Mercurial > repos > drosofff > metavisitor_workflows
comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga @ 0:4a47903bb4df draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
author | drosofff |
---|---|
date | Tue, 05 Apr 2016 06:42:47 -0400 |
parents | |
children | 48b020a0d2f7 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:4a47903bb4df |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "Metavisitor: Workflow for Use Case 2-1", | |
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 Collection" | |
16 } | |
17 ], | |
18 "label": null, | |
19 "name": "Input dataset collection", | |
20 "outputs": [], | |
21 "position": { | |
22 "left": 110.9375, | |
23 "top": 269.37501525878906 | |
24 }, | |
25 "tool_errors": null, | |
26 "tool_id": null, | |
27 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", | |
28 "tool_version": null, | |
29 "type": "data_collection_input", | |
30 "uuid": "None", | |
31 "workflow_outputs": [ | |
32 { | |
33 "label": null, | |
34 "output_name": "output", | |
35 "uuid": "4e1d736b-a314-441c-95ef-c4e7fbde52e6" | |
36 } | |
37 ] | |
38 }, | |
39 "1": { | |
40 "annotation": "", | |
41 "content_id": null, | |
42 "id": 1, | |
43 "input_connections": {}, | |
44 "inputs": [ | |
45 { | |
46 "description": "", | |
47 "name": "Blast Protein database" | |
48 } | |
49 ], | |
50 "label": null, | |
51 "name": "Input dataset", | |
52 "outputs": [], | |
53 "position": { | |
54 "left": 1088.5938110351562, | |
55 "top": 839.96533203125 | |
56 }, | |
57 "tool_errors": null, | |
58 "tool_id": null, | |
59 "tool_state": "{\"name\": \"Blast Protein database\"}", | |
60 "tool_version": null, | |
61 "type": "data_input", | |
62 "uuid": "ee9f8f76-6682-4688-88ad-8263109cf051", | |
63 "workflow_outputs": [ | |
64 { | |
65 "label": null, | |
66 "output_name": "output", | |
67 "uuid": "18d27e4d-ada8-48e3-b69a-ce878a19d260" | |
68 } | |
69 ] | |
70 }, | |
71 "2": { | |
72 "annotation": "", | |
73 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3", | |
74 "id": 2, | |
75 "input_connections": {}, | |
76 "inputs": [], | |
77 "label": null, | |
78 "name": "Retrieve FASTA from NCBI", | |
79 "outputs": [ | |
80 { | |
81 "name": "outfilename", | |
82 "type": "fasta" | |
83 }, | |
84 { | |
85 "name": "logfile", | |
86 "type": "txt" | |
87 } | |
88 ], | |
89 "position": { | |
90 "left": 1736.5973052978516, | |
91 "top": 1034.4966125488281 | |
92 }, | |
93 "post_job_actions": { | |
94 "HideDatasetActionlogfile": { | |
95 "action_arguments": {}, | |
96 "action_type": "HideDatasetAction", | |
97 "output_name": "logfile" | |
98 }, | |
99 "HideDatasetActionoutfilename": { | |
100 "action_arguments": {}, | |
101 "action_type": "HideDatasetAction", | |
102 "output_name": "outfilename" | |
103 }, | |
104 "RenameDatasetActionoutfilename": { | |
105 "action_arguments": { | |
106 "newname": "DCV NC_001834.1 Guide" | |
107 }, | |
108 "action_type": "RenameDatasetAction", | |
109 "output_name": "outfilename" | |
110 } | |
111 }, | |
112 "tool_errors": null, | |
113 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3", | |
114 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"NC_001834.1\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}", | |
115 "tool_version": "0.9.3", | |
116 "type": "tool", | |
117 "uuid": "None", | |
118 "workflow_outputs": [] | |
119 }, | |
120 "3": { | |
121 "annotation": "", | |
122 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", | |
123 "id": 3, | |
124 "input_connections": { | |
125 "input": { | |
126 "id": 0, | |
127 "output_name": "output" | |
128 } | |
129 }, | |
130 "inputs": [], | |
131 "label": null, | |
132 "name": "Clip adapter", | |
133 "outputs": [ | |
134 { | |
135 "name": "output", | |
136 "type": "fasta" | |
137 } | |
138 ], | |
139 "position": { | |
140 "left": 254.84375, | |
141 "top": 419.3750247955322 | |
142 }, | |
143 "post_job_actions": { | |
144 "HideDatasetActionoutput": { | |
145 "action_arguments": {}, | |
146 "action_type": "HideDatasetAction", | |
147 "output_name": "output" | |
148 } | |
149 }, | |
150 "tool_errors": null, | |
151 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", | |
152 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"50\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"TGGAATTCTCGGGTGCCAAG\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"Nmode\": \"\\\"accept\\\"\"}", | |
153 "tool_version": "1.3.6", | |
154 "type": "tool", | |
155 "uuid": "None", | |
156 "workflow_outputs": [] | |
157 }, | |
158 "4": { | |
159 "annotation": "", | |
160 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", | |
161 "id": 4, | |
162 "input_connections": { | |
163 "input_file": { | |
164 "id": 2, | |
165 "output_name": "outfilename" | |
166 } | |
167 }, | |
168 "inputs": [], | |
169 "label": null, | |
170 "name": "NCBI BLAST+ makeblastdb", | |
171 "outputs": [ | |
172 { | |
173 "name": "outfile", | |
174 "type": "data" | |
175 } | |
176 ], | |
177 "position": { | |
178 "left": 2035.6077270507812, | |
179 "top": 918.4896545410156 | |
180 }, | |
181 "post_job_actions": { | |
182 "HideDatasetActionoutfile": { | |
183 "action_arguments": {}, | |
184 "action_type": "HideDatasetAction", | |
185 "output_name": "outfile" | |
186 } | |
187 }, | |
188 "tool_errors": null, | |
189 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", | |
190 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"title\": \"\\\"DCV NC_001834.1\\\"\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\", \"parse_seqids\": \"\\\"False\\\"\"}", | |
191 "tool_version": "0.1.06", | |
192 "type": "tool", | |
193 "uuid": "None", | |
194 "workflow_outputs": [] | |
195 }, | |
196 "5": { | |
197 "annotation": "", | |
198 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", | |
199 "id": 5, | |
200 "input_connections": { | |
201 "input": { | |
202 "id": 3, | |
203 "output_name": "output" | |
204 } | |
205 }, | |
206 "inputs": [], | |
207 "label": null, | |
208 "name": "Concatenate multiple datasets", | |
209 "outputs": [ | |
210 { | |
211 "name": "out_file1", | |
212 "type": "input" | |
213 } | |
214 ], | |
215 "position": { | |
216 "left": 312.77783203125, | |
217 "top": 621.3715667724609 | |
218 }, | |
219 "post_job_actions": { | |
220 "ChangeDatatypeActionout_file1": { | |
221 "action_arguments": { | |
222 "newtype": "fasta" | |
223 }, | |
224 "action_type": "ChangeDatatypeAction", | |
225 "output_name": "out_file1" | |
226 }, | |
227 "HideDatasetActionout_file1": { | |
228 "action_arguments": {}, | |
229 "action_type": "HideDatasetAction", | |
230 "output_name": "out_file1" | |
231 } | |
232 }, | |
233 "tool_errors": null, | |
234 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", | |
235 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
236 "tool_version": "0.2", | |
237 "type": "tool", | |
238 "uuid": "None", | |
239 "workflow_outputs": [] | |
240 }, | |
241 "6": { | |
242 "annotation": "", | |
243 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", | |
244 "id": 6, | |
245 "input_connections": { | |
246 "switch|input": { | |
247 "id": 5, | |
248 "output_name": "out_file1" | |
249 } | |
250 }, | |
251 "inputs": [], | |
252 "label": null, | |
253 "name": "fasta - tabular", | |
254 "outputs": [ | |
255 { | |
256 "name": "output", | |
257 "type": "fasta" | |
258 } | |
259 ], | |
260 "position": { | |
261 "left": 482.5694580078125, | |
262 "top": 420.9722480773926 | |
263 }, | |
264 "post_job_actions": { | |
265 "HideDatasetActionoutput": { | |
266 "action_arguments": {}, | |
267 "action_type": "HideDatasetAction", | |
268 "output_name": "output" | |
269 } | |
270 }, | |
271 "tool_errors": null, | |
272 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", | |
273 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"fasta2tabular\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null}", | |
274 "tool_version": "1.1.0", | |
275 "type": "tool", | |
276 "uuid": "890947a5-b6c3-4905-9659-9f4cb58ae3de", | |
277 "workflow_outputs": [] | |
278 }, | |
279 "7": { | |
280 "annotation": "", | |
281 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", | |
282 "id": 7, | |
283 "input_connections": { | |
284 "switch|input": { | |
285 "id": 6, | |
286 "output_name": "output" | |
287 } | |
288 }, | |
289 "inputs": [], | |
290 "label": null, | |
291 "name": "fasta - tabular", | |
292 "outputs": [ | |
293 { | |
294 "name": "output", | |
295 "type": "fasta" | |
296 } | |
297 ], | |
298 "position": { | |
299 "left": 729.6007080078125, | |
300 "top": 374.9653015136719 | |
301 }, | |
302 "post_job_actions": { | |
303 "RenameDatasetActionoutput": { | |
304 "action_arguments": { | |
305 "newname": "Initial Clipped sequences" | |
306 }, | |
307 "action_type": "RenameDatasetAction", | |
308 "output_name": "output" | |
309 } | |
310 }, | |
311 "tool_errors": null, | |
312 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", | |
313 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"tabular2fastaweight\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null}", | |
314 "tool_version": "1.1.0", | |
315 "type": "tool", | |
316 "uuid": "5807c11d-856f-466a-80b3-2854a13ed901", | |
317 "workflow_outputs": [ | |
318 { | |
319 "label": null, | |
320 "output_name": "output", | |
321 "uuid": "0104c422-daac-45f9-b56c-2b899f4f4c6f" | |
322 } | |
323 ] | |
324 }, | |
325 "8": { | |
326 "annotation": "", | |
327 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", | |
328 "id": 8, | |
329 "input_connections": { | |
330 "input": { | |
331 "id": 7, | |
332 "output_name": "output" | |
333 } | |
334 }, | |
335 "inputs": [], | |
336 "label": null, | |
337 "name": "sRbowtie", | |
338 "outputs": [ | |
339 { | |
340 "name": "output", | |
341 "type": "tabular" | |
342 }, | |
343 { | |
344 "name": "aligned", | |
345 "type": "fasta" | |
346 }, | |
347 { | |
348 "name": "unaligned", | |
349 "type": "fasta" | |
350 } | |
351 ], | |
352 "position": { | |
353 "left": 722.482666015625, | |
354 "top": 602.3785095214844 | |
355 }, | |
356 "post_job_actions": { | |
357 "HideDatasetActionaligned": { | |
358 "action_arguments": {}, | |
359 "action_type": "HideDatasetAction", | |
360 "output_name": "aligned" | |
361 }, | |
362 "HideDatasetActionoutput": { | |
363 "action_arguments": {}, | |
364 "action_type": "HideDatasetAction", | |
365 "output_name": "output" | |
366 }, | |
367 "RenameDatasetActionunaligned": { | |
368 "action_arguments": { | |
369 "newname": "Non A. gambiae sequences" | |
370 }, | |
371 "action_type": "RenameDatasetAction", | |
372 "output_name": "unaligned" | |
373 } | |
374 }, | |
375 "tool_errors": null, | |
376 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", | |
377 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"AgamP4\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", | |
378 "tool_version": "1.1.2", | |
379 "type": "tool", | |
380 "uuid": "None", | |
381 "workflow_outputs": [ | |
382 { | |
383 "label": null, | |
384 "output_name": "unaligned", | |
385 "uuid": "e00fc25f-c655-4854-a3e3-e1f6ae204302" | |
386 } | |
387 ] | |
388 }, | |
389 "9": { | |
390 "annotation": "", | |
391 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", | |
392 "id": 9, | |
393 "input_connections": { | |
394 "input": { | |
395 "id": 8, | |
396 "output_name": "unaligned" | |
397 } | |
398 }, | |
399 "inputs": [], | |
400 "label": null, | |
401 "name": "sRbowtie", | |
402 "outputs": [ | |
403 { | |
404 "name": "output", | |
405 "type": "tabular" | |
406 }, | |
407 { | |
408 "name": "aligned", | |
409 "type": "fasta" | |
410 }, | |
411 { | |
412 "name": "unaligned", | |
413 "type": "fasta" | |
414 } | |
415 ], | |
416 "position": { | |
417 "left": 724.96533203125, | |
418 "top": 780.3819885253906 | |
419 }, | |
420 "post_job_actions": { | |
421 "HideDatasetActionaligned": { | |
422 "action_arguments": {}, | |
423 "action_type": "HideDatasetAction", | |
424 "output_name": "aligned" | |
425 }, | |
426 "HideDatasetActionoutput": { | |
427 "action_arguments": {}, | |
428 "action_type": "HideDatasetAction", | |
429 "output_name": "output" | |
430 }, | |
431 "HideDatasetActionunaligned": { | |
432 "action_arguments": {}, | |
433 "action_type": "HideDatasetAction", | |
434 "output_name": "unaligned" | |
435 }, | |
436 "RenameDatasetActionunaligned": { | |
437 "action_arguments": { | |
438 "newname": "unmatched Plasmodium Berghei" | |
439 }, | |
440 "action_type": "RenameDatasetAction", | |
441 "output_name": "unaligned" | |
442 } | |
443 }, | |
444 "tool_errors": null, | |
445 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", | |
446 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", | |
447 "tool_version": "1.1.2", | |
448 "type": "tool", | |
449 "uuid": "None", | |
450 "workflow_outputs": [] | |
451 }, | |
452 "10": { | |
453 "annotation": "", | |
454 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", | |
455 "id": 10, | |
456 "input_connections": { | |
457 "input": { | |
458 "id": 9, | |
459 "output_name": "unaligned" | |
460 } | |
461 }, | |
462 "inputs": [], | |
463 "label": null, | |
464 "name": "sRbowtie", | |
465 "outputs": [ | |
466 { | |
467 "name": "output", | |
468 "type": "tabular" | |
469 }, | |
470 { | |
471 "name": "aligned", | |
472 "type": "fasta" | |
473 }, | |
474 { | |
475 "name": "unaligned", | |
476 "type": "fasta" | |
477 } | |
478 ], | |
479 "position": { | |
480 "left": 725.920166015625, | |
481 "top": 996.3889465332031 | |
482 }, | |
483 "post_job_actions": { | |
484 "HideDatasetActionaligned": { | |
485 "action_arguments": {}, | |
486 "action_type": "HideDatasetAction", | |
487 "output_name": "aligned" | |
488 }, | |
489 "HideDatasetActionoutput": { | |
490 "action_arguments": {}, | |
491 "action_type": "HideDatasetAction", | |
492 "output_name": "output" | |
493 }, | |
494 "HideDatasetActionunaligned": { | |
495 "action_arguments": {}, | |
496 "action_type": "HideDatasetAction", | |
497 "output_name": "unaligned" | |
498 }, | |
499 "RenameDatasetActionunaligned": { | |
500 "action_arguments": { | |
501 "newname": "Unaligned PhiX174" | |
502 }, | |
503 "action_type": "RenameDatasetAction", | |
504 "output_name": "unaligned" | |
505 } | |
506 }, | |
507 "tool_errors": null, | |
508 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", | |
509 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", | |
510 "tool_version": "1.1.2", | |
511 "type": "tool", | |
512 "uuid": "None", | |
513 "workflow_outputs": [] | |
514 }, | |
515 "11": { | |
516 "annotation": "", | |
517 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", | |
518 "id": 11, | |
519 "input_connections": { | |
520 "inputs_0|input": { | |
521 "id": 10, | |
522 "output_name": "unaligned" | |
523 } | |
524 }, | |
525 "inputs": [], | |
526 "label": null, | |
527 "name": "Oases_optimiser", | |
528 "outputs": [ | |
529 { | |
530 "name": "transcripts", | |
531 "type": "fasta" | |
532 } | |
533 ], | |
534 "position": { | |
535 "left": 1090.4688110351562, | |
536 "top": 339.39238357543945 | |
537 }, | |
538 "post_job_actions": { | |
539 "RenameDatasetActiontranscripts": { | |
540 "action_arguments": { | |
541 "newname": "Oases Contigs" | |
542 }, | |
543 "action_type": "RenameDatasetAction", | |
544 "output_name": "transcripts" | |
545 } | |
546 }, | |
547 "tool_errors": null, | |
548 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", | |
549 "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", | |
550 "tool_version": "1.1.4", | |
551 "type": "tool", | |
552 "uuid": "None", | |
553 "workflow_outputs": [ | |
554 { | |
555 "label": null, | |
556 "output_name": "transcripts", | |
557 "uuid": "68909f85-3532-47e2-956b-73dfad6bdc5f" | |
558 } | |
559 ] | |
560 }, | |
561 "12": { | |
562 "annotation": "", | |
563 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", | |
564 "id": 12, | |
565 "input_connections": { | |
566 "db_opts|histdb": { | |
567 "id": 1, | |
568 "output_name": "output" | |
569 }, | |
570 "query": { | |
571 "id": 11, | |
572 "output_name": "transcripts" | |
573 } | |
574 }, | |
575 "inputs": [], | |
576 "label": null, | |
577 "name": "NCBI BLAST+ blastx", | |
578 "outputs": [ | |
579 { | |
580 "name": "output1", | |
581 "type": "tabular" | |
582 } | |
583 ], | |
584 "position": { | |
585 "left": 1149.49658203125, | |
586 "top": 607.3785095214844 | |
587 }, | |
588 "post_job_actions": {}, | |
589 "tool_errors": null, | |
590 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", | |
591 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\"}", | |
592 "tool_version": "0.1.06", | |
593 "type": "tool", | |
594 "uuid": "None", | |
595 "workflow_outputs": [ | |
596 { | |
597 "label": null, | |
598 "output_name": "output1", | |
599 "uuid": "2bcd52a4-3023-4f30-918d-0383c0ef4455" | |
600 } | |
601 ] | |
602 }, | |
603 "13": { | |
604 "annotation": "", | |
605 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", | |
606 "id": 13, | |
607 "input_connections": { | |
608 "blast": { | |
609 "id": 12, | |
610 "output_name": "output1" | |
611 }, | |
612 "sequences": { | |
613 "id": 11, | |
614 "output_name": "transcripts" | |
615 } | |
616 }, | |
617 "inputs": [], | |
618 "label": null, | |
619 "name": "Parse blast output and compile hits", | |
620 "outputs": [ | |
621 { | |
622 "name": "tabularOutput", | |
623 "type": "tabular" | |
624 }, | |
625 { | |
626 "name": "fastaOutput", | |
627 "type": "fasta" | |
628 }, | |
629 { | |
630 "name": "al_sequences", | |
631 "type": "fasta" | |
632 }, | |
633 { | |
634 "name": "un_sequences", | |
635 "type": "fasta" | |
636 } | |
637 ], | |
638 "position": { | |
639 "left": 1454.5486907958984, | |
640 "top": 436.9097480773926 | |
641 }, | |
642 "post_job_actions": { | |
643 "HideDatasetActional_sequences": { | |
644 "action_arguments": {}, | |
645 "action_type": "HideDatasetAction", | |
646 "output_name": "al_sequences" | |
647 }, | |
648 "HideDatasetActionun_sequences": { | |
649 "action_arguments": {}, | |
650 "action_type": "HideDatasetAction", | |
651 "output_name": "un_sequences" | |
652 } | |
653 }, | |
654 "tool_errors": null, | |
655 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", | |
656 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"use_filters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", | |
657 "tool_version": "2.4.3", | |
658 "type": "tool", | |
659 "uuid": "32401021-0c03-4c16-a8a3-b08c54d34ce5", | |
660 "workflow_outputs": [ | |
661 { | |
662 "label": null, | |
663 "output_name": "tabularOutput", | |
664 "uuid": "0ecb04ea-b8fe-45ce-aa11-c4a67f1e17dd" | |
665 }, | |
666 { | |
667 "label": null, | |
668 "output_name": "fastaOutput", | |
669 "uuid": "f37bfebc-7b87-4dfc-a98c-2cdc3b18a84a" | |
670 } | |
671 ] | |
672 }, | |
673 "14": { | |
674 "annotation": "", | |
675 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", | |
676 "id": 14, | |
677 "input_connections": { | |
678 "input": { | |
679 "id": 13, | |
680 "output_name": "fastaOutput" | |
681 } | |
682 }, | |
683 "inputs": [], | |
684 "label": null, | |
685 "name": "Pick Fasta sequences", | |
686 "outputs": [ | |
687 { | |
688 "name": "output", | |
689 "type": "fasta" | |
690 } | |
691 ], | |
692 "position": { | |
693 "left": 1746.0938415527344, | |
694 "top": 672.5000305175781 | |
695 }, | |
696 "post_job_actions": { | |
697 "HideDatasetActionoutput": { | |
698 "action_arguments": {}, | |
699 "action_type": "HideDatasetAction", | |
700 "output_name": "output" | |
701 } | |
702 }, | |
703 "tool_errors": null, | |
704 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", | |
705 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"query\": \"\\\"Drosophila_C_virus\\\"\"}", | |
706 "tool_version": "0.9.0", | |
707 "type": "tool", | |
708 "uuid": "None", | |
709 "workflow_outputs": [] | |
710 }, | |
711 "15": { | |
712 "annotation": "", | |
713 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", | |
714 "id": 15, | |
715 "input_connections": { | |
716 "input": { | |
717 "id": 13, | |
718 "output_name": "fastaOutput" | |
719 } | |
720 }, | |
721 "inputs": [], | |
722 "label": null, | |
723 "name": "Pick Fasta sequences", | |
724 "outputs": [ | |
725 { | |
726 "name": "output", | |
727 "type": "fasta" | |
728 } | |
729 ], | |
730 "position": { | |
731 "left": 1745.104248046875, | |
732 "top": 765.4861450195312 | |
733 }, | |
734 "post_job_actions": { | |
735 "HideDatasetActionoutput": { | |
736 "action_arguments": {}, | |
737 "action_type": "HideDatasetAction", | |
738 "output_name": "output" | |
739 } | |
740 }, | |
741 "tool_errors": null, | |
742 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", | |
743 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"query\": \"\\\"Cricket_paralysis_virus\\\"\"}", | |
744 "tool_version": "0.9.0", | |
745 "type": "tool", | |
746 "uuid": "None", | |
747 "workflow_outputs": [] | |
748 }, | |
749 "16": { | |
750 "annotation": "", | |
751 "content_id": "cat1", | |
752 "id": 16, | |
753 "input_connections": { | |
754 "input1": { | |
755 "id": 14, | |
756 "output_name": "output" | |
757 }, | |
758 "queries_0|input2": { | |
759 "id": 15, | |
760 "output_name": "output" | |
761 } | |
762 }, | |
763 "inputs": [], | |
764 "label": null, | |
765 "name": "Concatenate datasets", | |
766 "outputs": [ | |
767 { | |
768 "name": "out_file1", | |
769 "type": "input" | |
770 } | |
771 ], | |
772 "position": { | |
773 "left": 1983.5938415527344, | |
774 "top": 680.4861450195312 | |
775 }, | |
776 "post_job_actions": { | |
777 "RenameDatasetActionout_file1": { | |
778 "action_arguments": { | |
779 "newname": "Dicistroviridae Hits" | |
780 }, | |
781 "action_type": "RenameDatasetAction", | |
782 "output_name": "out_file1" | |
783 } | |
784 }, | |
785 "tool_errors": null, | |
786 "tool_id": "cat1", | |
787 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", | |
788 "tool_version": "1.0.0", | |
789 "type": "tool", | |
790 "uuid": "None", | |
791 "workflow_outputs": [ | |
792 { | |
793 "label": null, | |
794 "output_name": "out_file1", | |
795 "uuid": "f73ab6cc-279f-4a9e-8860-73e3b206b9ca" | |
796 } | |
797 ] | |
798 }, | |
799 "17": { | |
800 "annotation": "", | |
801 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", | |
802 "id": 17, | |
803 "input_connections": { | |
804 "inputSequences": { | |
805 "id": 16, | |
806 "output_name": "out_file1" | |
807 } | |
808 }, | |
809 "inputs": [], | |
810 "label": null, | |
811 "name": "cap3", | |
812 "outputs": [ | |
813 { | |
814 "name": "contigsandsinglets", | |
815 "type": "fasta" | |
816 }, | |
817 { | |
818 "name": "cap3stdout", | |
819 "type": "txt" | |
820 }, | |
821 { | |
822 "name": "contigs", | |
823 "type": "fasta" | |
824 }, | |
825 { | |
826 "name": "contigsqual", | |
827 "type": "txt" | |
828 }, | |
829 { | |
830 "name": "contigslink", | |
831 "type": "txt" | |
832 }, | |
833 { | |
834 "name": "ace", | |
835 "type": "txt" | |
836 }, | |
837 { | |
838 "name": "info", | |
839 "type": "txt" | |
840 }, | |
841 { | |
842 "name": "singlets", | |
843 "type": "txt" | |
844 } | |
845 ], | |
846 "position": { | |
847 "left": 2192.100830078125, | |
848 "top": 513.489616394043 | |
849 }, | |
850 "post_job_actions": { | |
851 "HideDatasetActionace": { | |
852 "action_arguments": {}, | |
853 "action_type": "HideDatasetAction", | |
854 "output_name": "ace" | |
855 }, | |
856 "HideDatasetActioncap3stdout": { | |
857 "action_arguments": {}, | |
858 "action_type": "HideDatasetAction", | |
859 "output_name": "cap3stdout" | |
860 }, | |
861 "HideDatasetActioncontigs": { | |
862 "action_arguments": {}, | |
863 "action_type": "HideDatasetAction", | |
864 "output_name": "contigs" | |
865 }, | |
866 "HideDatasetActioncontigslink": { | |
867 "action_arguments": {}, | |
868 "action_type": "HideDatasetAction", | |
869 "output_name": "contigslink" | |
870 }, | |
871 "HideDatasetActioncontigsqual": { | |
872 "action_arguments": {}, | |
873 "action_type": "HideDatasetAction", | |
874 "output_name": "contigsqual" | |
875 }, | |
876 "HideDatasetActioninfo": { | |
877 "action_arguments": {}, | |
878 "action_type": "HideDatasetAction", | |
879 "output_name": "info" | |
880 }, | |
881 "HideDatasetActionsinglets": { | |
882 "action_arguments": {}, | |
883 "action_type": "HideDatasetAction", | |
884 "output_name": "singlets" | |
885 }, | |
886 "RenameDatasetActioncontigs": { | |
887 "action_arguments": { | |
888 "newname": "CAP assemblies of Dicistroviridae hits" | |
889 }, | |
890 "action_type": "RenameDatasetAction", | |
891 "output_name": "contigs" | |
892 } | |
893 }, | |
894 "tool_errors": null, | |
895 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", | |
896 "tool_state": "{\"overlapidentity\": \"\\\"90\\\"\", \"inputSequences\": \"null\", \"__rerun_remap_job_id__\": null, \"overlaplength\": \"\\\"40\\\"\", \"__page__\": 0}", | |
897 "tool_version": "1.2.0", | |
898 "type": "tool", | |
899 "uuid": "None", | |
900 "workflow_outputs": [ | |
901 { | |
902 "label": null, | |
903 "output_name": "contigsandsinglets", | |
904 "uuid": "e413fdea-3b18-40c1-b423-cf2bd33eeadf" | |
905 } | |
906 ] | |
907 }, | |
908 "18": { | |
909 "annotation": "", | |
910 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.06", | |
911 "id": 18, | |
912 "input_connections": { | |
913 "db_opts|histdb": { | |
914 "id": 4, | |
915 "output_name": "outfile" | |
916 }, | |
917 "query": { | |
918 "id": 17, | |
919 "output_name": "contigsandsinglets" | |
920 } | |
921 }, | |
922 "inputs": [], | |
923 "label": null, | |
924 "name": "NCBI BLAST+ tblastx", | |
925 "outputs": [ | |
926 { | |
927 "name": "output1", | |
928 "type": "tabular" | |
929 } | |
930 ], | |
931 "position": { | |
932 "left": 2424.0973510742188, | |
933 "top": 837.5000305175781 | |
934 }, | |
935 "post_job_actions": {}, | |
936 "tool_errors": null, | |
937 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.06", | |
938 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"query\": \"null\"}", | |
939 "tool_version": "0.1.06", | |
940 "type": "tool", | |
941 "uuid": "None", | |
942 "workflow_outputs": [ | |
943 { | |
944 "label": null, | |
945 "output_name": "output1", | |
946 "uuid": "7ad377ba-ad8f-421f-af4c-6835a1994f46" | |
947 } | |
948 ] | |
949 }, | |
950 "19": { | |
951 "annotation": "", | |
952 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", | |
953 "id": 19, | |
954 "input_connections": { | |
955 "blast_tab": { | |
956 "id": 18, | |
957 "output_name": "output1" | |
958 }, | |
959 "guideSequence": { | |
960 "id": 2, | |
961 "output_name": "outfilename" | |
962 }, | |
963 "sequences": { | |
964 "id": 17, | |
965 "output_name": "contigsandsinglets" | |
966 } | |
967 }, | |
968 "inputs": [], | |
969 "label": null, | |
970 "name": "blast_to_scaffold", | |
971 "outputs": [ | |
972 { | |
973 "name": "output", | |
974 "type": "fasta" | |
975 } | |
976 ], | |
977 "position": { | |
978 "left": 2718.003662109375, | |
979 "top": 597.9167022705078 | |
980 }, | |
981 "post_job_actions": { | |
982 "RenameDatasetActionoutput": { | |
983 "action_arguments": { | |
984 "newname": "New AnCV sequences in DCV scaffold" | |
985 }, | |
986 "action_type": "RenameDatasetAction", | |
987 "output_name": "output" | |
988 } | |
989 }, | |
990 "tool_errors": null, | |
991 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", | |
992 "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}", | |
993 "tool_version": "0.9.0", | |
994 "type": "tool", | |
995 "uuid": "d6fcfcf9-1b9b-4ac3-8217-f7ddbc84be91", | |
996 "workflow_outputs": [ | |
997 { | |
998 "label": null, | |
999 "output_name": "output", | |
1000 "uuid": "c052be17-d78e-4a17-891c-7154936c7935" | |
1001 } | |
1002 ] | |
1003 } | |
1004 }, | |
1005 "uuid": "ac35209c-d243-403c-95c7-5500b022ae10" | |
1006 } |