Mercurial > repos > chrisd > amrplusplus_workflow
comparison amrplusplus_wf.ga @ 1:11cb57237849 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
author | chrisd |
---|---|
date | Thu, 24 Mar 2016 04:16:47 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
0:834c10340bce | 1:11cb57237849 |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "amrplusplus_wf_pe", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "content_id": null, | |
10 "id": 0, | |
11 "input_connections": {}, | |
12 "inputs": [ | |
13 { | |
14 "description": "", | |
15 "name": "Input Dataset" | |
16 } | |
17 ], | |
18 "label": "AMR Database", | |
19 "name": "Input dataset", | |
20 "outputs": [], | |
21 "position": { | |
22 "left": 200, | |
23 "top": 200 | |
24 }, | |
25 "tool_errors": null, | |
26 "tool_id": null, | |
27 "tool_state": "{\"name\": \"Input Dataset\"}", | |
28 "tool_version": null, | |
29 "type": "data_input", | |
30 "uuid": "c33b3302-86dd-4020-920b-e91904994b0b", | |
31 "workflow_outputs": [] | |
32 }, | |
33 "1": { | |
34 "annotation": "", | |
35 "content_id": null, | |
36 "id": 1, | |
37 "input_connections": {}, | |
38 "inputs": [ | |
39 { | |
40 "description": "", | |
41 "name": "Input Dataset" | |
42 } | |
43 ], | |
44 "label": "Host Genome", | |
45 "name": "Input dataset", | |
46 "outputs": [], | |
47 "position": { | |
48 "left": 200, | |
49 "top": 285 | |
50 }, | |
51 "tool_errors": null, | |
52 "tool_id": null, | |
53 "tool_state": "{\"name\": \"Input Dataset\"}", | |
54 "tool_version": null, | |
55 "type": "data_input", | |
56 "uuid": "828c1738-4db6-4548-89b8-85e68a00491a", | |
57 "workflow_outputs": [] | |
58 }, | |
59 "2": { | |
60 "annotation": "", | |
61 "content_id": null, | |
62 "id": 2, | |
63 "input_connections": {}, | |
64 "inputs": [ | |
65 { | |
66 "description": "", | |
67 "name": "Input Dataset" | |
68 } | |
69 ], | |
70 "label": "FastQ Forward", | |
71 "name": "Input dataset", | |
72 "outputs": [], | |
73 "position": { | |
74 "left": 200, | |
75 "top": 370 | |
76 }, | |
77 "tool_errors": null, | |
78 "tool_id": null, | |
79 "tool_state": "{\"name\": \"Input Dataset\"}", | |
80 "tool_version": null, | |
81 "type": "data_input", | |
82 "uuid": "1956acf3-af87-497d-bced-1dc18003b4ee", | |
83 "workflow_outputs": [] | |
84 }, | |
85 "3": { | |
86 "annotation": "", | |
87 "content_id": null, | |
88 "id": 3, | |
89 "input_connections": {}, | |
90 "inputs": [ | |
91 { | |
92 "description": "", | |
93 "name": "Input Dataset" | |
94 } | |
95 ], | |
96 "label": "FastQ Reverse", | |
97 "name": "Input dataset", | |
98 "outputs": [], | |
99 "position": { | |
100 "left": 200, | |
101 "top": 455 | |
102 }, | |
103 "tool_errors": null, | |
104 "tool_id": null, | |
105 "tool_state": "{\"name\": \"Input Dataset\"}", | |
106 "tool_version": null, | |
107 "type": "data_input", | |
108 "uuid": "0e020fbd-697d-4ebc-bd3d-0b45d5104b44", | |
109 "workflow_outputs": [] | |
110 }, | |
111 "4": { | |
112 "annotation": "", | |
113 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | |
114 "id": 4, | |
115 "input_connections": { | |
116 "paired_end|paired_input_type_conditional|fastq_r1_in": { | |
117 "id": 2, | |
118 "output_name": "output" | |
119 }, | |
120 "paired_end|paired_input_type_conditional|fastq_r2_in": { | |
121 "id": 3, | |
122 "output_name": "output" | |
123 } | |
124 }, | |
125 "inputs": [], | |
126 "label": null, | |
127 "name": "Trimmomatic", | |
128 "outputs": [ | |
129 { | |
130 "name": "fastq_out_paired", | |
131 "type": "input" | |
132 }, | |
133 { | |
134 "name": "fastq_out_unpaired", | |
135 "type": "input" | |
136 }, | |
137 { | |
138 "name": "fastq_out_r1_paired", | |
139 "type": "fastqsanger" | |
140 }, | |
141 { | |
142 "name": "fastq_out_r2_paired", | |
143 "type": "fastqsanger" | |
144 }, | |
145 { | |
146 "name": "fastq_out_r1_unpaired", | |
147 "type": "fastqsanger" | |
148 }, | |
149 { | |
150 "name": "fastq_out_r2_unpaired", | |
151 "type": "fastqsanger" | |
152 }, | |
153 { | |
154 "name": "fastq_out", | |
155 "type": "fastqsanger" | |
156 } | |
157 ], | |
158 "position": { | |
159 "left": 435, | |
160 "top": 200 | |
161 }, | |
162 "post_job_actions": { | |
163 "DeleteIntermediatesActionfastq_out_paired": { | |
164 "action_arguments": {}, | |
165 "action_type": "DeleteIntermediatesAction", | |
166 "output_name": "fastq_out_paired" | |
167 }, | |
168 "HideDatasetActionfastq_out": { | |
169 "action_arguments": {}, | |
170 "action_type": "HideDatasetAction", | |
171 "output_name": "fastq_out" | |
172 }, | |
173 "HideDatasetActionfastq_out_paired": { | |
174 "action_arguments": {}, | |
175 "action_type": "HideDatasetAction", | |
176 "output_name": "fastq_out_paired" | |
177 }, | |
178 "HideDatasetActionfastq_out_r1_unpaired": { | |
179 "action_arguments": {}, | |
180 "action_type": "HideDatasetAction", | |
181 "output_name": "fastq_out_r1_unpaired" | |
182 }, | |
183 "HideDatasetActionfastq_out_r2_unpaired": { | |
184 "action_arguments": {}, | |
185 "action_type": "HideDatasetAction", | |
186 "output_name": "fastq_out_r2_unpaired" | |
187 }, | |
188 "HideDatasetActionfastq_out_unpaired": { | |
189 "action_arguments": {}, | |
190 "action_type": "HideDatasetAction", | |
191 "output_name": "fastq_out_unpaired" | |
192 } | |
193 }, | |
194 "tool_errors": null, | |
195 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | |
196 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"True\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}", | |
197 "tool_version": "0.32.3", | |
198 "type": "tool", | |
199 "uuid": "68fbd2ce-d667-4f34-a3e0-4381d93bfbaa", | |
200 "workflow_outputs": [ | |
201 { | |
202 "label": null, | |
203 "output_name": "fastq_out_r1_paired", | |
204 "uuid": "59ce771e-1cad-486b-ab2e-3ed1c85a195c" | |
205 }, | |
206 { | |
207 "label": null, | |
208 "output_name": "fastq_out_r2_paired", | |
209 "uuid": "29696b1d-f675-4255-b902-f7ded1cf6fad" | |
210 } | |
211 ] | |
212 }, | |
213 "5": { | |
214 "annotation": "", | |
215 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
216 "id": 5, | |
217 "input_connections": { | |
218 "input_type|fastq_input1": { | |
219 "id": 4, | |
220 "output_name": "fastq_out_r1_paired" | |
221 }, | |
222 "input_type|fastq_input2": { | |
223 "id": 4, | |
224 "output_name": "fastq_out_r2_paired" | |
225 }, | |
226 "reference_source|ref_file": { | |
227 "id": 1, | |
228 "output_name": "output" | |
229 } | |
230 }, | |
231 "inputs": [], | |
232 "label": null, | |
233 "name": "Map with BWA", | |
234 "outputs": [ | |
235 { | |
236 "name": "bam_output", | |
237 "type": "bam" | |
238 } | |
239 ], | |
240 "position": { | |
241 "left": 763, | |
242 "top": 200 | |
243 }, | |
244 "post_job_actions": { | |
245 "DeleteIntermediatesActionbam_output": { | |
246 "action_arguments": {}, | |
247 "action_type": "DeleteIntermediatesAction", | |
248 "output_name": "bam_output" | |
249 } | |
250 }, | |
251 "tool_errors": null, | |
252 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
253 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | |
254 "tool_version": "0.7.12.1", | |
255 "type": "tool", | |
256 "uuid": "ddf4de24-ceec-4dd7-a4a2-cd91994b4346", | |
257 "workflow_outputs": [ | |
258 { | |
259 "label": null, | |
260 "output_name": "bam_output", | |
261 "uuid": "ad467c2c-4b48-4f06-9c68-ced14296afb8" | |
262 } | |
263 ] | |
264 }, | |
265 "6": { | |
266 "annotation": "", | |
267 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0", | |
268 "id": 6, | |
269 "input_connections": { | |
270 "inputFile": { | |
271 "id": 5, | |
272 "output_name": "bam_output" | |
273 } | |
274 }, | |
275 "inputs": [], | |
276 "label": null, | |
277 "name": "FilterSamReads", | |
278 "outputs": [ | |
279 { | |
280 "name": "outFile", | |
281 "type": "bam" | |
282 } | |
283 ], | |
284 "position": { | |
285 "left": 1028, | |
286 "top": 200 | |
287 }, | |
288 "post_job_actions": { | |
289 "DeleteIntermediatesActionoutFile": { | |
290 "action_arguments": {}, | |
291 "action_type": "DeleteIntermediatesAction", | |
292 "output_name": "outFile" | |
293 } | |
294 }, | |
295 "tool_errors": null, | |
296 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0", | |
297 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", | |
298 "tool_version": "1.136.0", | |
299 "type": "tool", | |
300 "uuid": "bf824957-0907-4c1f-983d-f26a88826253", | |
301 "workflow_outputs": [ | |
302 { | |
303 "label": null, | |
304 "output_name": "outFile", | |
305 "uuid": "7aeb6a2f-a869-44df-bb2a-188e44036d1e" | |
306 } | |
307 ] | |
308 }, | |
309 "7": { | |
310 "annotation": "", | |
311 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
312 "id": 7, | |
313 "input_connections": { | |
314 "input_type|bam_input": { | |
315 "id": 6, | |
316 "output_name": "outFile" | |
317 }, | |
318 "reference_source|ref_file": { | |
319 "id": 0, | |
320 "output_name": "output" | |
321 } | |
322 }, | |
323 "inputs": [], | |
324 "label": null, | |
325 "name": "Map with BWA", | |
326 "outputs": [ | |
327 { | |
328 "name": "bam_output", | |
329 "type": "bam" | |
330 } | |
331 ], | |
332 "position": { | |
333 "left": 1356, | |
334 "top": 200 | |
335 }, | |
336 "post_job_actions": { | |
337 "DeleteIntermediatesActionbam_output": { | |
338 "action_arguments": {}, | |
339 "action_type": "DeleteIntermediatesAction", | |
340 "output_name": "bam_output" | |
341 } | |
342 }, | |
343 "tool_errors": null, | |
344 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
345 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": null, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"__current_case__\\\": 3, \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", | |
346 "tool_version": "0.7.12.1", | |
347 "type": "tool", | |
348 "uuid": "9d1d2fe9-c3c6-4a34-a28d-50b2f7a06e11", | |
349 "workflow_outputs": [ | |
350 { | |
351 "label": null, | |
352 "output_name": "bam_output", | |
353 "uuid": "981cdac9-e993-471c-87c2-c667431ed47f" | |
354 } | |
355 ] | |
356 }, | |
357 "8": { | |
358 "annotation": "", | |
359 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1", | |
360 "id": 8, | |
361 "input_connections": { | |
362 "inputFile": { | |
363 "id": 7, | |
364 "output_name": "bam_output" | |
365 } | |
366 }, | |
367 "inputs": [], | |
368 "label": null, | |
369 "name": "SortSam", | |
370 "outputs": [ | |
371 { | |
372 "name": "outFile", | |
373 "type": "bam" | |
374 } | |
375 ], | |
376 "position": { | |
377 "left": 1621, | |
378 "top": 200 | |
379 }, | |
380 "post_job_actions": { | |
381 "DeleteIntermediatesActionoutFile": { | |
382 "action_arguments": {}, | |
383 "action_type": "DeleteIntermediatesAction", | |
384 "output_name": "outFile" | |
385 } | |
386 }, | |
387 "tool_errors": null, | |
388 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1", | |
389 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", | |
390 "tool_version": "1.136.1", | |
391 "type": "tool", | |
392 "uuid": "42d32394-d968-4cb0-ae06-69e551a8d328", | |
393 "workflow_outputs": [ | |
394 { | |
395 "label": null, | |
396 "output_name": "outFile", | |
397 "uuid": "30ae35f3-4cda-4feb-bfbe-6005ea4dcd22" | |
398 } | |
399 ] | |
400 }, | |
401 "9": { | |
402 "annotation": "", | |
403 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
404 "id": 9, | |
405 "input_connections": { | |
406 "input1": { | |
407 "id": 8, | |
408 "output_name": "outFile" | |
409 } | |
410 }, | |
411 "inputs": [], | |
412 "label": null, | |
413 "name": "BAM-to-SAM", | |
414 "outputs": [ | |
415 { | |
416 "name": "output1", | |
417 "type": "sam" | |
418 } | |
419 ], | |
420 "position": { | |
421 "left": 1949, | |
422 "top": 200 | |
423 }, | |
424 "post_job_actions": { | |
425 "DeleteIntermediatesActionoutput1": { | |
426 "action_arguments": {}, | |
427 "action_type": "DeleteIntermediatesAction", | |
428 "output_name": "output1" | |
429 } | |
430 }, | |
431 "tool_errors": null, | |
432 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
433 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}", | |
434 "tool_version": "2.0", | |
435 "type": "tool", | |
436 "uuid": "9fe23b03-b221-4007-a406-44b05be85066", | |
437 "workflow_outputs": [ | |
438 { | |
439 "label": null, | |
440 "output_name": "output1", | |
441 "uuid": "c34f9ca8-8d2d-4d8a-bb24-c3a030ff45af" | |
442 } | |
443 ] | |
444 }, | |
445 "10": { | |
446 "annotation": "", | |
447 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", | |
448 "id": 10, | |
449 "input_connections": { | |
450 "input1": { | |
451 "id": 0, | |
452 "output_name": "output" | |
453 }, | |
454 "input2": { | |
455 "id": 9, | |
456 "output_name": "output1" | |
457 } | |
458 }, | |
459 "inputs": [], | |
460 "label": null, | |
461 "name": "Coverage Sampler", | |
462 "outputs": [ | |
463 { | |
464 "name": "output1", | |
465 "type": "tabular" | |
466 } | |
467 ], | |
468 "position": { | |
469 "left": 2184, | |
470 "top": 200 | |
471 }, | |
472 "post_job_actions": { | |
473 "RenameDatasetActionoutput1": { | |
474 "action_arguments": { | |
475 "newname": "Coverage Results" | |
476 }, | |
477 "action_type": "RenameDatasetAction", | |
478 "output_name": "output1" | |
479 } | |
480 }, | |
481 "tool_errors": null, | |
482 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", | |
483 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", | |
484 "tool_version": "0.1.0", | |
485 "type": "tool", | |
486 "uuid": "8305b84c-ceb2-41bb-9f07-4c7bedff5d0a", | |
487 "workflow_outputs": [ | |
488 { | |
489 "label": null, | |
490 "output_name": "output1", | |
491 "uuid": "1db38476-e927-44aa-bac5-0ff46b81a2b7" | |
492 } | |
493 ] | |
494 }, | |
495 "11": { | |
496 "annotation": "", | |
497 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", | |
498 "id": 11, | |
499 "input_connections": { | |
500 "input1": { | |
501 "id": 0, | |
502 "output_name": "output" | |
503 }, | |
504 "sam_type|sampe_input2": { | |
505 "id": 9, | |
506 "output_name": "output1" | |
507 } | |
508 }, | |
509 "inputs": [], | |
510 "label": null, | |
511 "name": "Snip Finder", | |
512 "outputs": [ | |
513 { | |
514 "name": "output1", | |
515 "type": "tabular" | |
516 } | |
517 ], | |
518 "position": { | |
519 "left": 2184, | |
520 "top": 341 | |
521 }, | |
522 "post_job_actions": { | |
523 "RenameDatasetActionoutput1": { | |
524 "action_arguments": { | |
525 "newname": "Snip Results" | |
526 }, | |
527 "action_type": "RenameDatasetAction", | |
528 "output_name": "output1" | |
529 } | |
530 }, | |
531 "tool_errors": null, | |
532 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", | |
533 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"False\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}", | |
534 "tool_version": "0.1.0", | |
535 "type": "tool", | |
536 "uuid": "b7bac673-aed8-4abd-a873-f842b9497ac8", | |
537 "workflow_outputs": [ | |
538 { | |
539 "label": null, | |
540 "output_name": "output1", | |
541 "uuid": "fb7fbbba-05bd-4477-a0ee-8e51bcbeddd2" | |
542 } | |
543 ] | |
544 } | |
545 }, | |
546 "uuid": "6c6ee2ed-be38-4787-9a8e-5ab9a872a00e" | |
547 } |