comparison Galaxy-Workflow-dada2_for_paired_data.ga @ 3:cf166b8a8e27 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
author matthias
date Mon, 29 Apr 2019 08:57:18 -0400
parents
children
comparison
equal deleted inserted replaced
2:4095456821e2 3:cf166b8a8e27
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "dada2 for paired data",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "errors": null,
11 "id": 0,
12 "input_connections": {},
13 "inputs": [
14 {
15 "description": "",
16 "name": "Input Dataset Collection"
17 }
18 ],
19 "label": null,
20 "name": "Input dataset collection",
21 "outputs": [],
22 "position": {
23 "left": 100,
24 "top": 591
25 },
26 "tool_id": null,
27 "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}",
28 "tool_version": null,
29 "type": "data_collection_input",
30 "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f",
31 "workflow_outputs": []
32 },
33 "1": {
34 "annotation": "",
35 "content_id": "dada2_plotQualityProfile",
36 "errors": null,
37 "id": 1,
38 "input_connections": {
39 "paired_cond|reads": {
40 "id": 0,
41 "output_name": "output"
42 }
43 },
44 "inputs": [],
45 "label": null,
46 "name": "dada2: plotQualityProfile",
47 "outputs": [
48 {
49 "name": "output",
50 "type": "pdf"
51 }
52 ],
53 "position": {
54 "left": 406,
55 "top": 473
56 },
57 "post_job_actions": {},
58 "tool_id": "dada2_plotQualityProfile",
59 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"paired\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"n\": \"\\\"500000\\\"\", \"aggregate\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
60 "tool_version": "1.10.0+galaxy0",
61 "type": "tool",
62 "uuid": "f6e0a2ea-a639-48d9-ae3c-c1ec2bab93e5",
63 "workflow_outputs": []
64 },
65 "2": {
66 "annotation": "",
67 "content_id": "dada2_filterAndTrim",
68 "errors": null,
69 "id": 2,
70 "input_connections": {
71 "paired_cond|reads": {
72 "id": 0,
73 "output_name": "output"
74 }
75 },
76 "inputs": [],
77 "label": null,
78 "name": "dada2: filterAndTrim",
79 "outputs": [
80 {
81 "name": "paired_output",
82 "type": "input"
83 },
84 {
85 "name": "outtab",
86 "type": "tabular"
87 }
88 ],
89 "position": {
90 "left": 384,
91 "top": 612
92 },
93 "post_job_actions": {},
94 "tool_id": "dada2_filterAndTrim",
95 "tool_state": "{\"trim\": \"{\\\"trimLeft\\\": \\\"0\\\", \\\"trimRight\\\": \\\"0\\\", \\\"truncLen\\\": \\\"0\\\", \\\"truncQ\\\": \\\"2\\\"}\", \"__page__\": null, \"rmPhiX\": \"\\\"true\\\"\", \"seprev_cond\": \"{\\\"__current_case__\\\": 0, \\\"seprev_select\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"paired_cond\": \"{\\\"__current_case__\\\": 0, \\\"paired_select\\\": \\\"TRUE\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"filter\": \"{\\\"maxEE\\\": \\\"\\\", \\\"maxLen\\\": \\\"\\\", \\\"maxN\\\": \\\"0\\\", \\\"minLen\\\": \\\"20\\\", \\\"minQ\\\": \\\"0\\\"}\", \"output_statistics\": \"\\\"true\\\"\", \"orientFwd\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
96 "tool_version": "1.10.0+galaxy0",
97 "type": "tool",
98 "uuid": "353103fd-afc3-4fe0-a4a3-8dca75b59107",
99 "workflow_outputs": []
100 },
101 "3": {
102 "annotation": "",
103 "content_id": "__UNZIP_COLLECTION__",
104 "errors": null,
105 "id": 3,
106 "input_connections": {
107 "input": {
108 "id": 2,
109 "output_name": "paired_output"
110 }
111 },
112 "inputs": [],
113 "label": null,
114 "name": "Unzip Collection",
115 "outputs": [
116 {
117 "name": "forward",
118 "type": "data"
119 },
120 {
121 "name": "reverse",
122 "type": "data"
123 }
124 ],
125 "position": {
126 "left": 718,
127 "top": 609
128 },
129 "post_job_actions": {},
130 "tool_id": "__UNZIP_COLLECTION__",
131 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
132 "tool_version": "1.0.0",
133 "type": "tool",
134 "uuid": "41ab27fe-f07d-4653-b4b5-e77408957a9a",
135 "workflow_outputs": []
136 },
137 "4": {
138 "annotation": "",
139 "content_id": "dada2_derepFastq",
140 "errors": null,
141 "id": 4,
142 "input_connections": {
143 "reads": {
144 "id": 3,
145 "output_name": "forward"
146 }
147 },
148 "inputs": [],
149 "label": null,
150 "name": "dada2: derepFastq",
151 "outputs": [
152 {
153 "name": "derep",
154 "type": "dada2_derep"
155 }
156 ],
157 "position": {
158 "left": 987,
159 "top": 466
160 },
161 "post_job_actions": {},
162 "tool_id": "dada2_derepFastq",
163 "tool_state": "{\"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"reads|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
164 "tool_version": "1.10.0+galaxy0",
165 "type": "tool",
166 "uuid": "ad42a0b6-c3f1-4152-ba24-61f7905d896d",
167 "workflow_outputs": []
168 },
169 "5": {
170 "annotation": "",
171 "content_id": "dada2_learnErrors",
172 "errors": null,
173 "id": 5,
174 "input_connections": {
175 "reads": {
176 "id": 3,
177 "output_name": "forward"
178 }
179 },
180 "inputs": [],
181 "label": null,
182 "name": "dada2: learnErrors",
183 "outputs": [
184 {
185 "name": "errors",
186 "type": "dada2_errorrates"
187 },
188 {
189 "name": "plot",
190 "type": "pdf"
191 }
192 ],
193 "position": {
194 "left": 984,
195 "top": 592
196 },
197 "post_job_actions": {},
198 "tool_id": "dada2_learnErrors",
199 "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"errin\\\": \\\"false\\\", \\\"errout\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"__rerun_remap_job_id__\": null, \"nbases\": \"\\\"8\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0\\\", \\\"randomize\\\": \\\"false\\\"}\"}",
200 "tool_version": "1.10.0+galaxy0",
201 "type": "tool",
202 "uuid": "e8c86ffd-118c-44f6-a58d-5c1704bb6ed6",
203 "workflow_outputs": []
204 },
205 "6": {
206 "annotation": "",
207 "content_id": "dada2_derepFastq",
208 "errors": null,
209 "id": 6,
210 "input_connections": {
211 "reads": {
212 "id": 3,
213 "output_name": "reverse"
214 }
215 },
216 "inputs": [],
217 "label": null,
218 "name": "dada2: derepFastq",
219 "outputs": [
220 {
221 "name": "derep",
222 "type": "dada2_derep"
223 }
224 ],
225 "position": {
226 "left": 979,
227 "top": 794
228 },
229 "post_job_actions": {},
230 "tool_id": "dada2_derepFastq",
231 "tool_state": "{\"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"reads|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
232 "tool_version": "1.10.0+galaxy0",
233 "type": "tool",
234 "uuid": "19c7747c-a3c3-498f-8a0a-a351aa2e408d",
235 "workflow_outputs": []
236 },
237 "7": {
238 "annotation": "",
239 "content_id": "dada2_learnErrors",
240 "errors": null,
241 "id": 7,
242 "input_connections": {
243 "reads": {
244 "id": 3,
245 "output_name": "reverse"
246 }
247 },
248 "inputs": [],
249 "label": null,
250 "name": "dada2: learnErrors",
251 "outputs": [
252 {
253 "name": "errors",
254 "type": "dada2_errorrates"
255 },
256 {
257 "name": "plot",
258 "type": "pdf"
259 }
260 ],
261 "position": {
262 "left": 970,
263 "top": 922
264 },
265 "post_job_actions": {},
266 "tool_id": "dada2_learnErrors",
267 "tool_state": "{\"__page__\": null, \"plotopt\": \"{\\\"errin\\\": \\\"false\\\", \\\"errout\\\": \\\"true\\\", \\\"nominalQ\\\": \\\"true\\\", \\\"obs\\\": \\\"true\\\"}\", \"__rerun_remap_job_id__\": null, \"nbases\": \"\\\"8\\\"\", \"reads\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"errfoo\\\": \\\"loessErrfun\\\", \\\"maxconsist\\\": \\\"10\\\", \\\"omegac\\\": \\\"0\\\", \\\"randomize\\\": \\\"false\\\"}\"}",
268 "tool_version": "1.10.0+galaxy0",
269 "type": "tool",
270 "uuid": "2cbc5056-7cc7-4e3e-a283-959a261ca4c5",
271 "workflow_outputs": []
272 },
273 "8": {
274 "annotation": "",
275 "content_id": "dada2_dada",
276 "errors": null,
277 "id": 8,
278 "input_connections": {
279 "batch_cond|derep": {
280 "id": 4,
281 "output_name": "derep"
282 },
283 "errorrates": {
284 "id": 5,
285 "output_name": "errors"
286 }
287 },
288 "inputs": [],
289 "label": null,
290 "name": "dada2: dada",
291 "outputs": [
292 {
293 "name": "data_collection",
294 "type": "input"
295 }
296 ],
297 "position": {
298 "left": 1294,
299 "top": 562
300 },
301 "post_job_actions": {},
302 "tool_id": "dada2_dada",
303 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"errorrates\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
304 "tool_version": "1.10.0+galaxy0",
305 "type": "tool",
306 "uuid": "44bab152-645c-43f1-8356-8ef3f45de057",
307 "workflow_outputs": []
308 },
309 "9": {
310 "annotation": "",
311 "content_id": "dada2_dada",
312 "errors": null,
313 "id": 9,
314 "input_connections": {
315 "batch_cond|derep": {
316 "id": 6,
317 "output_name": "derep"
318 },
319 "errorrates": {
320 "id": 7,
321 "output_name": "errors"
322 }
323 },
324 "inputs": [],
325 "label": null,
326 "name": "dada2: dada",
327 "outputs": [
328 {
329 "name": "data_collection",
330 "type": "input"
331 }
332 ],
333 "position": {
334 "left": 1280,
335 "top": 881
336 },
337 "post_job_actions": {},
338 "tool_id": "dada2_dada",
339 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"batch_cond\": \"{\\\"__current_case__\\\": 1, \\\"batch_select\\\": \\\"no\\\", \\\"derep\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"pool\\\": \\\"FALSE\\\"}\", \"errorrates\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
340 "tool_version": "1.10.0+galaxy0",
341 "type": "tool",
342 "uuid": "c9045469-5cd6-44f1-bffd-b61290d23145",
343 "workflow_outputs": []
344 },
345 "10": {
346 "annotation": "",
347 "content_id": "dada2_mergePairs",
348 "errors": null,
349 "id": 10,
350 "input_connections": {
351 "dadaf": {
352 "id": 8,
353 "output_name": "data_collection"
354 },
355 "dadar": {
356 "id": 9,
357 "output_name": "data_collection"
358 },
359 "derepf": {
360 "id": 4,
361 "output_name": "derep"
362 },
363 "derepr": {
364 "id": 6,
365 "output_name": "derep"
366 }
367 },
368 "inputs": [],
369 "label": null,
370 "name": "dada2: mergePairs",
371 "outputs": [
372 {
373 "name": "merged",
374 "type": "dada2_mergepairs"
375 }
376 ],
377 "position": {
378 "left": 1520,
379 "top": 704
380 },
381 "post_job_actions": {},
382 "tool_id": "dada2_mergePairs",
383 "tool_state": "{\"__page__\": null, \"minOverlap\": \"\\\"12\\\"\", \"dadaf\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"dadaf|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"derepr\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"derepr|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"maxMismatch\": \"\\\"0\\\"\", \"trimOverhang\": \"\\\"false\\\"\", \"dadar\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"derepf|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"justConcatenate\": \"\\\"false\\\"\", \"dadar|__identifier__\": \"\\\"F3D0_S188_L001_001.fastq\\\"\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"derepf\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
384 "tool_version": "1.10.0+galaxy0",
385 "type": "tool",
386 "uuid": "ca8f7d96-9c9c-40f8-ab23-7cb4fb49ab47",
387 "workflow_outputs": []
388 },
389 "11": {
390 "annotation": "",
391 "content_id": "dada2_makeSequenceTable",
392 "errors": null,
393 "id": 11,
394 "input_connections": {
395 "samples": {
396 "id": 10,
397 "output_name": "merged"
398 }
399 },
400 "inputs": [],
401 "label": null,
402 "name": "dada2: makeSequenceTable",
403 "outputs": [
404 {
405 "name": "stable",
406 "type": "dada2_sequencetable"
407 },
408 {
409 "name": "plot_output",
410 "type": "pdf"
411 }
412 ],
413 "position": {
414 "left": 1829,
415 "top": 707
416 },
417 "post_job_actions": {},
418 "tool_id": "dada2_makeSequenceTable",
419 "tool_state": "{\"orderBy\": \"\\\"abundance\\\"\", \"plot\": \"\\\"true\\\"\", \"__page__\": null, \"filter_cond\": \"{\\\"__current_case__\\\": 0, \\\"filter_select\\\": \\\"no\\\"}\", \"samples\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
420 "tool_version": "1.10.0+galaxy0",
421 "type": "tool",
422 "uuid": "3cd64745-bb03-4bfa-b425-a16db0888967",
423 "workflow_outputs": []
424 },
425 "12": {
426 "annotation": "",
427 "content_id": "dada2_removeBimeraDenovo",
428 "errors": null,
429 "id": 12,
430 "input_connections": {
431 "unqs": {
432 "id": 11,
433 "output_name": "stable"
434 }
435 },
436 "inputs": [],
437 "label": null,
438 "name": "dada2: removeBimeraDenovo",
439 "outputs": [
440 {
441 "name": "stable_uniques",
442 "type": "dada2_uniques"
443 },
444 {
445 "name": "stable_mergepairs",
446 "type": "dada2_mergepairs"
447 },
448 {
449 "name": "stable_sequencetable",
450 "type": "dada2_sequencetable"
451 }
452 ],
453 "position": {
454 "left": 2137,
455 "top": 710
456 },
457 "post_job_actions": {},
458 "tool_id": "dada2_removeBimeraDenovo",
459 "tool_state": "{\"unqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"method\": \"\\\"consensus\\\"\", \"__page__\": null}",
460 "tool_version": "1.10.0+galaxy0",
461 "type": "tool",
462 "uuid": "4c001b98-d20d-4255-96ee-2b9829aa815b",
463 "workflow_outputs": []
464 },
465 "13": {
466 "annotation": "",
467 "content_id": "dada2_seqCounts",
468 "errors": null,
469 "id": 13,
470 "input_connections": {
471 "inrep_0|input": {
472 "id": 2,
473 "output_name": "outtab"
474 },
475 "inrep_1|input": {
476 "id": 8,
477 "output_name": "data_collection"
478 },
479 "inrep_2|input": {
480 "id": 9,
481 "output_name": "data_collection"
482 },
483 "inrep_3|input": {
484 "id": 10,
485 "output_name": "merged"
486 },
487 "inrep_4|input": {
488 "id": 11,
489 "output_name": "stable"
490 },
491 "inrep_5|input": {
492 "id": 12,
493 "output_name": "stable_sequencetable"
494 }
495 },
496 "inputs": [],
497 "label": null,
498 "name": "dada2: sequence counts",
499 "outputs": [
500 {
501 "name": "counts",
502 "type": "tabular"
503 }
504 ],
505 "position": {
506 "left": 1870,
507 "top": 277
508 },
509 "post_job_actions": {},
510 "tool_id": "dada2_seqCounts",
511 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"inrep\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"filt\\\"}, {\\\"__index__\\\": 1, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised fwd\\\"}, {\\\"__index__\\\": 2, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"denoised rev\\\"}, {\\\"__index__\\\": 3, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"merged\\\"}, {\\\"__index__\\\": 4, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"tabled\\\"}, {\\\"__index__\\\": 5, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"name\\\": \\\"nochim\\\"}]\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
512 "tool_version": "1.10.0+galaxy0",
513 "type": "tool",
514 "uuid": "cbdb7105-6e81-418e-98fb-7f36df117fb5",
515 "workflow_outputs": []
516 },
517 "14": {
518 "annotation": "",
519 "content_id": "dada2_assignTaxonomyAddspecies",
520 "errors": null,
521 "id": 14,
522 "input_connections": {
523 "seqs": {
524 "id": 12,
525 "output_name": "stable_sequencetable"
526 }
527 },
528 "inputs": [],
529 "label": null,
530 "name": "dada2: assignTaxonomy and addSpecies",
531 "outputs": [
532 {
533 "name": "output",
534 "type": "tabular"
535 }
536 ],
537 "position": {
538 "left": 2444,
539 "top": 710
540 },
541 "post_job_actions": {},
542 "tool_id": "dada2_assignTaxonomyAddspecies",
543 "tool_state": "{\"__page__\": null, \"tryRC\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"addSpecies_cond\": \"{\\\"__current_case__\\\": 1, \\\"addSpecies_select\\\": \\\"TRUE\\\", \\\"allowMultiple_cond\\\": {\\\"__current_case__\\\": 0, \\\"allowMultiple\\\": \\\"FALSE\\\"}, \\\"speciesreference_cond\\\": {\\\"__current_case__\\\": 0, \\\"speciesrefFasta\\\": \\\"rdp16\\\", \\\"speciesreference_select\\\": \\\"builtin\\\"}, \\\"tryRC\\\": \\\"false\\\"}\", \"reference_cond\": \"{\\\"__current_case__\\\": 0, \\\"refFasta\\\": \\\"rdp16\\\", \\\"reference_select\\\": \\\"builtin\\\"}\", \"outputBootstraps\": \"\\\"false\\\"\", \"minBoot\": \"\\\"50\\\"\", \"seqs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"chromInfo\": \"\\\"/home/berntm/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
544 "tool_version": "1.10.0+galaxy0",
545 "type": "tool",
546 "uuid": "babc7594-ae73-4818-919f-561836c45c17",
547 "workflow_outputs": []
548 }
549 },
550 "tags": [],
551 "uuid": "48912525-da2b-44b4-b225-f3e3adecad96",
552 "version": 1
553 }