Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs
comparison Galaxy-Workflow-microsatellite_profiling.ga @ 7:3c05abb4452e default tip
add missing files
author | devteam@galaxyproject.org |
---|---|
date | Wed, 22 Apr 2015 12:22:50 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
6:dccd7a3ee717 | 7:3c05abb4452e |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "Profile length of microsatellites or short tandem repeats from short read data", | |
4 "format-version": "0.1", | |
5 "name": "microsatellite_profiling", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", | |
14 "name": "single end fastq" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 200, | |
21 "top": 274.765625 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"single end fastq\"}", | |
26 "tool_version": null, | |
27 "type": "data_input", | |
28 "user_outputs": [] | |
29 }, | |
30 "1": { | |
31 "annotation": "need to be prepared by user using TR genome profiling", | |
32 "id": 1, | |
33 "input_connections": {}, | |
34 "inputs": [ | |
35 { | |
36 "description": "need to be prepared by user using TR genome profiling", | |
37 "name": "TR in genome" | |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
41 "outputs": [], | |
42 "position": { | |
43 "left": 177, | |
44 "top": 412.953125 | |
45 }, | |
46 "tool_errors": null, | |
47 "tool_id": null, | |
48 "tool_state": "{\"name\": \"TR in genome\"}", | |
49 "tool_version": null, | |
50 "type": "data_input", | |
51 "user_outputs": [] | |
52 }, | |
53 "2": { | |
54 "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", | |
55 "id": 2, | |
56 "input_connections": {}, | |
57 "inputs": [ | |
58 { | |
59 "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", | |
60 "name": "error rate file" | |
61 } | |
62 ], | |
63 "name": "Input dataset", | |
64 "outputs": [], | |
65 "position": { | |
66 "left": 1412.875, | |
67 "top": 384.671875 | |
68 }, | |
69 "tool_errors": null, | |
70 "tool_id": null, | |
71 "tool_state": "{\"name\": \"error rate file\"}", | |
72 "tool_version": null, | |
73 "type": "data_input", | |
74 "user_outputs": [] | |
75 }, | |
76 "3": { | |
77 "annotation": "", | |
78 "id": 3, | |
79 "input_connections": { | |
80 "filePath": { | |
81 "id": 0, | |
82 "output_name": "output" | |
83 } | |
84 }, | |
85 "inputs": [], | |
86 "name": "Microsatellite detection", | |
87 "outputs": [ | |
88 { | |
89 "name": "stdout", | |
90 "type": "tabular" | |
91 } | |
92 ], | |
93 "position": { | |
94 "left": 441.953125, | |
95 "top": 252 | |
96 }, | |
97 "post_job_actions": { | |
98 "ChangeDatatypeActionstdout": { | |
99 "action_arguments": { | |
100 "newtype": "tabular" | |
101 }, | |
102 "action_type": "ChangeDatatypeAction", | |
103 "output_name": "stdout" | |
104 }, | |
105 "RenameDatasetActionstdout": { | |
106 "action_arguments": { | |
107 "newname": "TR in raw reads" | |
108 }, | |
109 "action_type": "RenameDatasetAction", | |
110 "output_name": "stdout" | |
111 } | |
112 }, | |
113 "tool_errors": null, | |
114 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatellite/1.0.0", | |
115 "tool_state": "{\"__page__\": 0, \"flankSetting\": \"{\\\"noflankdisplay\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"filePath\": \"null\", \"minlength\": \"\\\"5\\\"\", \"hammingThreshold\": \"\\\"0\\\"\", \"period\": \"\\\"1\\\"\", \"surfix\": \"\\\"20\\\"\", \"prefix\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"inputFileSource\": \"{\\\"inputFileType\\\": \\\"fastq\\\", \\\"__current_case__\\\": 3}\", \"partialmotifs\": \"\\\"True\\\"\", \"multipleruns\": \"\\\"True\\\"\"}", | |
116 "tool_version": "1.0.0", | |
117 "type": "tool", | |
118 "user_outputs": [] | |
119 }, | |
120 "4": { | |
121 "annotation": "", | |
122 "id": 4, | |
123 "input_connections": { | |
124 "input": { | |
125 "id": 3, | |
126 "output_name": "stdout" | |
127 } | |
128 }, | |
129 "inputs": [], | |
130 "name": "Read name modifier", | |
131 "outputs": [ | |
132 { | |
133 "name": "output", | |
134 "type": "tabular" | |
135 } | |
136 ], | |
137 "position": { | |
138 "left": 418.484375, | |
139 "top": 385.03125 | |
140 }, | |
141 "post_job_actions": {}, | |
142 "tool_errors": null, | |
143 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/space2underscore_readname/1.0.0", | |
144 "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"6\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\"}", | |
145 "tool_version": "1.0.0", | |
146 "type": "tool", | |
147 "user_outputs": [] | |
148 }, | |
149 "5": { | |
150 "annotation": "", | |
151 "id": 5, | |
152 "input_connections": { | |
153 "microsat_in_read": { | |
154 "id": 4, | |
155 "output_name": "output" | |
156 } | |
157 }, | |
158 "inputs": [], | |
159 "name": "Fetch flanking bases", | |
160 "outputs": [ | |
161 { | |
162 "name": "Leftflanking", | |
163 "type": "fastq" | |
164 }, | |
165 { | |
166 "name": "Rightflanking", | |
167 "type": "fastq" | |
168 } | |
169 ], | |
170 "position": { | |
171 "left": 390.9375, | |
172 "top": 509.046875 | |
173 }, | |
174 "post_job_actions": { | |
175 "ChangeDatatypeActionLeftflanking": { | |
176 "action_arguments": { | |
177 "newtype": "fastqsanger" | |
178 }, | |
179 "action_type": "ChangeDatatypeAction", | |
180 "output_name": "Leftflanking" | |
181 }, | |
182 "ChangeDatatypeActionRightflanking": { | |
183 "action_arguments": { | |
184 "newtype": "fastqsanger" | |
185 }, | |
186 "action_type": "ChangeDatatypeAction", | |
187 "output_name": "Rightflanking" | |
188 }, | |
189 "HideDatasetActionLeftflanking": { | |
190 "action_arguments": {}, | |
191 "action_type": "HideDatasetAction", | |
192 "output_name": "Leftflanking" | |
193 }, | |
194 "HideDatasetActionRightflanking": { | |
195 "action_arguments": {}, | |
196 "action_type": "HideDatasetAction", | |
197 "output_name": "Rightflanking" | |
198 } | |
199 }, | |
200 "tool_errors": null, | |
201 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/fetchflank/1.0.0", | |
202 "tool_state": "{\"qualitycutoff\": \"\\\"20\\\"\", \"lengthofbasetocheckquality\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"microsat_in_read\": \"null\", \"__page__\": 0}", | |
203 "tool_version": "1.0.0", | |
204 "type": "tool", | |
205 "user_outputs": [] | |
206 }, | |
207 "6": { | |
208 "annotation": "this tool has problems with parameter setting when you run it from pipeline. If you want different parameter, it's recommend that you clone pipleline and modify it.", | |
209 "id": 6, | |
210 "input_connections": { | |
211 "paired|input1": { | |
212 "id": 5, | |
213 "output_name": "Leftflanking" | |
214 }, | |
215 "paired|input2": { | |
216 "id": 5, | |
217 "output_name": "Rightflanking" | |
218 } | |
219 }, | |
220 "inputs": [], | |
221 "name": "Map with BWA for Illumina", | |
222 "outputs": [ | |
223 { | |
224 "name": "output", | |
225 "type": "sam" | |
226 } | |
227 ], | |
228 "position": { | |
229 "left": 403, | |
230 "top": 686 | |
231 }, | |
232 "post_job_actions": { | |
233 "HideDatasetActionoutput": { | |
234 "action_arguments": {}, | |
235 "action_type": "HideDatasetAction", | |
236 "output_name": "output" | |
237 } | |
238 }, | |
239 "tool_errors": null, | |
240 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", | |
241 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"outputTopN\\\": \\\"3\\\", \\\"suboptAlign\\\": \\\"\\\", \\\"gapOpenPenalty\\\": \\\"11\\\", \\\"maxGapOpens\\\": \\\"1\\\", \\\"mismatchPenalty\\\": \\\"3\\\", \\\"fracMissingAligns\\\": \\\"0.04\\\", \\\"disallowIndel\\\": \\\"5\\\", \\\"outputTopNDisc\\\": \\\"10\\\", \\\"disallowLongDel\\\": \\\"16\\\", \\\"readGroup\\\": {\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}, \\\"maxInsertSize\\\": \\\"500\\\", \\\"__current_case__\\\": 1, \\\"maxEditDist\\\": \\\"0\\\", \\\"gapExtensPenalty\\\": \\\"4\\\", \\\"maxGapExtens\\\": \\\"-1\\\", \\\"maxEditDistSeed\\\": \\\"2\\\", \\\"noIterSearch\\\": \\\"False\\\", \\\"seed\\\": \\\"-1\\\", \\\"maxOccurPairing\\\": \\\"100000\\\", \\\"source_select\\\": \\\"full\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}", | |
242 "tool_version": "1.2.3", | |
243 "type": "tool", | |
244 "user_outputs": [] | |
245 }, | |
246 "7": { | |
247 "annotation": "", | |
248 "id": 7, | |
249 "input_connections": { | |
250 "input1": { | |
251 "id": 6, | |
252 "output_name": "output" | |
253 } | |
254 }, | |
255 "inputs": [], | |
256 "name": "Filter SAM", | |
257 "outputs": [ | |
258 { | |
259 "name": "out_file1", | |
260 "type": "sam" | |
261 } | |
262 ], | |
263 "position": { | |
264 "left": 778, | |
265 "top": 489.953125 | |
266 }, | |
267 "post_job_actions": { | |
268 "HideDatasetActionout_file1": { | |
269 "action_arguments": {}, | |
270 "action_type": "HideDatasetAction", | |
271 "output_name": "out_file1" | |
272 } | |
273 }, | |
274 "tool_errors": null, | |
275 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0", | |
276 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"bits\": \"[{\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 0, \\\"flags\\\": \\\"--0x0004\\\"}]\"}", | |
277 "tool_version": "1.0.0", | |
278 "type": "tool", | |
279 "user_outputs": [] | |
280 }, | |
281 "8": { | |
282 "annotation": "remove all mapped read with soft mask", | |
283 "id": 8, | |
284 "input_connections": { | |
285 "input": { | |
286 "id": 7, | |
287 "output_name": "out_file1" | |
288 } | |
289 }, | |
290 "inputs": [], | |
291 "name": "Filter", | |
292 "outputs": [ | |
293 { | |
294 "name": "out_file1", | |
295 "type": "input" | |
296 } | |
297 ], | |
298 "position": { | |
299 "left": 781.5, | |
300 "top": 602 | |
301 }, | |
302 "post_job_actions": { | |
303 "HideDatasetActionout_file1": { | |
304 "action_arguments": {}, | |
305 "action_type": "HideDatasetAction", | |
306 "output_name": "out_file1" | |
307 } | |
308 }, | |
309 "tool_errors": null, | |
310 "tool_id": "Filter1", | |
311 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c6.count('S')==0\\\"\", \"__page__\": 0}", | |
312 "tool_version": "1.1.0", | |
313 "type": "tool", | |
314 "user_outputs": [] | |
315 }, | |
316 "9": { | |
317 "annotation": "", | |
318 "id": 9, | |
319 "input_connections": { | |
320 "input": { | |
321 "id": 8, | |
322 "output_name": "out_file1" | |
323 } | |
324 }, | |
325 "inputs": [], | |
326 "name": "Sort", | |
327 "outputs": [ | |
328 { | |
329 "name": "out_file1", | |
330 "type": "input" | |
331 } | |
332 ], | |
333 "position": { | |
334 "left": 777.5, | |
335 "top": 739 | |
336 }, | |
337 "post_job_actions": { | |
338 "HideDatasetActionout_file1": { | |
339 "action_arguments": {}, | |
340 "action_type": "HideDatasetAction", | |
341 "output_name": "out_file1" | |
342 } | |
343 }, | |
344 "tool_errors": null, | |
345 "tool_id": "sort1", | |
346 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", | |
347 "tool_version": "1.0.3", | |
348 "type": "tool", | |
349 "user_outputs": [] | |
350 }, | |
351 "10": { | |
352 "annotation": "", | |
353 "id": 10, | |
354 "input_connections": { | |
355 "flankedbasesSAM": { | |
356 "id": 9, | |
357 "output_name": "out_file1" | |
358 } | |
359 }, | |
360 "inputs": [], | |
361 "name": "Combine mapped flaked bases", | |
362 "outputs": [ | |
363 { | |
364 "name": "output", | |
365 "type": "tabular" | |
366 } | |
367 ], | |
368 "position": { | |
369 "left": 723.328125, | |
370 "top": 887.828125 | |
371 }, | |
372 "post_job_actions": { | |
373 "HideDatasetActionoutput": { | |
374 "action_arguments": {}, | |
375 "action_type": "HideDatasetAction", | |
376 "output_name": "output" | |
377 } | |
378 }, | |
379 "tool_errors": null, | |
380 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/PEsortedSAM2readprofile/1.0.0", | |
381 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"maxoriginalreadlength\": \"\\\"101\\\"\", \"maxTRlength\": \"\\\"100\\\"\", \"flankedbasesSAM\": \"null\", \"twobitref\": \"null\"}", | |
382 "tool_version": "1.0.0", | |
383 "type": "tool", | |
384 "user_outputs": [] | |
385 }, | |
386 "11": { | |
387 "annotation": "", | |
388 "id": 11, | |
389 "input_connections": { | |
390 "input1": { | |
391 "id": 4, | |
392 "output_name": "output" | |
393 }, | |
394 "input2": { | |
395 "id": 10, | |
396 "output_name": "output" | |
397 } | |
398 }, | |
399 "inputs": [], | |
400 "name": "Join two Datasets", | |
401 "outputs": [ | |
402 { | |
403 "name": "out_file1", | |
404 "type": "input" | |
405 } | |
406 ], | |
407 "position": { | |
408 "left": 1116.375, | |
409 "top": 431.84375 | |
410 }, | |
411 "post_job_actions": { | |
412 "ColumnSetActionout_file1": { | |
413 "action_arguments": { | |
414 "chromCol": "10", | |
415 "endCol": "14", | |
416 "nameCol": "", | |
417 "startCol": "13", | |
418 "strandCol": "" | |
419 }, | |
420 "action_type": "ColumnSetAction", | |
421 "output_name": "out_file1" | |
422 }, | |
423 "HideDatasetActionout_file1": { | |
424 "action_arguments": {}, | |
425 "action_type": "HideDatasetAction", | |
426 "output_name": "out_file1" | |
427 } | |
428 }, | |
429 "tool_errors": null, | |
430 "tool_id": "join1", | |
431 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\"}", | |
432 "tool_version": "2.0.2", | |
433 "type": "tool", | |
434 "user_outputs": [] | |
435 }, | |
436 "12": { | |
437 "annotation": "", | |
438 "id": 12, | |
439 "input_connections": { | |
440 "input1": { | |
441 "id": 1, | |
442 "output_name": "output" | |
443 }, | |
444 "input2": { | |
445 "id": 11, | |
446 "output_name": "out_file1" | |
447 } | |
448 }, | |
449 "inputs": [], | |
450 "name": "Join", | |
451 "outputs": [ | |
452 { | |
453 "name": "output", | |
454 "type": "interval" | |
455 } | |
456 ], | |
457 "position": { | |
458 "left": 1113.96875, | |
459 "top": 560.296875 | |
460 }, | |
461 "post_job_actions": { | |
462 "HideDatasetActionoutput": { | |
463 "action_arguments": {}, | |
464 "action_type": "HideDatasetAction", | |
465 "output_name": "output" | |
466 } | |
467 }, | |
468 "tool_errors": null, | |
469 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0", | |
470 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"fill\": \"\\\"none\\\"\"}", | |
471 "tool_version": "1.0.0", | |
472 "type": "tool", | |
473 "user_outputs": [] | |
474 }, | |
475 "13": { | |
476 "annotation": "", | |
477 "id": 13, | |
478 "input_connections": { | |
479 "input": { | |
480 "id": 12, | |
481 "output_name": "output" | |
482 } | |
483 }, | |
484 "inputs": [], | |
485 "name": "Check microsatellites motif compatibility", | |
486 "outputs": [ | |
487 { | |
488 "name": "output", | |
489 "type": "tabular" | |
490 } | |
491 ], | |
492 "position": { | |
493 "left": 1122.328125, | |
494 "top": 710.84375 | |
495 }, | |
496 "post_job_actions": { | |
497 "HideDatasetActionoutput": { | |
498 "action_arguments": {}, | |
499 "action_type": "HideDatasetAction", | |
500 "output_name": "output" | |
501 } | |
502 }, | |
503 "tool_errors": null, | |
504 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatcompat/1.0.0", | |
505 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"column1\": \"\\\"4\\\"\", \"column2\": \"\\\"10\\\"\"}", | |
506 "tool_version": "1.0.0", | |
507 "type": "tool", | |
508 "user_outputs": [] | |
509 }, | |
510 "14": { | |
511 "annotation": "", | |
512 "id": 14, | |
513 "input_connections": { | |
514 "input": { | |
515 "id": 13, | |
516 "output_name": "output" | |
517 } | |
518 }, | |
519 "inputs": [], | |
520 "name": "Select uninterrupted microsatellites", | |
521 "outputs": [ | |
522 { | |
523 "name": "output", | |
524 "type": "tabular" | |
525 } | |
526 ], | |
527 "position": { | |
528 "left": 1131.21875, | |
529 "top": 852.90625 | |
530 }, | |
531 "post_job_actions": { | |
532 "HideDatasetActionoutput": { | |
533 "action_arguments": {}, | |
534 "action_type": "HideDatasetAction", | |
535 "output_name": "output" | |
536 } | |
537 }, | |
538 "tool_errors": null, | |
539 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatpurity/1.0.0", | |
540 "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"period\": \"\\\"1\\\"\", \"input\": \"null\"}", | |
541 "tool_version": "1.0.0", | |
542 "type": "tool", | |
543 "user_outputs": [] | |
544 }, | |
545 "15": { | |
546 "annotation": "", | |
547 "id": 15, | |
548 "input_connections": { | |
549 "input": { | |
550 "id": 14, | |
551 "output_name": "output" | |
552 } | |
553 }, | |
554 "inputs": [], | |
555 "name": "Cut", | |
556 "outputs": [ | |
557 { | |
558 "name": "out_file1", | |
559 "type": "tabular" | |
560 } | |
561 ], | |
562 "position": { | |
563 "left": 1161, | |
564 "top": 963.953125 | |
565 }, | |
566 "post_job_actions": { | |
567 "HideDatasetActionout_file1": { | |
568 "action_arguments": {}, | |
569 "action_type": "HideDatasetAction", | |
570 "output_name": "out_file1" | |
571 } | |
572 }, | |
573 "tool_errors": null, | |
574 "tool_id": "Cut1", | |
575 "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c5,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", | |
576 "tool_version": "1.0.2", | |
577 "type": "tool", | |
578 "user_outputs": [] | |
579 }, | |
580 "16": { | |
581 "annotation": "", | |
582 "id": 16, | |
583 "input_connections": { | |
584 "input": { | |
585 "id": 15, | |
586 "output_name": "out_file1" | |
587 } | |
588 }, | |
589 "inputs": [], | |
590 "name": "Add column", | |
591 "outputs": [ | |
592 { | |
593 "name": "out_file1", | |
594 "type": "input" | |
595 } | |
596 ], | |
597 "position": { | |
598 "left": 1168, | |
599 "top": 1069.953125 | |
600 }, | |
601 "post_job_actions": { | |
602 "HideDatasetActionout_file1": { | |
603 "action_arguments": {}, | |
604 "action_type": "HideDatasetAction", | |
605 "output_name": "out_file1" | |
606 } | |
607 }, | |
608 "tool_errors": null, | |
609 "tool_id": "addValue", | |
610 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"_\\\"\", \"iterate\": \"\\\"no\\\"\"}", | |
611 "tool_version": "1.0.0", | |
612 "type": "tool", | |
613 "user_outputs": [] | |
614 }, | |
615 "17": { | |
616 "annotation": "", | |
617 "id": 17, | |
618 "input_connections": { | |
619 "input1": { | |
620 "id": 16, | |
621 "output_name": "out_file1" | |
622 } | |
623 }, | |
624 "inputs": [], | |
625 "name": "Merge Columns", | |
626 "outputs": [ | |
627 { | |
628 "name": "out_file1", | |
629 "type": "tabular" | |
630 } | |
631 ], | |
632 "position": { | |
633 "left": 1175, | |
634 "top": 1184.953125 | |
635 }, | |
636 "post_job_actions": { | |
637 "HideDatasetActionout_file1": { | |
638 "action_arguments": {}, | |
639 "action_type": "HideDatasetAction", | |
640 "output_name": "out_file1" | |
641 } | |
642 }, | |
643 "tool_errors": null, | |
644 "tool_id": "mergeCols1", | |
645 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"columns\": \"[{\\\"__index__\\\": 0, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}}, {\\\"__index__\\\": 1, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}}, {\\\"__index__\\\": 2, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}}]\"}", | |
646 "tool_version": "1.0.1", | |
647 "type": "tool", | |
648 "user_outputs": [] | |
649 }, | |
650 "18": { | |
651 "annotation": "", | |
652 "id": 18, | |
653 "input_connections": { | |
654 "input1": { | |
655 "id": 17, | |
656 "output_name": "out_file1" | |
657 } | |
658 }, | |
659 "inputs": [], | |
660 "name": "Group", | |
661 "outputs": [ | |
662 { | |
663 "name": "out_file1", | |
664 "type": "tabular" | |
665 } | |
666 ], | |
667 "position": { | |
668 "left": 1175, | |
669 "top": 1297.953125 | |
670 }, | |
671 "post_job_actions": { | |
672 "HideDatasetActionout_file1": { | |
673 "action_arguments": {}, | |
674 "action_type": "HideDatasetAction", | |
675 "output_name": "out_file1" | |
676 } | |
677 }, | |
678 "tool_errors": null, | |
679 "tool_id": "Grouping1", | |
680 "tool_state": "{\"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"cat\\\", \\\"opround\\\": \\\"no\\\"}, {\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"4\\\"}, \\\"__index__\\\": 1, \\\"optype\\\": \\\"cat_uniq\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}", | |
681 "tool_version": "2.1.0", | |
682 "type": "tool", | |
683 "user_outputs": [] | |
684 }, | |
685 "19": { | |
686 "annotation": "", | |
687 "id": 19, | |
688 "input_connections": { | |
689 "input": { | |
690 "id": 18, | |
691 "output_name": "out_file1" | |
692 } | |
693 }, | |
694 "inputs": [], | |
695 "name": "Filter", | |
696 "outputs": [ | |
697 { | |
698 "name": "out_file1", | |
699 "type": "input" | |
700 } | |
701 ], | |
702 "position": { | |
703 "left": 1186, | |
704 "top": 1405.953125 | |
705 }, | |
706 "post_job_actions": { | |
707 "RenameDatasetActionout_file1": { | |
708 "action_arguments": { | |
709 "newname": "TR profile" | |
710 }, | |
711 "action_type": "RenameDatasetAction", | |
712 "output_name": "out_file1" | |
713 } | |
714 }, | |
715 "tool_errors": null, | |
716 "tool_id": "Filter1", | |
717 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c2.count(\\\\\\\",\\\\\\\")>=4\\\"\", \"__page__\": 0}", | |
718 "tool_version": "1.1.0", | |
719 "type": "tool", | |
720 "user_outputs": [] | |
721 }, | |
722 "20": { | |
723 "annotation": "", | |
724 "id": 20, | |
725 "input_connections": { | |
726 "microsat_error_profile": { | |
727 "id": 2, | |
728 "output_name": "output" | |
729 }, | |
730 "microsat_raw": { | |
731 "id": 19, | |
732 "output_name": "out_file1" | |
733 } | |
734 }, | |
735 "inputs": [], | |
736 "name": "Correct genotype for microsatellite errors", | |
737 "outputs": [ | |
738 { | |
739 "name": "microsat_corrected", | |
740 "type": "tabular" | |
741 } | |
742 ], | |
743 "position": { | |
744 "left": 1591.328125, | |
745 "top": 456.8125 | |
746 }, | |
747 "post_job_actions": { | |
748 "RenameDatasetActionmicrosat_corrected": { | |
749 "action_arguments": { | |
750 "newname": "Genotype file" | |
751 }, | |
752 "action_type": "RenameDatasetAction", | |
753 "output_name": "microsat_corrected" | |
754 } | |
755 }, | |
756 "tool_errors": null, | |
757 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/GenotypeSTR/2.0.0", | |
758 "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}", | |
759 "tool_version": "2.0.0", | |
760 "type": "tool", | |
761 "user_outputs": [] | |
762 } | |
763 } | |
764 } |