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 }