Mercurial > repos > sjung > bdds

comparison Galaxy-Workflow-DNAse-footprints-singlesample-bamInput_wellington_hint_piq.ga @ 0:2d6315e241e4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author sjung
date Wed, 10 May 2017 13:55:47 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:2d6315e241e4
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "DNAse-footprints-singlesample-bamInput_wellington_hint_piq",
6 "steps": {
7 "0": {
8 "annotation": "0",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "0",
14 "name": "sorted Bam"
15 }
16 ],
17 "label": null,
18 "name": "Input dataset",
19 "outputs": [],
20 "position": {
21 "left": 226.383544921875,
22 "top": 220.94318389892578
23 },
24 "tool_errors": null,
25 "tool_id": null,
26 "tool_state": "{\"name\": \"sorted Bam\"}",
27 "tool_version": null,
28 "type": "data_input",
29 "user_outputs": [],
30 "uuid": "None"
31 },
32 "1": {
33 "annotation": "2",
34 "id": 1,
35 "input_connections": {},
36 "inputs": [],
37 "label": null,
38 "name": "Convert from BAM to BED",
39 "outputs": [
40 {
41 "name": "output",
42 "type": "bed"
43 }
44 ],
45 "position": {
46 "left": 466.2727355957031,
47 "top": 210.88920211791992
48 },
49 "post_job_actions": {
50 "HideDatasetActionoutput": {
51 "action_arguments": {},
52 "action_type": "HideDatasetAction",
53 "output_name": "output"
54 }
55 },
56 "tool_errors": null,
57 "tool_id": "bedtools_bamtobed",
58 "tool_state": "{\"__page__\": 0, \"option\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"input_source\": \"{\\\"input_type\\\": \\\"file\\\", \\\"__current_case__\\\": 1, \\\"input_file\\\": null}\", \"tag\": \"\\\"\\\"\", \"split\": \"\\\"False\\\"\", \"ed_score\": \"\\\"False\\\"\"}",
59 "tool_version": "BEDTOOLS: 2.17.0",
60 "type": "tool",
61 "user_outputs": [],
62 "uuid": "None"
63 },
64 "2": {
65 "annotation": "3",
66 "id": 2,
67 "input_connections": {
68 "input": {
69 "id": 0,
70 "output_name": "output"
71 }
72 },
73 "inputs": [],
74 "label": null,
75 "name": "piq",
76 "outputs": [
77 {
78 "name": "output",
79 "type": "csv"
80 }
81 ],
82 "position": {
83 "left": 1022.210205078125,
84 "top": 532.2102203369141
85 },
86 "post_job_actions": {
87 "HideDatasetActionoutput": {
88 "action_arguments": {},
89 "action_type": "HideDatasetAction",
90 "output_name": "output"
91 }
92 },
93 "tool_errors": null,
94 "tool_id": "piq",
95 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
96 "tool_version": "PIQ: 1.3",
97 "type": "tool",
98 "user_outputs": [],
99 "uuid": "None"
100 },
101 "3": {
102 "annotation": "4",
103 "id": 3,
104 "input_connections": {
105 "fd_0|input": {
106 "id": 1,
107 "output_name": "output"
108 }
109 },
110 "inputs": [],
111 "label": null,
112 "name": "FSeq",
113 "outputs": [
114 {
115 "name": "output",
116 "type": "bed,wig"
117 }
118 ],
119 "position": {
120 "left": 513.2613689899445,
121 "top": 375.875
122 },
123 "post_job_actions": {
124 "HideDatasetActionoutput": {
125 "action_arguments": {},
126 "action_type": "HideDatasetAction",
127 "output_name": "output"
128 }
129 },
130 "tool_errors": null,
131 "tool_id": "fseq",
132 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"bed\\\"\", \"wiggleTrackStep\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"featLen\": \"\\\"600\\\"\", \"fd\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"threshold\": \"\\\"2.5\\\"\", \"fragSize\": \"\\\"0\\\"\"}",
133 "tool_version": "F-Seq: 1.85",
134 "type": "tool",
135 "user_outputs": [],
136 "uuid": "None"
137 },
138 "4": {
139 "annotation": "16",
140 "id": 4,
141 "input_connections": {
142 "input": {
143 "id": 2,
144 "output_name": "output"
145 }
146 },
147 "inputs": [],
148 "label": null,
149 "name": "Uniq",
150 "outputs": [
151 {
152 "name": "output",
153 "type": "input"
154 }
155 ],
156 "position": {
157 "left": 1246.03125,
158 "top": 541.0170440673828
159 },
160 "post_job_actions": {
161 "RenameDatasetActionoutput": {
162 "action_arguments": {
163 "newname": "piq_uniq"
164 },
165 "action_type": "RenameDatasetAction",
166 "output_name": "output"
167 }
168 },
169 "tool_errors": null,
170 "tool_id": "uniq",
171 "tool_state": "{\"columnList\": \"\\\"1,2,3\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
172 "tool_version": "1.0.0",
173 "type": "tool",
174 "user_outputs": [],
175 "uuid": "7dcb1018-baa2-48a1-a0ee-478d8edced77"
176 },
177 "5": {
178 "annotation": "6",
179 "id": 5,
180 "input_connections": {
181 "input": {
182 "id": 3,
183 "output_name": "output"
184 }
185 },
186 "inputs": [],
187 "label": null,
188 "name": "Cut",
189 "outputs": [
190 {
191 "name": "out_file1",
192 "type": "tabular"
193 }
194 ],
195 "position": {
196 "left": 389.2841033935547,
197 "top": 528.8863372802734
198 },
199 "post_job_actions": {
200 "HideDatasetActionout_file1": {
201 "action_arguments": {},
202 "action_type": "HideDatasetAction",
203 "output_name": "out_file1"
204 }
205 },
206 "tool_errors": null,
207 "tool_id": "Cut1",
208 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
209 "tool_version": "1.0.1",
210 "type": "tool",
211 "user_outputs": [],
212 "uuid": "None"
213 },
214 "6": {
215 "annotation": "8",
216 "id": 6,
217 "input_connections": {
218 "input": {
219 "id": 5,
220 "output_name": "out_file1"
221 }
222 },
223 "inputs": [],
224 "label": null,
225 "name": "Compute",
226 "outputs": [
227 {
228 "name": "out_file1",
229 "type": "input"
230 }
231 ],
232 "position": {
233 "left": 587.28125,
234 "top": 531.8834991455078
235 },
236 "post_job_actions": {
237 "HideDatasetActionout_file1": {
238 "action_arguments": {},
239 "action_type": "HideDatasetAction",
240 "output_name": "out_file1"
241 }
242 },
243 "tool_errors": null,
244 "tool_id": "Add_a_column1",
245 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2-c3\\\"\", \"round\": \"\\\"no\\\"\", \"__page__\": 0}",
246 "tool_version": "1.1.0",
247 "type": "tool",
248 "user_outputs": [],
249 "uuid": "None"
250 },
251 "7": {
252 "annotation": "9",
253 "id": 7,
254 "input_connections": {
255 "input": {
256 "id": 6,
257 "output_name": "out_file1"
258 }
259 },
260 "inputs": [],
261 "label": null,
262 "name": "Filter",
263 "outputs": [
264 {
265 "name": "out_file1",
266 "type": "input"
267 }
268 ],
269 "position": {
270 "left": 788.2897644042969,
271 "top": 531.8834991455078
272 },
273 "post_job_actions": {
274 "HideDatasetActionout_file1": {
275 "action_arguments": {},
276 "action_type": "HideDatasetAction",
277 "output_name": "out_file1"
278 }
279 },
280 "tool_errors": null,
281 "tool_id": "Filter1",
282 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4<-400\\\"\", \"__page__\": 0}",
283 "tool_version": "1.1.0",
284 "type": "tool",
285 "user_outputs": [],
286 "uuid": "None"
287 },
288 "8": {
289 "annotation": "10",
290 "id": 8,
291 "input_connections": {
292 "input": {
293 "id": 7,
294 "output_name": "out_file1"
295 }
296 },
297 "inputs": [],
298 "label": null,
299 "name": "Cut",
300 "outputs": [
301 {
302 "name": "out_file1",
303 "type": "tabular"
304 }
305 ],
306 "position": {
307 "left": 784.7102355957031,
308 "top": 367.2670440673828
309 },
310 "post_job_actions": {
311 "HideDatasetActionout_file1": {
312 "action_arguments": {},
313 "action_type": "HideDatasetAction",
314 "output_name": "out_file1"
315 }
316 },
317 "tool_errors": null,
318 "tool_id": "Cut1",
319 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
320 "tool_version": "1.0.1",
321 "type": "tool",
322 "user_outputs": [],
323 "uuid": "None"
324 },
325 "9": {
326 "annotation": "11",
327 "id": 9,
328 "input_connections": {
329 "input": {
330 "id": 8,
331 "output_name": "out_file1"
332 }
333 },
334 "inputs": [],
335 "label": null,
336 "name": "Filter",
337 "outputs": [
338 {
339 "name": "out_file1",
340 "type": "input"
341 }
342 ],
343 "position": {
344 "left": 779.8806762695312,
345 "top": 221.44318389892578
346 },
347 "post_job_actions": {
348 "ChangeDatatypeActionout_file1": {
349 "action_arguments": {
350 "newtype": "bed"
351 },
352 "action_type": "ChangeDatatypeAction",
353 "output_name": "out_file1"
354 },
355 "HideDatasetActionout_file1": {
356 "action_arguments": {},
357 "action_type": "HideDatasetAction",
358 "output_name": "out_file1"
359 }
360 },
361 "tool_errors": null,
362 "tool_id": "Filter1",
363 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c1=='chr1' or c1=='chr2'or c1=='chr3' or c1=='chr4' or c1=='chr5' or c1=='chr6' or c1=='chr7' or c1=='chr8' or c1=='chr9' or c1=='chr10' or c1=='chr11' or c1=='chr12' or c1=='chr13' or c1=='chr14' or c1=='chr15' or c1=='chr16' or c1=='chr17' or c1=='chr18' or c1=='chr19' or c1=='chr20' or c1=='chr21' or c1=='chr22' or c1=='chrX' or c1=='chrY'\\\"\", \"__page__\": 0}",
364 "tool_version": "1.1.0",
365 "type": "tool",
366 "user_outputs": [],
367 "uuid": "None"
368 },
369 "10": {
370 "annotation": "12",
371 "id": 10,
372 "input_connections": {
373 "bam_file": {
374 "id": 0,
375 "output_name": "output"
376 },
377 "bed_file": {
378 "id": 9,
379 "output_name": "out_file1"
380 }
381 },
382 "inputs": [],
383 "label": null,
384 "name": "Wellington Footprints",
385 "outputs": [
386 {
387 "name": "output",
388 "type": "bed"
389 }
390 ],
391 "position": {
392 "left": 984.9090881347656,
393 "top": 207.96306610107422
394 },
395 "post_job_actions": {
396 "HideDatasetActionoutput": {
397 "action_arguments": {},
398 "action_type": "HideDatasetAction",
399 "output_name": "output"
400 }
401 },
402 "tool_errors": null,
403 "tool_id": "wellington_footprints",
404 "tool_state": "{\"__page__\": 0, \"bam_file\": \"null\", \"bed_file\": \"null\", \"__rerun_remap_job_id__\": null, \"fdrlimit\": \"\\\"0\\\"\"}",
405 "tool_version": "0.2.5",
406 "type": "tool",
407 "user_outputs": [],
408 "uuid": "None"
409 },
410 "11": {
411 "annotation": "13",
412 "id": 11,
413 "input_connections": {
414 "input": {
415 "id": 0,
416 "output_name": "output"
417 },
418 "region": {
419 "id": 9,
420 "output_name": "out_file1"
421 }
422 },
423 "inputs": [],
424 "label": null,
425 "name": "Hint",
426 "outputs": [
427 {
428 "name": "output",
429 "type": "bed"
430 }
431 ],
432 "position": {
433 "left": 996.897705078125,
434 "top": 371.9545440673828
435 },
436 "post_job_actions": {
437 "HideDatasetActionoutput": {
438 "action_arguments": {},
439 "action_type": "HideDatasetAction",
440 "output_name": "output"
441 }
442 },
443 "tool_errors": null,
444 "tool_id": "hint",
445 "tool_state": "{\"input\": \"null\", \"region\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
446 "tool_version": "HINT: 1.1.1",
447 "type": "tool",
448 "user_outputs": [],
449 "uuid": "None"
450 },
451 "12": {
452 "annotation": "14",
453 "id": 12,
454 "input_connections": {
455 "input": {
456 "id": 10,
457 "output_name": "output"
458 }
459 },
460 "inputs": [],
461 "label": null,
462 "name": "Sort",
463 "outputs": [
464 {
465 "name": "out_file1",
466 "type": "input"
467 }
468 ],
469 "position": {
470 "left": 1225.9176025390625,
471 "top": 206.9545440673828
472 },
473 "post_job_actions": {
474 "RenameDatasetActionout_file1": {
475 "action_arguments": {
476 "newname": "wellington_sorted"
477 },
478 "action_type": "RenameDatasetAction",
479 "output_name": "out_file1"
480 }
481 },
482 "tool_errors": null,
483 "tool_id": "sort1",
484 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}",
485 "tool_version": "1.0.1",
486 "type": "tool",
487 "user_outputs": [],
488 "uuid": "None"
489 },
490 "13": {
491 "annotation": "15",
492 "id": 13,
493 "input_connections": {
494 "input": {
495 "id": 11,
496 "output_name": "output"
497 }
498 },
499 "inputs": [],
500 "label": null,
501 "name": "Sort",
502 "outputs": [
503 {
504 "name": "out_file1",
505 "type": "input"
506 }
507 ],
508 "position": {
509 "left": 1231.897705078125,
510 "top": 395.9460144042969
511 },
512 "post_job_actions": {
513 "RenameDatasetActionout_file1": {
514 "action_arguments": {
515 "newname": "hint_sorted"
516 },
517 "action_type": "RenameDatasetAction",
518 "output_name": "out_file1"
519 }
520 },
521 "tool_errors": null,
522 "tool_id": "sort1",
523 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}",
524 "tool_version": "1.0.1",
525 "type": "tool",
526 "user_outputs": [],
527 "uuid": "None"
528 }
529 },
530 "uuid": "a1168692-fb6d-4143-b956-fe7f10370bec"
531 }