Mercurial > repos > chrisd > amrplusplus_workflow
comparison Galaxy-Workflow-AmrPlusPlus_PE.ga @ 0:834c10340bce draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
author | chrisd |
---|---|
date | Wed, 23 Mar 2016 21:49:48 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:834c10340bce |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "AmrPlusPlus_PE", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "The genome to align non-host reads to", | |
9 "content_id": null, | |
10 "id": 0, | |
11 "input_connections": {}, | |
12 "inputs": [ | |
13 { | |
14 "description": "The genome to align non-host reads to", | |
15 "name": "AMR Database" | |
16 } | |
17 ], | |
18 "label": "AMR Database", | |
19 "name": "Input dataset", | |
20 "outputs": [], | |
21 "position": { | |
22 "left": 391, | |
23 "top": 200 | |
24 }, | |
25 "tool_errors": null, | |
26 "tool_id": null, | |
27 "tool_state": "{\"name\": \"AMR Database\"}", | |
28 "tool_version": null, | |
29 "type": "data_input", | |
30 "uuid": "66a5eb48-4b35-46cc-9b93-fd88d97d2218", | |
31 "workflow_outputs": [ | |
32 { | |
33 "label": null, | |
34 "output_name": "output", | |
35 "uuid": "d30b93c8-aa9f-49eb-801f-5a02e68a876b" | |
36 } | |
37 ] | |
38 }, | |
39 "1": { | |
40 "annotation": "Genome used to filter reads on", | |
41 "content_id": null, | |
42 "id": 1, | |
43 "input_connections": {}, | |
44 "inputs": [ | |
45 { | |
46 "description": "Genome used to filter reads on", | |
47 "name": "Host Genome" | |
48 } | |
49 ], | |
50 "label": "Host Genome", | |
51 "name": "Input dataset", | |
52 "outputs": [], | |
53 "position": { | |
54 "left": 391, | |
55 "top": 285 | |
56 }, | |
57 "tool_errors": null, | |
58 "tool_id": null, | |
59 "tool_state": "{\"name\": \"Host Genome\"}", | |
60 "tool_version": null, | |
61 "type": "data_input", | |
62 "uuid": "02603c1f-b5f0-4121-9b57-005a98411364", | |
63 "workflow_outputs": [ | |
64 { | |
65 "label": null, | |
66 "output_name": "output", | |
67 "uuid": "6b4607b2-f4d8-4b24-ade6-30b2a6377017" | |
68 } | |
69 ] | |
70 }, | |
71 "2": { | |
72 "annotation": "Forward reads", | |
73 "content_id": null, | |
74 "id": 2, | |
75 "input_connections": {}, | |
76 "inputs": [ | |
77 { | |
78 "description": "Forward reads", | |
79 "name": "FastQ Forward" | |
80 } | |
81 ], | |
82 "label": "FastQ Forward", | |
83 "name": "Input dataset", | |
84 "outputs": [], | |
85 "position": { | |
86 "left": 391, | |
87 "top": 370 | |
88 }, | |
89 "tool_errors": null, | |
90 "tool_id": null, | |
91 "tool_state": "{\"name\": \"FastQ Forward\"}", | |
92 "tool_version": null, | |
93 "type": "data_input", | |
94 "uuid": "f25b69be-a40e-4d89-8535-84e2c3784148", | |
95 "workflow_outputs": [ | |
96 { | |
97 "label": null, | |
98 "output_name": "output", | |
99 "uuid": "cd11b688-012e-4d6e-bac7-a35c97057e8e" | |
100 } | |
101 ] | |
102 }, | |
103 "3": { | |
104 "annotation": "Reverse reads", | |
105 "content_id": null, | |
106 "id": 3, | |
107 "input_connections": {}, | |
108 "inputs": [ | |
109 { | |
110 "description": "Reverse reads", | |
111 "name": "FastQ Reverse" | |
112 } | |
113 ], | |
114 "label": "FastQ Reverse", | |
115 "name": "Input dataset", | |
116 "outputs": [], | |
117 "position": { | |
118 "left": 391, | |
119 "top": 455 | |
120 }, | |
121 "tool_errors": null, | |
122 "tool_id": null, | |
123 "tool_state": "{\"name\": \"FastQ Reverse\"}", | |
124 "tool_version": null, | |
125 "type": "data_input", | |
126 "uuid": "837dabbc-eec6-4490-8944-ab408d02631e", | |
127 "workflow_outputs": [ | |
128 { | |
129 "label": null, | |
130 "output_name": "output", | |
131 "uuid": "3a4ab0ae-6842-42ce-b41c-0bc02f2f1ea5" | |
132 } | |
133 ] | |
134 }, | |
135 "4": { | |
136 "annotation": "", | |
137 "content_id": "testtoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | |
138 "id": 4, | |
139 "input_connections": { | |
140 "paired_end|paired_input_type_conditional|fastq_r1_in": { | |
141 "id": 2, | |
142 "output_name": "output" | |
143 }, | |
144 "paired_end|paired_input_type_conditional|fastq_r2_in": { | |
145 "id": 3, | |
146 "output_name": "output" | |
147 } | |
148 }, | |
149 "inputs": [], | |
150 "label": null, | |
151 "name": "Trimmomatic", | |
152 "outputs": [ | |
153 { | |
154 "name": "fastq_out_paired", | |
155 "type": "input" | |
156 }, | |
157 { | |
158 "name": "fastq_out_unpaired", | |
159 "type": "input" | |
160 }, | |
161 { | |
162 "name": "fastq_out_r1_paired", | |
163 "type": "fastqsanger" | |
164 }, | |
165 { | |
166 "name": "fastq_out_r2_paired", | |
167 "type": "fastqsanger" | |
168 }, | |
169 { | |
170 "name": "fastq_out_r1_unpaired", | |
171 "type": "fastqsanger" | |
172 }, | |
173 { | |
174 "name": "fastq_out_r2_unpaired", | |
175 "type": "fastqsanger" | |
176 }, | |
177 { | |
178 "name": "fastq_out", | |
179 "type": "fastqsanger" | |
180 } | |
181 ], | |
182 "position": { | |
183 "left": 626, | |
184 "top": 200 | |
185 }, | |
186 "post_job_actions": { | |
187 "DeleteIntermediatesActionfastq_out_paired": { | |
188 "action_arguments": {}, | |
189 "action_type": "DeleteIntermediatesAction", | |
190 "output_name": "fastq_out_paired" | |
191 }, | |
192 "HideDatasetActionfastq_out": { | |
193 "action_arguments": {}, | |
194 "action_type": "HideDatasetAction", | |
195 "output_name": "fastq_out" | |
196 }, | |
197 "HideDatasetActionfastq_out_paired": { | |
198 "action_arguments": {}, | |
199 "action_type": "HideDatasetAction", | |
200 "output_name": "fastq_out_paired" | |
201 }, | |
202 "HideDatasetActionfastq_out_r1_unpaired": { | |
203 "action_arguments": {}, | |
204 "action_type": "HideDatasetAction", | |
205 "output_name": "fastq_out_r1_unpaired" | |
206 }, | |
207 "HideDatasetActionfastq_out_r2_unpaired": { | |
208 "action_arguments": {}, | |
209 "action_type": "HideDatasetAction", | |
210 "output_name": "fastq_out_r2_unpaired" | |
211 }, | |
212 "HideDatasetActionfastq_out_unpaired": { | |
213 "action_arguments": {}, | |
214 "action_type": "HideDatasetAction", | |
215 "output_name": "fastq_out_unpaired" | |
216 } | |
217 }, | |
218 "tool_errors": null, | |
219 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", | |
220 "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}\"}", | |
221 "tool_version": "0.32.3", | |
222 "type": "tool", | |
223 "uuid": "fd478986-09be-4758-9360-a4a345f1efc0", | |
224 "workflow_outputs": [ | |
225 { | |
226 "label": null, | |
227 "output_name": "fastq_out_r1_paired", | |
228 "uuid": "955d6928-ebc0-4dc9-be6c-f2f6f888ca45" | |
229 }, | |
230 { | |
231 "label": null, | |
232 "output_name": "fastq_out_r2_paired", | |
233 "uuid": "19e51c6f-b0b7-46d0-9885-a5701938f310" | |
234 } | |
235 ] | |
236 }, | |
237 "5": { | |
238 "annotation": "", | |
239 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
240 "id": 5, | |
241 "input_connections": { | |
242 "input_type|fastq_input1": { | |
243 "id": 4, | |
244 "output_name": "fastq_out_r1_paired" | |
245 }, | |
246 "input_type|fastq_input2": { | |
247 "id": 4, | |
248 "output_name": "fastq_out_r2_paired" | |
249 }, | |
250 "reference_source|ref_file": { | |
251 "id": 1, | |
252 "output_name": "output" | |
253 } | |
254 }, | |
255 "inputs": [], | |
256 "label": null, | |
257 "name": "Map with BWA", | |
258 "outputs": [ | |
259 { | |
260 "name": "bam_output", | |
261 "type": "bam" | |
262 } | |
263 ], | |
264 "position": { | |
265 "left": 954, | |
266 "top": 200 | |
267 }, | |
268 "post_job_actions": {}, | |
269 "tool_errors": null, | |
270 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
271 "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\\\"}\"}", | |
272 "tool_version": "0.7.12.1", | |
273 "type": "tool", | |
274 "uuid": "6d53f77e-8f8a-4b9a-a674-8f7c55824260", | |
275 "workflow_outputs": [ | |
276 { | |
277 "label": null, | |
278 "output_name": "bam_output", | |
279 "uuid": "efa12320-805e-4d96-aa50-2607b1952c6d" | |
280 } | |
281 ] | |
282 }, | |
283 "6": { | |
284 "annotation": "", | |
285 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0", | |
286 "id": 6, | |
287 "input_connections": { | |
288 "inputFile": { | |
289 "id": 5, | |
290 "output_name": "bam_output" | |
291 } | |
292 }, | |
293 "inputs": [], | |
294 "label": null, | |
295 "name": "FilterSamReads", | |
296 "outputs": [ | |
297 { | |
298 "name": "outFile", | |
299 "type": "bam" | |
300 } | |
301 ], | |
302 "position": { | |
303 "left": 1282, | |
304 "top": 200 | |
305 }, | |
306 "post_job_actions": { | |
307 "DeleteIntermediatesActionoutFile": { | |
308 "action_arguments": {}, | |
309 "action_type": "DeleteIntermediatesAction", | |
310 "output_name": "outFile" | |
311 } | |
312 }, | |
313 "tool_errors": null, | |
314 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0", | |
315 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", | |
316 "tool_version": "1.136.0", | |
317 "type": "tool", | |
318 "uuid": "031b872f-1554-4a3e-bd3d-bc7a00b009fe", | |
319 "workflow_outputs": [ | |
320 { | |
321 "label": null, | |
322 "output_name": "outFile", | |
323 "uuid": "c74b2b4e-517e-400c-acdf-4360e31e7289" | |
324 } | |
325 ] | |
326 }, | |
327 "7": { | |
328 "annotation": "", | |
329 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
330 "id": 7, | |
331 "input_connections": { | |
332 "input_type|bam_input": { | |
333 "id": 6, | |
334 "output_name": "outFile" | |
335 }, | |
336 "reference_source|ref_file": { | |
337 "id": 0, | |
338 "output_name": "output" | |
339 } | |
340 }, | |
341 "inputs": [], | |
342 "label": null, | |
343 "name": "Map with BWA", | |
344 "outputs": [ | |
345 { | |
346 "name": "bam_output", | |
347 "type": "bam" | |
348 } | |
349 ], | |
350 "position": { | |
351 "left": 1610, | |
352 "top": 200 | |
353 }, | |
354 "post_job_actions": {}, | |
355 "tool_errors": null, | |
356 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", | |
357 "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\\\"}\"}", | |
358 "tool_version": "0.7.12.1", | |
359 "type": "tool", | |
360 "uuid": "0a5b629f-5fbd-45c0-97cc-67a54ce242ae", | |
361 "workflow_outputs": [ | |
362 { | |
363 "label": null, | |
364 "output_name": "bam_output", | |
365 "uuid": "196d789d-3ed1-41a9-9e28-92e8135e8ee5" | |
366 } | |
367 ] | |
368 }, | |
369 "8": { | |
370 "annotation": "", | |
371 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1", | |
372 "id": 8, | |
373 "input_connections": { | |
374 "inputFile": { | |
375 "id": 7, | |
376 "output_name": "bam_output" | |
377 } | |
378 }, | |
379 "inputs": [], | |
380 "label": null, | |
381 "name": "SortSam", | |
382 "outputs": [ | |
383 { | |
384 "name": "outFile", | |
385 "type": "bam" | |
386 } | |
387 ], | |
388 "position": { | |
389 "left": 1938, | |
390 "top": 200 | |
391 }, | |
392 "post_job_actions": { | |
393 "DeleteIntermediatesActionoutFile": { | |
394 "action_arguments": {}, | |
395 "action_type": "DeleteIntermediatesAction", | |
396 "output_name": "outFile" | |
397 } | |
398 }, | |
399 "tool_errors": null, | |
400 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1", | |
401 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}", | |
402 "tool_version": "1.136.1", | |
403 "type": "tool", | |
404 "uuid": "efe328ad-11fa-4e3b-9c9f-6037c5ea4262", | |
405 "workflow_outputs": [ | |
406 { | |
407 "label": null, | |
408 "output_name": "outFile", | |
409 "uuid": "5b0b2f60-116f-40ee-acf8-f5ddacfc4bc7" | |
410 } | |
411 ] | |
412 }, | |
413 "9": { | |
414 "annotation": "", | |
415 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
416 "id": 9, | |
417 "input_connections": { | |
418 "input1": { | |
419 "id": 8, | |
420 "output_name": "outFile" | |
421 } | |
422 }, | |
423 "inputs": [], | |
424 "label": null, | |
425 "name": "BAM-to-SAM", | |
426 "outputs": [ | |
427 { | |
428 "name": "output1", | |
429 "type": "sam" | |
430 } | |
431 ], | |
432 "position": { | |
433 "left": 2266, | |
434 "top": 200 | |
435 }, | |
436 "post_job_actions": { | |
437 "DeleteIntermediatesActionoutput1": { | |
438 "action_arguments": {}, | |
439 "action_type": "DeleteIntermediatesAction", | |
440 "output_name": "output1" | |
441 } | |
442 }, | |
443 "tool_errors": null, | |
444 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", | |
445 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}", | |
446 "tool_version": "2.0", | |
447 "type": "tool", | |
448 "uuid": "e4900e78-feb5-4cd6-9194-3131e227388e", | |
449 "workflow_outputs": [ | |
450 { | |
451 "label": null, | |
452 "output_name": "output1", | |
453 "uuid": "356bdab0-a907-4c07-a096-fab658a794ba" | |
454 } | |
455 ] | |
456 }, | |
457 "10": { | |
458 "annotation": "", | |
459 "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", | |
460 "id": 10, | |
461 "input_connections": { | |
462 "input1": { | |
463 "id": 0, | |
464 "output_name": "output" | |
465 }, | |
466 "sam_type|sampe_input2": { | |
467 "id": 9, | |
468 "output_name": "output1" | |
469 } | |
470 }, | |
471 "inputs": [], | |
472 "label": null, | |
473 "name": "Snip Finder", | |
474 "outputs": [ | |
475 { | |
476 "name": "output1", | |
477 "type": "tabular" | |
478 } | |
479 ], | |
480 "position": { | |
481 "left": 2501, | |
482 "top": 200 | |
483 }, | |
484 "post_job_actions": { | |
485 "RenameDatasetActionoutput1": { | |
486 "action_arguments": { | |
487 "newname": "Snip Results" | |
488 }, | |
489 "action_type": "RenameDatasetAction", | |
490 "output_name": "output1" | |
491 } | |
492 }, | |
493 "tool_errors": null, | |
494 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", | |
495 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"False\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}", | |
496 "tool_version": "0.1.0", | |
497 "type": "tool", | |
498 "uuid": "197e5f9d-b4e5-449b-9b2d-67c939f34e32", | |
499 "workflow_outputs": [ | |
500 { | |
501 "label": null, | |
502 "output_name": "output1", | |
503 "uuid": "768cb726-399b-490e-82c1-8d523f7208ee" | |
504 } | |
505 ] | |
506 }, | |
507 "11": { | |
508 "annotation": "", | |
509 "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", | |
510 "id": 11, | |
511 "input_connections": { | |
512 "input1": { | |
513 "id": 0, | |
514 "output_name": "output" | |
515 }, | |
516 "input2": { | |
517 "id": 9, | |
518 "output_name": "output1" | |
519 } | |
520 }, | |
521 "inputs": [], | |
522 "label": null, | |
523 "name": "Coverage Sampler", | |
524 "outputs": [ | |
525 { | |
526 "name": "output1", | |
527 "type": "tabular" | |
528 } | |
529 ], | |
530 "position": { | |
531 "left": 2501, | |
532 "top": 341 | |
533 }, | |
534 "post_job_actions": { | |
535 "RenameDatasetActionoutput1": { | |
536 "action_arguments": { | |
537 "newname": "Coverage Results" | |
538 }, | |
539 "action_type": "RenameDatasetAction", | |
540 "output_name": "output1" | |
541 } | |
542 }, | |
543 "tool_errors": null, | |
544 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", | |
545 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", | |
546 "tool_version": "0.1.0", | |
547 "type": "tool", | |
548 "uuid": "8ffc98a9-82b8-429c-bd1d-fa4f24b22148", | |
549 "workflow_outputs": [ | |
550 { | |
551 "label": null, | |
552 "output_name": "output1", | |
553 "uuid": "207d0359-f140-47bb-9e2c-4882e2697e82" | |
554 } | |
555 ] | |
556 } | |
557 }, | |
558 "uuid": "c3b33138-479d-4709-9a3a-8ba49bb06673" | |
559 } |