Mercurial > repos > artbio > metavisitor_2_workflows
comparison Galaxy-Workflow-Metavisitor__Workflow_for_small_RNA_profiling_of_contigs.ga @ 0:c375489bbcb0 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows/metavisitor_2_workflows commit ecf95caa7d5e9ab001a75cbf5fb306e7ecd3def3
author | artbio |
---|---|
date | Sun, 21 Jul 2019 19:22:52 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:c375489bbcb0 |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "uuid": "691e3812-602f-4492-93f3-f1355698b197", | |
4 "tags": [], | |
5 "format-version": "0.1", | |
6 "version": 1, | |
7 "steps": { | |
8 "1": { | |
9 "tool_id": null, | |
10 "errors": null, | |
11 "uuid": "9b24b7ef-5eb5-4c87-9272-42f9f05e109f", | |
12 "tool_version": null, | |
13 "outputs": [], | |
14 "workflow_outputs": [ | |
15 { | |
16 "output_name": "output", | |
17 "uuid": "aa452f52-79bc-4b65-b230-6bcd9badfb2f", | |
18 "label": null | |
19 } | |
20 ], | |
21 "annotation": "", | |
22 "content_id": null, | |
23 "input_connections": {}, | |
24 "inputs": [], | |
25 "position": { | |
26 "top": 439, | |
27 "left": 304 | |
28 }, | |
29 "tool_state": "{}", | |
30 "label": "de novo assembled Oases contigs", | |
31 "type": "data_input", | |
32 "id": 1, | |
33 "name": "Input dataset" | |
34 }, | |
35 "0": { | |
36 "tool_id": null, | |
37 "errors": null, | |
38 "uuid": "ed07d831-9b23-4def-b883-f6fe24eb55a0", | |
39 "tool_version": null, | |
40 "outputs": [], | |
41 "workflow_outputs": [ | |
42 { | |
43 "output_name": "output", | |
44 "uuid": "e73d1517-c1f3-4a7f-8fbd-e2297906ee1f", | |
45 "label": null | |
46 } | |
47 ], | |
48 "annotation": "", | |
49 "content_id": null, | |
50 "input_connections": {}, | |
51 "inputs": [], | |
52 "position": { | |
53 "top": 289, | |
54 "left": 271 | |
55 }, | |
56 "tool_state": "{\"collection_type\": \"list\"}", | |
57 "label": "Input Dataset Collection of fastq reads", | |
58 "type": "data_collection_input", | |
59 "id": 0, | |
60 "name": "Input dataset collection" | |
61 }, | |
62 "3": { | |
63 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", | |
64 "errors": null, | |
65 "uuid": "88093ee6-2279-4398-8350-6c0e6f59720c", | |
66 "tool_version": "1.1", | |
67 "outputs": [ | |
68 { | |
69 "type": "fasta", | |
70 "name": "output" | |
71 } | |
72 ], | |
73 "post_job_actions": { | |
74 "RenameDatasetActionoutput": { | |
75 "output_name": "output", | |
76 "action_type": "RenameDatasetAction", | |
77 "action_arguments": { | |
78 "newname": "Contig (>300 nt)" | |
79 } | |
80 } | |
81 }, | |
82 "workflow_outputs": [ | |
83 { | |
84 "output_name": "output", | |
85 "uuid": "7eaafc91-9c84-4307-bbff-6ad629170bdc", | |
86 "label": null | |
87 } | |
88 ], | |
89 "annotation": "", | |
90 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", | |
91 "input_connections": { | |
92 "input": { | |
93 "output_name": "output", | |
94 "id": 1 | |
95 } | |
96 }, | |
97 "inputs": [ | |
98 { | |
99 "name": "input", | |
100 "description": "runtime parameter for tool Filter sequences by length" | |
101 } | |
102 ], | |
103 "position": { | |
104 "top": 451, | |
105 "left": 569 | |
106 }, | |
107 "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"300\\\"\"}", | |
108 "label": null, | |
109 "type": "tool", | |
110 "id": 3, | |
111 "tool_shed_repository": { | |
112 "owner": "devteam", | |
113 "changeset_revision": "2fd6033d0e9c", | |
114 "name": "fasta_filter_by_length", | |
115 "tool_shed": "toolshed.g2.bx.psu.edu" | |
116 }, | |
117 "name": "Filter sequences by length" | |
118 }, | |
119 "2": { | |
120 "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/yac_clipper/yac/2.3.0", | |
121 "errors": null, | |
122 "uuid": "a07a6d78-bdd3-4092-b463-c0bd7f796efe", | |
123 "tool_version": "2.3.0", | |
124 "outputs": [ | |
125 { | |
126 "type": "input", | |
127 "name": "output" | |
128 } | |
129 ], | |
130 "post_job_actions": { | |
131 "RenameDatasetActionoutput": { | |
132 "output_name": "output", | |
133 "action_type": "RenameDatasetAction", | |
134 "action_arguments": { | |
135 "newname": "Clipped reads" | |
136 } | |
137 } | |
138 }, | |
139 "workflow_outputs": [ | |
140 { | |
141 "output_name": "output", | |
142 "uuid": "890a91ad-07e6-421d-a40f-b75aff18f95b", | |
143 "label": null | |
144 } | |
145 ], | |
146 "annotation": "", | |
147 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/yac_clipper/yac/2.3.0", | |
148 "input_connections": { | |
149 "input": { | |
150 "output_name": "output", | |
151 "id": 0 | |
152 } | |
153 }, | |
154 "inputs": [ | |
155 { | |
156 "name": "input", | |
157 "description": "runtime parameter for tool Clip adapter" | |
158 } | |
159 ], | |
160 "position": { | |
161 "top": 294, | |
162 "left": 587 | |
163 }, | |
164 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": null, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"__current_case__\\\": 0, \\\"clip_sequence\\\": \\\"TGGAATTCTCGGGTGCCAAG\\\", \\\"clip_source_list\\\": \\\"prebuilt\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"Nmode\": \"\\\"reject\\\"\"}", | |
165 "label": null, | |
166 "type": "tool", | |
167 "id": 2, | |
168 "tool_shed_repository": { | |
169 "owner": "artbio", | |
170 "changeset_revision": "f7947c5a18b8", | |
171 "name": "yac_clipper", | |
172 "tool_shed": "toolshed.g2.bx.psu.edu" | |
173 }, | |
174 "name": "Clip adapter" | |
175 }, | |
176 "5": { | |
177 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", | |
178 "errors": null, | |
179 "uuid": "a069c8db-14ef-4708-89be-3a5d5a926498", | |
180 "tool_version": "1.0.0", | |
181 "outputs": [ | |
182 { | |
183 "type": "input", | |
184 "name": "out_file1" | |
185 } | |
186 ], | |
187 "post_job_actions": { | |
188 "RenameDatasetActionout_file1": { | |
189 "output_name": "out_file1", | |
190 "action_type": "RenameDatasetAction", | |
191 "action_arguments": { | |
192 "newname": "contig (>300t, simplified names)" | |
193 } | |
194 } | |
195 }, | |
196 "workflow_outputs": [ | |
197 { | |
198 "output_name": "out_file1", | |
199 "uuid": "fa095644-f7e0-4c44-a555-4d24f8fddc85", | |
200 "label": null | |
201 } | |
202 ], | |
203 "annotation": "", | |
204 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", | |
205 "input_connections": { | |
206 "input": { | |
207 "output_name": "output", | |
208 "id": 3 | |
209 } | |
210 }, | |
211 "inputs": [ | |
212 { | |
213 "name": "input", | |
214 "description": "runtime parameter for tool Regex Find And Replace" | |
215 } | |
216 ], | |
217 "position": { | |
218 "top": 443, | |
219 "left": 842 | |
220 }, | |
221 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"pattern\\\": \\\"_Confidence_.+\\\", \\\"replacement\\\": \\\"\\\"}]\", \"__page__\": null}", | |
222 "label": null, | |
223 "type": "tool", | |
224 "id": 5, | |
225 "tool_shed_repository": { | |
226 "owner": "galaxyp", | |
227 "changeset_revision": "209b7c5ee9d7", | |
228 "name": "regex_find_replace", | |
229 "tool_shed": "toolshed.g2.bx.psu.edu" | |
230 }, | |
231 "name": "Regex Find And Replace" | |
232 }, | |
233 "4": { | |
234 "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", | |
235 "errors": null, | |
236 "uuid": "a10d3b12-9018-4b96-9492-18e1b1e87a83", | |
237 "tool_version": "1.4.1", | |
238 "outputs": [ | |
239 { | |
240 "type": "input", | |
241 "name": "paired_output" | |
242 }, | |
243 { | |
244 "type": "input", | |
245 "name": "list_output" | |
246 }, | |
247 { | |
248 "type": "input", | |
249 "name": "out_file1" | |
250 }, | |
251 { | |
252 "type": "_sniff_", | |
253 "name": "paired_out_file" | |
254 } | |
255 ], | |
256 "post_job_actions": { | |
257 "HideDatasetActionpaired_out_file": { | |
258 "output_name": "paired_out_file", | |
259 "action_type": "HideDatasetAction", | |
260 "action_arguments": {} | |
261 }, | |
262 "RenameDatasetActionout_file1": { | |
263 "output_name": "out_file1", | |
264 "action_type": "RenameDatasetAction", | |
265 "action_arguments": { | |
266 "newname": "Merged clipped reads" | |
267 } | |
268 }, | |
269 "HideDatasetActionpaired_output": { | |
270 "output_name": "paired_output", | |
271 "action_type": "HideDatasetAction", | |
272 "action_arguments": {} | |
273 }, | |
274 "HideDatasetActionlist_output": { | |
275 "output_name": "list_output", | |
276 "action_type": "HideDatasetAction", | |
277 "action_arguments": {} | |
278 } | |
279 }, | |
280 "workflow_outputs": [ | |
281 { | |
282 "output_name": "out_file1", | |
283 "uuid": "362a4d36-9fd9-4f68-a271-d068a245d307", | |
284 "label": null | |
285 } | |
286 ], | |
287 "annotation": "", | |
288 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", | |
289 "input_connections": { | |
290 "global_condition|inputs": { | |
291 "output_name": "output", | |
292 "id": 2 | |
293 } | |
294 }, | |
295 "inputs": [ | |
296 { | |
297 "name": "global_condition", | |
298 "description": "runtime parameter for tool Concatenate multiple datasets" | |
299 } | |
300 ], | |
301 "position": { | |
302 "top": 221.5, | |
303 "left": 831 | |
304 }, | |
305 "tool_state": "{\"dataset_names\": \"\\\"false\\\"\", \"headers\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"global_condition\": \"{\\\"__current_case__\\\": 0, \\\"input_type\\\": \\\"singles\\\", \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", | |
306 "label": null, | |
307 "type": "tool", | |
308 "id": 4, | |
309 "tool_shed_repository": { | |
310 "owner": "artbio", | |
311 "changeset_revision": "55cf9d9defd1", | |
312 "name": "concatenate_multiple_datasets", | |
313 "tool_shed": "toolshed.g2.bx.psu.edu" | |
314 }, | |
315 "name": "Concatenate multiple datasets" | |
316 }, | |
317 "7": { | |
318 "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/small_rna_maps/small_rna_maps/2.14.0", | |
319 "errors": null, | |
320 "uuid": "95dc4ba8-402f-4d64-b5e9-8706589bc7fc", | |
321 "tool_version": "2.14.0", | |
322 "outputs": [ | |
323 { | |
324 "type": "tabular", | |
325 "name": "output_tab" | |
326 }, | |
327 { | |
328 "type": "bed", | |
329 "name": "output_bed" | |
330 }, | |
331 { | |
332 "type": "tabular", | |
333 "name": "extra_output_tab" | |
334 }, | |
335 { | |
336 "type": "pdf", | |
337 "name": "output_pdf" | |
338 } | |
339 ], | |
340 "post_job_actions": { | |
341 "HideDatasetActionextra_output_tab": { | |
342 "output_name": "extra_output_tab", | |
343 "action_type": "HideDatasetAction", | |
344 "action_arguments": {} | |
345 }, | |
346 "HideDatasetActionoutput_tab": { | |
347 "output_name": "output_tab", | |
348 "action_type": "HideDatasetAction", | |
349 "action_arguments": {} | |
350 } | |
351 }, | |
352 "workflow_outputs": [ | |
353 { | |
354 "output_name": "output_bed", | |
355 "uuid": "cab2a668-47c6-4e86-aab6-22155d6a3e4d", | |
356 "label": null | |
357 }, | |
358 { | |
359 "output_name": "output_pdf", | |
360 "uuid": "9436b9c9-2dda-4649-8367-10e71d3a429e", | |
361 "label": null | |
362 } | |
363 ], | |
364 "annotation": "", | |
365 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/small_rna_maps/small_rna_maps/2.14.0", | |
366 "input_connections": { | |
367 "inputs": { | |
368 "output_name": "output", | |
369 "id": 6 | |
370 } | |
371 }, | |
372 "inputs": [ | |
373 { | |
374 "name": "inputs", | |
375 "description": "runtime parameter for tool small_rna_maps" | |
376 } | |
377 ], | |
378 "position": { | |
379 "top": 383, | |
380 "left": 1496.5 | |
381 }, | |
382 "tool_state": "{\"inputs\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"series\": \"[{\\\"__index__\\\": 0, \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"normalization\\\": \\\"1.0\\\"}]\", \"__rerun_remap_job_id__\": null, \"ylimits_cond\": \"{\\\"__current_case__\\\": 1, \\\"ylimits\\\": \\\"false\\\"}\", \"minsize\": \"\\\"18\\\"\", \"cluster\": \"\\\"0\\\"\", \"maxsize\": \"\\\"30\\\"\", \"normalization\": \"\\\"1\\\"\", \"plots_options\": \"{\\\"__current_case__\\\": 0, \\\"extra_plot\\\": \\\"Size\\\", \\\"first_plot\\\": \\\"Counts\\\", \\\"plots_options_selector\\\": \\\"two_plot\\\"}\"}", | |
383 "label": null, | |
384 "type": "tool", | |
385 "id": 7, | |
386 "tool_shed_repository": { | |
387 "owner": "artbio", | |
388 "changeset_revision": "14adf24603b6", | |
389 "name": "small_rna_maps", | |
390 "tool_shed": "toolshed.g2.bx.psu.edu" | |
391 }, | |
392 "name": "small_rna_maps" | |
393 }, | |
394 "6": { | |
395 "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", | |
396 "errors": null, | |
397 "uuid": "7e4be478-ae45-4282-812c-e72dc15c3d2d", | |
398 "tool_version": "2.1.1", | |
399 "outputs": [ | |
400 { | |
401 "type": "tabular", | |
402 "name": "output" | |
403 }, | |
404 { | |
405 "type": "input", | |
406 "name": "aligned" | |
407 }, | |
408 { | |
409 "type": "input", | |
410 "name": "unaligned" | |
411 } | |
412 ], | |
413 "post_job_actions": { | |
414 "HideDatasetActionunaligned": { | |
415 "output_name": "unaligned", | |
416 "action_type": "HideDatasetAction", | |
417 "action_arguments": {} | |
418 }, | |
419 "HideDatasetActionaligned": { | |
420 "output_name": "aligned", | |
421 "action_type": "HideDatasetAction", | |
422 "action_arguments": {} | |
423 } | |
424 }, | |
425 "workflow_outputs": [ | |
426 { | |
427 "output_name": "output", | |
428 "uuid": "39529cb2-4ae9-4b89-bab0-9cb59f577046", | |
429 "label": null | |
430 } | |
431 ], | |
432 "annotation": "", | |
433 "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/sr_bowtie/bowtieForSmallRNA/2.1.1", | |
434 "input_connections": { | |
435 "input": { | |
436 "output_name": "out_file1", | |
437 "id": 4 | |
438 }, | |
439 "refGenomeSource|ownFile": { | |
440 "output_name": "out_file1", | |
441 "id": 5 | |
442 } | |
443 }, | |
444 "inputs": [ | |
445 { | |
446 "name": "input", | |
447 "description": "runtime parameter for tool sR_bowtie" | |
448 }, | |
449 { | |
450 "name": "refGenomeSource", | |
451 "description": "runtime parameter for tool sR_bowtie" | |
452 } | |
453 ], | |
454 "position": { | |
455 "top": 368, | |
456 "left": 1164 | |
457 }, | |
458 "tool_state": "{\"__page__\": null, \"output_format\": \"\\\"tabular\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"__current_case__\\\": 1, \\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"method\": \"\\\"a_option\\\"\"}", | |
459 "label": "Align reads against contigs", | |
460 "type": "tool", | |
461 "id": 6, | |
462 "tool_shed_repository": { | |
463 "owner": "artbio", | |
464 "changeset_revision": "0281bb245635", | |
465 "name": "sr_bowtie", | |
466 "tool_shed": "toolshed.g2.bx.psu.edu" | |
467 }, | |
468 "name": "sR_bowtie" | |
469 } | |
470 }, | |
471 "annotation": "", | |
472 "name": "Metavisitor: Workflow for small RNA profiling of contigs" | |
473 } |