | |
339 "input_connections": { | |
340 "inputs|left_input": { | |
341 "id": 10, | |
342 "output_name": "left_normalized_read" | |
343 }, | |
344 "inputs|right_input": { | |
345 "id": 10, | |
346 "output_name": "right_normalized_read" | |
347 } | |
348 }, | |
349 "inputs": [], | |
350 "label": null, | |
351 "name": "Trinity", | |
352 "outputs": [ | |
353 { | |
354 "name": "trinity_log", | |
355 "type": "txt" | |
356 }, | |
357 { | |
358 "name": "assembled_transcripts", | |
359 "type": "fasta" | |
360 } | |
361 ], | |
362 "position": { | |
363 "left": 980.0000305175781, | |
364 "top": 200 | |
365 }, | |
366 "post_job_actions": {}, | |
367 "tool_errors": null, | |
368 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/trinityrnaseq/0.0.1", | |
369 "tool_state": "{\"__page__\": 0, \"additional_params\": \"{\\\"use_additional\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"inputs\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"library_type\\\": \\\"None\\\", \\\"group_pairs_distance\\\": \\\"500\\\", \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"path_reinforcement_distance\\\": \\\"75\\\", \\\"right_input\\\": null}\", \"__rerun_remap_job_id__\": null, \"JM\": \"\\\"1G\\\"\", \"CPU\": \"\\\"2\\\"\"}", | |
370 "tool_version": "0.0.1", | |
371 "type": "tool", | |
372 "user_outputs": [], | |
373 "uuid": "990fa822-9962-4d2d-99ae-67674fbb8607" | |
374 }, | |
375 "12": { | |
376 "annotation": "", | |
377 "id": 12, | |
378 "input_connections": { | |
379 "reads|left_input": { | |
380 "id": 0, | |
381 "output_name": "output" | |
382 }, | |
383 "reads|right_input": { | |
384 "id": 1, | |
385 "output_name": "output" | |
386 }, | |
387 "transcripts": { | |
388 "id": 11, | |
389 "output_name": "assembled_transcripts" | |
390 } | |
391 }, | |
392 "inputs": [], | |
393 "label": null, | |
394 "name": "align_and_estimate_abundance", | |
395 "outputs": [ | |
396 { | |
397 "name": "align_and_estimate_abundance_log", | |
398 "type": "txt" | |
399 }, | |
400 { | |
401 "name": "bowtie_bam", | |
402 "type": "bam" | |
403 }, | |
404 { | |
405 "name": "rsem_isoforms", | |
406 "type": "tabular" | |
407 }, | |
408 { | |
409 "name": "rsem_genes", | |
410 "type": "tabular" | |
411 } | |
412 ], | |
413 "position": { | |
414 "left": 1261.0000305175781, | |
415 "top": 200 | |
416 }, | |
417 "post_job_actions": {}, | |
418 "tool_errors": null, | |
419 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/id_align_and_estimate_abundance/1.0", | |
420 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}", | |
421 "tool_version": "1.0", | |
422 "type": "tool", | |
423 "user_outputs": [], | |
424 "uuid": "d8feddcc-b4b8-4037-89a8-f0bb416146fc" | |
425 }, | |
426 "13": { | |
427 "annotation": "", | |
428 "id": 13, | |
429 "input_connections": { | |
430 "fastafile": { | |
431 "id": 11, | |
432 "output_name": "assembled_transcripts" | |
433 } | |
434 }, | |
435 "inputs": [], | |
436 "label": null, | |
437 "name": "Trinity Stats", | |
438 "outputs": [ | |
439 { | |
440 "name": "statsfile", | |
441 "type": "text" | |
442 } | |
443 ], | |
444 "position": { | |
445 "left": 1261.0000305175781, | |
446 "top": 449 | |
447 }, | |
448 "post_job_actions": {}, | |
449 "tool_errors": null, | |
450 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/id_trinity_stats/1.0", | |
451 "tool_state": "{\"fastafile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", | |
452 "tool_version": "1.0", | |
453 "type": "tool", | |
454 "user_outputs": [], | |
455 "uuid": "ccb6162f-e84b-4aae-bf7d-22dcc8fa16d5" | |
456 }, | |
457 "14": { | |
458 "annotation": "", | |
459 "id": 14, | |
460 "input_connections": { | |
461 "reads|left_input": { | |
462 "id": 2, | |
463 "output_name": "output" | |
464 }, | |
465 "reads|right_input": { | |
466 "id": 5, | |
467 "output_name": "output" | |
468 }, | |
469 "transcripts": { | |
470 "id": 11, | |
471 "output_name": "assembled_transcripts" | |
472 } | |
473 }, | |
474 "inputs": [], | |
475 "label": null, | |
476 "name": "align_and_estimate_abundance", | |
477 "outputs": [ | |
478 { | |
479 "name": "align_and_estimate_abundance_log", | |
480 "type": "txt" | |
481 }, | |
482 { | |
483 "name": "bowtie_bam", | |
484 "type": "bam" | |
485 }, | |
486 { | |
487 "name": "rsem_isoforms", | |
488 "type": "tabular" | |
489 }, | |
490 { | |
491 "name": "rsem_genes", | |
492 "type": "tabular" | |
493 } | |
494 ], | |
495 "position": { | |
496 "left": 1261.0000305175781, | |
497 "top": 561.9999694824219 | |
498 }, | |
499 "post_job_actions": {}, | |
500 "tool_errors": null, | |
501 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/id_align_and_estimate_abundance/1.0", | |
502 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}", | |
503 "tool_version": "1.0", | |
504 "type": "tool", | |
505 "user_outputs": [], | |
506 "uuid": "769db165-573c-4359-84ee-e1bb7518a430" | |
507 }, | |
508 "15": { | |
509 "annotation": "", | |
510 "id": 15, | |
511 "input_connections": { | |
512 "transcript": { | |
513 "id": 11, | |
514 "output_name": "assembled_transcripts" | |
515 } | |
516 }, | |
517 "inputs": [], | |
518 "label": null, | |
519 "name": "transDecoder", | |
520 "outputs": [ | |
521 { | |
522 "name": "transdecoder_pep", | |
523 "type": "fasta" | |
524 }, | |
525 { | |
526 "name": "transdecoder_cds", | |
527 "type": "fasta" | |
528 }, | |
529 { | |
530 "name": "transdecoder_bed", | |
531 "type": "bed" | |
532 }, | |
533 { | |
534 "name": "transdecoder_gff3", | |
535 "type": "tabular" | |
536 }, | |
537 { | |
538 "name": "transdecoder_mRNA", | |
539 "type": "fasta" | |
540 }, | |
541 { | |
542 "name": "transdecoder_log", | |
543 "type": "txt" | |
544 } | |
545 ], | |
546 "position": { | |
547 "left": 1261.0000305175781, | |
548 "top": 810.9999694824219 | |
549 }, | |
550 "post_job_actions": {}, | |
551 "tool_errors": null, | |
552 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/id_transDecoder/1.0", | |
553 "tool_state": "{\"pfam\": \"{\\\"options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"optional\": \"{\\\"parameters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"transcript\": \"null\", \"__page__\": 0}", | |
554 "tool_version": "1.0", | |
555 "type": "tool", | |
556 "user_outputs": [], | |
557 "uuid": "c4b3457c-57d2-4287-8c17-360a352f1d78" | |
558 }, | |
559 "16": { | |
560 "annotation": "", | |
561 "id": 16, | |
562 "input_connections": { | |
563 "reads|left_input": { | |
564 "id": 4, | |
565 "output_name": "output" | |
566 }, | |
567 "reads|right_input": { | |
568 "id": 7, | |
569 "output_name": "output" | |
570 }, | |
571 "transcripts": { | |
572 "id": 11, | |
573 "output_name": "assembled_transcripts" | |
574 } | |
575 }, | |
576 "inputs": [], | |
577 "label": null, | |
578 "name": "align_and_estimate_abundance", | |
579 "outputs": [ | |
580 { | |
581 "name": "align_and_estimate_abundance_log", | |
582 "type": "txt" | |
583 }, | |
584 { | |
585 "name": "bowtie_bam", | |
586 "type": "bam" | |
587 }, | |
588 { | |
589 "name": "rsem_isoforms", | |
590 "type": "tabular" | |
591 }, | |
592 { | |
593 "name": "rsem_genes", | |
594 "type": "tabular" | |
595 } | |
596 ], | |
597 "position": { | |
598 "left": 1261.0000305175781, | |
599 "top": 1059.9999694824219 | |
600 }, | |
601 "post_job_actions": {}, | |
602 "tool_errors": null, | |
603 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/id_align_and_estimate_abundance/1.0", | |
604 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}", | |
605 "tool_version": "1.0", | |
606 "type": "tool", | |
607 "user_outputs": [], | |
608 "uuid": "77776860-d7ed-45c6-9280-7326e4e8c486" | |
609 }, | |
610 "17": { | |
611 "annotation": "", | |
612 "id": 17, | |
613 "input_connections": { | |
614 "reads|left_input": { | |
615 "id": 3, | |
616 "output_name": "output" | |
617 }, | |
618 "reads|right_input": { | |
619 "id": 6, | |
620 "output_name": "output" | |
621 }, | |
622 "transcripts": { | |
623 "id": 11, | |
624 "output_name": "assembled_transcripts" | |
625 } | |
626 }, | |
627 "inputs": [], | |
628 "label": null, | |
629 "name": "align_and_estimate_abundance", | |
630 "outputs": [ | |
631 { | |
632 "name": "align_and_estimate_abundance_log", | |
633 "type": "txt" | |
634 }, | |
635 { | |
636 "name": "bowtie_bam", | |
637 "type": "bam" | |
638 }, | |
639 { | |
640 "name": "rsem_isoforms", | |
641 "type": "tabular" | |
642 }, | |
643 { | |
644 "name": "rsem_genes", | |
645 "type": "tabular" | |
646 } | |
647 ], | |
648 "position": { | |
649 "left": 1261.0000305175781, | |
650 "top": 1308.9999694824219 | |
651 }, | |
652 "post_job_actions": {}, | |
653 "tool_errors": null, | |
654 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/id_align_and_estimate_abundance/1.0", | |
655 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}", | |
656 "tool_version": "1.0", | |
657 "type": "tool", | |
658 "user_outputs": [], | |
659 "uuid": "f0db45a0-2a1b-422b-912e-b371778b46c6" | |
660 }, | |
661 "18": { | |
662 "annotation": "", | |
663 "id": 18, | |
664 "input_connections": { | |
665 "query": { | |
666 "id": 15, | |
667 "output_name": "transdecoder_pep" | |
668 } | |
669 }, | |
670 "inputs": [], | |
671 "label": null, | |
672 "name": "NCBI BLAST+ blastp", | |
673 "outputs": [ | |
674 { | |
675 "name": "output1", | |
676 "type": "tabular" | |
677 } | |
678 ], | |
679 "position": { | |
680 "left": 1589.0000305175781, | |
681 "top": 200 | |
682 }, | |
683 "post_job_actions": {}, | |
684 "tool_errors": null, | |
685 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.01", | |
686 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastp\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": null}}\", \"output\": \"{\\\"out_format\\\": \\\"ext\\\", \\\"__current_case__\\\": 1}\", \"query\": \"null\"}", | |
687 "tool_version": "0.1.01", | |
688 "type": "tool", | |
689 "user_outputs": [], | |
690 "uuid": "2e4f1945-4d2a-47e6-932c-f6f5b55c8089" | |
691 }, | |
692 "19": { | |
693 "annotation": "", | |
694 "id": 19, | |
695 "input_connections": { | |
696 "isoform_sample_0|isoform_sample_matrix": { | |
697 "id": 12, | |
698 "output_name": "rsem_isoforms" | |
699 }, | |
700 "isoform_sample_2|isoform_sample_matrix": { | |
701 "id": 14, | |
702 "output_name": "rsem_isoforms" | |
703 }, | |
704 "isoform_sample_3|isoform_sample_matrix": { | |
705 "id": 16, | |
706 "output_name": "rsem_isoforms" | |
707 }, | |
708 "isoform_sample_4|isoform_sample_matrix": { | |
709 "id": 17, | |
710 "output_name": "rsem_isoforms" | |
711 } | |
712 }, | |
713 "inputs": [], | |
714 "label": null, | |
715 "name": "Differential Expression", | |
716 "outputs": [ | |
717 { | |
718 "name": "de_output", | |
719 "type": "zip" | |
720 }, | |
721 { | |
722 "name": "output_log", | |
723 "type": "txt" | |
724 } | |
725 ], | |
726 "position": { | |
727 "left": 1589.0000305175781, | |
728 "top": 313 | |
729 }, | |
730 "post_job_actions": {}, | |
731 "tool_errors": null, | |
732 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/differential_expression/1.0", | |
733 "tool_state": "{\"isoform_sample\": \"[{\\\"__index__\\\": 0, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample1\\\"}, {\\\"__index__\\\": 2, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample2\\\"}, {\\\"__index__\\\": 3, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample3\\\"}, {\\\"__index__\\\": 4, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample4\\\"}]\", \"__page__\": 0, \"est_method\": \"\\\"RSEM\\\"\", \"__rerun_remap_job_id__\": null, \"method\": \"\\\"edgeR\\\"\"}", | |
734 "tool_version": "1.0", | |
735 "type": "tool", | |
736 "user_outputs": [], | |
737 "uuid": "ad56b1ff-e6d3-492e-b17b-72d68285ae17" | |
738 }, | |
739 "20": { | |
740 "annotation": "", | |
741 "id": 20, | |
742 "input_connections": { | |
743 "blastoutfile": { | |
744 "id": 18, | |
745 "output_name": "output1" | |
746 }, | |
747 "trinityassembledfile": { | |
748 "id": 15, | |
749 "output_name": "transdecoder_pep" | |
750 } | |
751 }, | |
752 "inputs": [], | |
753 "label": null, | |
754 "name": "BLAST OUTPUT PARSER", | |
755 "outputs": [ | |
756 { | |
757 "name": "parsed_blastfile_above_cutoff", | |
758 "type": "tabular" | |
759 }, | |
760 { | |
761 "name": "parsed_blastfile_below_cutoff", | |
762 "type": "tabular" | |
763 }, | |
764 { | |
765 "name": "oneline_file", | |
766 "type": "fasta" | |
767 }, | |
768 { | |
769 "name": "blastfile_below_cutoff", | |
770 "type": "fasta" | |
771 }, | |
772 { | |
773 "name": "blastfile_above_cutoff", | |
774 "type": "fasta" | |
775 } | |
776 ], | |
777 "position": { | |
778 "left": 1912.9999084472656, | |
779 "top": 200 | |
780 }, | |
781 "post_job_actions": {}, | |
782 "tool_errors": null, | |
783 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/ngsap1/blast_parser_using_awk/0.0.1", | |
784 "tool_state": "{\"__page__\": 0, \"blastoutfile\": \"null\", \"evalue\": \"\\\"1e-05\\\"\", \"trinityassembledfile\": \"null\", \"qcovs\": \"\\\"95\\\"\", \"__rerun_remap_job_id__\": null}", | |
785 "tool_version": "0.0.1", | |
786 "type": "tool", | |
787 "user_outputs": [], | |
788 "uuid": "a3e88afe-a154-43b3-8f7c-8baa37e529c0" | |
789 } | |
790 }, | |
791 "uuid": "7bbee726-311d-420a-92f8-fed0c0d00e1a" | |
792 } |