comparison Galaxy-Workflow-microsatellite_profiling.ga @ 0:70f8259b0b30 draft

Uploaded
author arkarachai-fungtammasan
date Wed, 01 Apr 2015 16:48:58 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:70f8259b0b30
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 }