Mercurial > repos > gandres > sniplay_workflow
comparison Galaxy-Workflow-SNiPlay_workflow_final.ga @ 0:66cb91afe9ea draft
Uploaded
author | gandres |
---|---|
date | Wed, 23 Sep 2015 11:09:10 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:66cb91afe9ea |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "SNiPlay_workflow_final", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "VCF" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 253.63333129882812, | |
21 "top": 239.61666870117188 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"VCF\"}", | |
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": "Fasta" | |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
41 "outputs": [], | |
42 "position": { | |
43 "left": 223.63333129882812, | |
44 "top": 417.6166687011719 | |
45 }, | |
46 "tool_errors": null, | |
47 "tool_id": null, | |
48 "tool_state": "{\"name\": \"Fasta\"}", | |
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": "GFF" | |
61 } | |
62 ], | |
63 "name": "Input dataset", | |
64 "outputs": [], | |
65 "position": { | |
66 "left": 306.63330078125, | |
67 "top": 580.61669921875 | |
68 }, | |
69 "tool_errors": null, | |
70 "tool_id": null, | |
71 "tool_state": "{\"name\": \"GFF\"}", | |
72 "tool_version": null, | |
73 "type": "data_input", | |
74 "user_outputs": [] | |
75 }, | |
76 "3": { | |
77 "annotation": "", | |
78 "id": 3, | |
79 "input_connections": { | |
80 "genome": { | |
81 "id": 1, | |
82 "output_name": "output" | |
83 }, | |
84 "gff": { | |
85 "id": 2, | |
86 "output_name": "output" | |
87 }, | |
88 "vcf": { | |
89 "id": 0, | |
90 "output_name": "output" | |
91 } | |
92 }, | |
93 "inputs": [], | |
94 "name": "SnpEff", | |
95 "outputs": [ | |
96 { | |
97 "name": "output", | |
98 "type": "vcf" | |
99 }, | |
100 { | |
101 "name": "statsFile", | |
102 "type": "html" | |
103 }, | |
104 { | |
105 "name": "log", | |
106 "type": "txt" | |
107 } | |
108 ], | |
109 "position": { | |
110 "left": 563.63330078125, | |
111 "top": 156.61666870117188 | |
112 }, | |
113 "post_job_actions": {}, | |
114 "tool_errors": null, | |
115 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/4.0", | |
116 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"gff\": \"null\", \"genome\": \"null\", \"vcf\": \"null\"}", | |
117 "tool_version": "4.0", | |
118 "type": "tool", | |
119 "user_outputs": [] | |
120 }, | |
121 "4": { | |
122 "annotation": "", | |
123 "id": 4, | |
124 "input_connections": { | |
125 "input": { | |
126 "id": 3, | |
127 "output_name": "output" | |
128 } | |
129 }, | |
130 "inputs": [ | |
131 { | |
132 "description": "runtime parameter for tool SnpSift Filter", | |
133 "name": "expr" | |
134 } | |
135 ], | |
136 "name": "SnpSift Filter", | |
137 "outputs": [ | |
138 { | |
139 "name": "output", | |
140 "type": "vcf" | |
141 } | |
142 ], | |
143 "position": { | |
144 "left": 863.63330078125, | |
145 "top": 334.6166687011719 | |
146 }, | |
147 "post_job_actions": {}, | |
148 "tool_errors": null, | |
149 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.0.0", | |
150 "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"expr\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"filtering\": \"{\\\"mode\\\": \\\"entries\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", | |
151 "tool_version": "4.0.0", | |
152 "type": "tool", | |
153 "user_outputs": [] | |
154 }, | |
155 "5": { | |
156 "annotation": "", | |
157 "id": 5, | |
158 "input_connections": { | |
159 "filein": { | |
160 "id": 4, | |
161 "output_name": "output" | |
162 } | |
163 }, | |
164 "inputs": [], | |
165 "name": "VCFtools Filter", | |
166 "outputs": [ | |
167 { | |
168 "name": "fileout", | |
169 "type": "vcf" | |
170 }, | |
171 { | |
172 "name": "fileout_map", | |
173 "type": "txt" | |
174 }, | |
175 { | |
176 "name": "filelog", | |
177 "type": "txt" | |
178 } | |
179 ], | |
180 "position": { | |
181 "left": 1164.63330078125, | |
182 "top": 300.6166687011719 | |
183 }, | |
184 "post_job_actions": {}, | |
185 "tool_errors": null, | |
186 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1", | |
187 "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"None\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"filein\": \"null\", \"samples\": \"\\\"None\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", | |
188 "tool_version": "1.1.1", | |
189 "type": "tool", | |
190 "user_outputs": [] | |
191 }, | |
192 "6": { | |
193 "annotation": "", | |
194 "id": 6, | |
195 "input_connections": { | |
196 "filein": { | |
197 "id": 5, | |
198 "output_name": "fileout" | |
199 } | |
200 }, | |
201 "inputs": [], | |
202 "name": "VCFtools Filter", | |
203 "outputs": [ | |
204 { | |
205 "name": "fileout", | |
206 "type": "vcf" | |
207 }, | |
208 { | |
209 "name": "fileout_map", | |
210 "type": "txt" | |
211 }, | |
212 { | |
213 "name": "filelog", | |
214 "type": "txt" | |
215 } | |
216 ], | |
217 "position": { | |
218 "left": 1194.433349609375, | |
219 "top": 770.88330078125 | |
220 }, | |
221 "post_job_actions": {}, | |
222 "tool_errors": null, | |
223 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1", | |
224 "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"plink\\\"\", \"filein\": \"null\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", | |
225 "tool_version": "1.1.1", | |
226 "type": "tool", | |
227 "user_outputs": [] | |
228 }, | |
229 "7": { | |
230 "annotation": "", | |
231 "id": 7, | |
232 "input_connections": { | |
233 "filein": { | |
234 "id": 5, | |
235 "output_name": "fileout" | |
236 } | |
237 }, | |
238 "inputs": [], | |
239 "name": "VCFtools Stats", | |
240 "outputs": [ | |
241 { | |
242 "name": "fileout_annot", | |
243 "type": "txt" | |
244 }, | |
245 { | |
246 "name": "fileout_het", | |
247 "type": "txt" | |
248 }, | |
249 { | |
250 "name": "fileout_imiss", | |
251 "type": "txt" | |
252 }, | |
253 { | |
254 "name": "fileout_sum", | |
255 "type": "txt" | |
256 }, | |
257 { | |
258 "name": "filelog", | |
259 "type": "txt" | |
260 } | |
261 ], | |
262 "position": { | |
263 "left": 1488.683349609375, | |
264 "top": 100.10000610351562 | |
265 }, | |
266 "post_job_actions": {}, | |
267 "tool_errors": null, | |
268 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsstats/1.0.0", | |
269 "tool_state": "{\"fileout_label\": \"\\\"vcf_stats\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", | |
270 "tool_version": "1.0.0", | |
271 "type": "tool", | |
272 "user_outputs": [] | |
273 }, | |
274 "8": { | |
275 "annotation": "", | |
276 "id": 8, | |
277 "input_connections": { | |
278 "filein": { | |
279 "id": 5, | |
280 "output_name": "fileout" | |
281 } | |
282 }, | |
283 "inputs": [], | |
284 "name": "VCF tools SlidingWindow", | |
285 "outputs": [ | |
286 { | |
287 "name": "fileout_snp", | |
288 "type": "tabular" | |
289 }, | |
290 { | |
291 "name": "fileout_taj", | |
292 "type": "tabular" | |
293 }, | |
294 { | |
295 "name": "fileout_tstv", | |
296 "type": "tabular" | |
297 }, | |
298 { | |
299 "name": "fileout_windowed", | |
300 "type": "tabular" | |
301 }, | |
302 { | |
303 "name": "filelog", | |
304 "type": "txt" | |
305 } | |
306 ], | |
307 "position": { | |
308 "left": 1488.683349609375, | |
309 "top": 309.1000061035156 | |
310 }, | |
311 "post_job_actions": {}, | |
312 "tool_errors": null, | |
313 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsslidingwindow/1.0.0", | |
314 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"window\": \"\\\"200000\\\"\", \"fileout_label\": \"\\\"snp_density\\\"\", \"step\": \"\\\"50000\\\"\", \"filein\": \"null\"}", | |
315 "tool_version": "1.0.0", | |
316 "type": "tool", | |
317 "user_outputs": [] | |
318 }, | |
319 "9": { | |
320 "annotation": "", | |
321 "id": 9, | |
322 "input_connections": { | |
323 "filein": { | |
324 "id": 5, | |
325 "output_name": "fileout" | |
326 }, | |
327 "optional|filefasta": { | |
328 "id": 1, | |
329 "output_name": "output" | |
330 }, | |
331 "optional|filegff": { | |
332 "id": 2, | |
333 "output_name": "output" | |
334 } | |
335 }, | |
336 "inputs": [], | |
337 "name": "VCF to Hapmap", | |
338 "outputs": [ | |
339 { | |
340 "name": "fileout", | |
341 "type": "txt" | |
342 }, | |
343 { | |
344 "name": "fileout_seq", | |
345 "type": "txt" | |
346 }, | |
347 { | |
348 "name": "fileout_fa1", | |
349 "type": "fasta" | |
350 } | |
351 ], | |
352 "position": { | |
353 "left": 1479.683349609375, | |
354 "top": 531.0999755859375 | |
355 }, | |
356 "post_job_actions": {}, | |
357 "tool_errors": null, | |
358 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_vcf2fastaandhapmap/1.1.0", | |
359 "tool_state": "{\"fileout_label\": \"\\\"input\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"optional\": \"{\\\"file_opt\\\": \\\"fasta_gff\\\", \\\"filefasta\\\": null, \\\"filegff\\\": null, \\\"__current_case__\\\": 2}\", \"filein\": \"null\"}", | |
360 "tool_version": "1.1.0", | |
361 "type": "tool", | |
362 "user_outputs": [] | |
363 }, | |
364 "10": { | |
365 "annotation": "", | |
366 "id": 10, | |
367 "input_connections": { | |
368 "map": { | |
369 "id": 6, | |
370 "output_name": "fileout_map" | |
371 }, | |
372 "ped": { | |
373 "id": 6, | |
374 "output_name": "fileout" | |
375 } | |
376 }, | |
377 "inputs": [], | |
378 "name": "plink: ped2bed", | |
379 "outputs": [ | |
380 { | |
381 "name": "bed", | |
382 "type": "txt" | |
383 }, | |
384 { | |
385 "name": "fam", | |
386 "type": "txt" | |
387 }, | |
388 { | |
389 "name": "bim", | |
390 "type": "txt" | |
391 }, | |
392 { | |
393 "name": "logs", | |
394 "type": "txt" | |
395 } | |
396 ], | |
397 "position": { | |
398 "left": 1488.1666259765625, | |
399 "top": 805.5833129882812 | |
400 }, | |
401 "post_job_actions": {}, | |
402 "tool_errors": null, | |
403 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/ped2bed/1.24", | |
404 "tool_state": "{\"ped\": \"null\", \"map\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
405 "tool_version": "1.24", | |
406 "type": "tool", | |
407 "user_outputs": [] | |
408 }, | |
409 "11": { | |
410 "annotation": "", | |
411 "id": 11, | |
412 "input_connections": { | |
413 "filein": { | |
414 "id": 6, | |
415 "output_name": "fileout" | |
416 } | |
417 }, | |
418 "inputs": [], | |
419 "name": "Ped2Fasta", | |
420 "outputs": [ | |
421 { | |
422 "name": "fileout", | |
423 "type": "fasta" | |
424 } | |
425 ], | |
426 "position": { | |
427 "left": 1491.4833984375, | |
428 "top": 1137.4666748046875 | |
429 }, | |
430 "post_job_actions": {}, | |
431 "tool_errors": null, | |
432 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_pedToFasta/1.0.0", | |
433 "tool_state": "{\"fileout_label\": \"\\\"filtered\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", | |
434 "tool_version": "1.0.0", | |
435 "type": "tool", | |
436 "user_outputs": [] | |
437 }, | |
438 "12": { | |
439 "annotation": "", | |
440 "id": 12, | |
441 "input_connections": { | |
442 "filein": { | |
443 "id": 9, | |
444 "output_name": "fileout" | |
445 } | |
446 }, | |
447 "inputs": [], | |
448 "name": "SNP density", | |
449 "outputs": [ | |
450 { | |
451 "name": "fileout", | |
452 "type": "tabular" | |
453 }, | |
454 { | |
455 "name": "fileout_bysample", | |
456 "type": "tabular" | |
457 } | |
458 ], | |
459 "position": { | |
460 "left": 1785.183349609375, | |
461 "top": 478.8499755859375 | |
462 }, | |
463 "post_job_actions": {}, | |
464 "tool_errors": null, | |
465 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_density/1.2.0", | |
466 "tool_state": "{\"fileout_label\": \"\\\"densities\\\"\", \"__page__\": 0, \"step\": \"\\\"200000\\\"\", \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", | |
467 "tool_version": "1.2.0", | |
468 "type": "tool", | |
469 "user_outputs": [] | |
470 }, | |
471 "13": { | |
472 "annotation": "", | |
473 "id": 13, | |
474 "input_connections": { | |
475 "input": { | |
476 "id": 9, | |
477 "output_name": "fileout_fa1" | |
478 } | |
479 }, | |
480 "inputs": [], | |
481 "name": "Diversity by gene", | |
482 "outputs": [ | |
483 { | |
484 "name": "output", | |
485 "type": "txt" | |
486 }, | |
487 { | |
488 "name": "log", | |
489 "type": "txt" | |
490 } | |
491 ], | |
492 "position": { | |
493 "left": 1764.183349609375, | |
494 "top": 655.63330078125 | |
495 }, | |
496 "post_job_actions": {}, | |
497 "tool_errors": null, | |
498 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/calculate_diversity/2.1.6", | |
499 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
500 "tool_version": "2.1.6", | |
501 "type": "tool", | |
502 "user_outputs": [] | |
503 }, | |
504 "14": { | |
505 "annotation": "", | |
506 "id": 14, | |
507 "input_connections": { | |
508 "bed": { | |
509 "id": 10, | |
510 "output_name": "bed" | |
511 }, | |
512 "bim": { | |
513 "id": 10, | |
514 "output_name": "bim" | |
515 }, | |
516 "fam": { | |
517 "id": 10, | |
518 "output_name": "fam" | |
519 } | |
520 }, | |
521 "inputs": [], | |
522 "name": "Admixture", | |
523 "outputs": [ | |
524 { | |
525 "name": "best_k_output", | |
526 "type": "txt" | |
527 }, | |
528 { | |
529 "name": "best_k_logfile", | |
530 "type": "txt" | |
531 }, | |
532 { | |
533 "name": "outputs", | |
534 "type": "txt" | |
535 }, | |
536 { | |
537 "name": "logs", | |
538 "type": "txt" | |
539 } | |
540 ], | |
541 "position": { | |
542 "left": 1784.1666259765625, | |
543 "top": 839.5833129882812 | |
544 }, | |
545 "post_job_actions": {}, | |
546 "tool_errors": null, | |
547 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/admixture/admixture/1.23", | |
548 "tool_state": "{\"__page__\": 0, \"bim\": \"null\", \"__rerun_remap_job_id__\": null, \"kmin\": \"\\\"1\\\"\", \"bed\": \"null\", \"kmax\": \"\\\"5\\\"\", \"fam\": \"null\"}", | |
549 "tool_version": "1.23", | |
550 "type": "tool", | |
551 "user_outputs": [] | |
552 }, | |
553 "15": { | |
554 "annotation": "", | |
555 "id": 15, | |
556 "input_connections": { | |
557 "filein": { | |
558 "id": 11, | |
559 "output_name": "fileout" | |
560 } | |
561 }, | |
562 "inputs": [], | |
563 "name": "Readseq", | |
564 "outputs": [ | |
565 { | |
566 "name": "fileout_log", | |
567 "type": "txt" | |
568 }, | |
569 { | |
570 "name": "fileout", | |
571 "type": "txt" | |
572 } | |
573 ], | |
574 "position": { | |
575 "left": 1734, | |
576 "top": 1156.75 | |
577 }, | |
578 "post_job_actions": {}, | |
579 "tool_errors": null, | |
580 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/readseq/sniplay_readseq/1.0.2", | |
581 "tool_state": "{\"fileout_label\": \"\\\"phylip conversion\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\", \"format\": \"\\\"12\\\"\"}", | |
582 "tool_version": "1.0.2", | |
583 "type": "tool", | |
584 "user_outputs": [] | |
585 }, | |
586 "16": { | |
587 "annotation": "", | |
588 "id": 16, | |
589 "input_connections": { | |
590 "input_data": { | |
591 "id": 15, | |
592 "output_name": "fileout_log" | |
593 } | |
594 }, | |
595 "inputs": [], | |
596 "name": "FastME", | |
597 "outputs": [ | |
598 { | |
599 "name": "fileout_log", | |
600 "type": "txt" | |
601 }, | |
602 { | |
603 "name": "fileout", | |
604 "type": "txt" | |
605 } | |
606 ], | |
607 "position": { | |
608 "left": 1969, | |
609 "top": 1143.75 | |
610 }, | |
611 "post_job_actions": {}, | |
612 "tool_errors": null, | |
613 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/fastme/sniplay_fastme/1.0.2", | |
614 "tool_state": "{\"distance\": \"\\\"I\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"fileout_label\": \"\\\"Newick tree\\\"\", \"input_data\": \"null\", \"model\": \"\\\"4\\\"\"}", | |
615 "tool_version": "1.0.2", | |
616 "type": "tool", | |
617 "user_outputs": [] | |
618 }, | |
619 "17": { | |
620 "annotation": "", | |
621 "id": 17, | |
622 "input_connections": { | |
623 "filein": { | |
624 "id": 16, | |
625 "output_name": "fileout" | |
626 } | |
627 }, | |
628 "inputs": [], | |
629 "name": "Rooting", | |
630 "outputs": [ | |
631 { | |
632 "name": "fileout_log", | |
633 "type": "txt" | |
634 }, | |
635 { | |
636 "name": "fileout", | |
637 "type": "txt" | |
638 } | |
639 ], | |
640 "position": { | |
641 "left": 2224, | |
642 "top": 1157.75 | |
643 }, | |
644 "post_job_actions": {}, | |
645 "tool_errors": null, | |
646 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/1.0.2", | |
647 "tool_state": "{\"fileout_label\": \"\\\"out tree\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"filein\": \"null\"}", | |
648 "tool_version": "1.0.2", | |
649 "type": "tool", | |
650 "user_outputs": [] | |
651 } | |
652 } | |
653 } |