7
|
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 } |