0
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "",
|
|
4 "format-version": "0.1",
|
7
|
5 "name": "linkX (imported from uploaded file)",
|
0
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
|
9 "id": 0,
|
|
10 "input_connections": {},
|
|
11 "inputs": [
|
|
12 {
|
|
13 "description": "",
|
|
14 "name": "mother_1.fastq"
|
|
15 }
|
|
16 ],
|
|
17 "name": "Input dataset",
|
|
18 "outputs": [],
|
|
19 "position": {
|
7
|
20 "left": 243.86113023757935,
|
|
21 "top": 294.6944737434387
|
0
|
22 },
|
|
23 "tool_errors": null,
|
|
24 "tool_id": null,
|
|
25 "tool_state": "{\"name\": \"mother_1.fastq\"}",
|
|
26 "tool_version": null,
|
|
27 "type": "data_input",
|
|
28 "user_outputs": []
|
|
29 },
|
|
30 "1": {
|
|
31 "annotation": "",
|
|
32 "id": 1,
|
|
33 "input_connections": {},
|
|
34 "inputs": [
|
|
35 {
|
|
36 "description": "",
|
|
37 "name": "mother_2.fastq"
|
|
38 }
|
|
39 ],
|
|
40 "name": "Input dataset",
|
|
41 "outputs": [],
|
|
42 "position": {
|
7
|
43 "left": 229.8506932258606,
|
|
44 "top": 442.68058824539185
|
0
|
45 },
|
|
46 "tool_errors": null,
|
|
47 "tool_id": null,
|
|
48 "tool_state": "{\"name\": \"mother_2.fastq\"}",
|
|
49 "tool_version": null,
|
|
50 "type": "data_input",
|
|
51 "user_outputs": []
|
|
52 },
|
|
53 "2": {
|
|
54 "annotation": "",
|
|
55 "id": 2,
|
|
56 "input_connections": {},
|
|
57 "inputs": [
|
|
58 {
|
|
59 "description": "",
|
|
60 "name": "father_1.fastq"
|
|
61 }
|
|
62 ],
|
|
63 "name": "Input dataset",
|
|
64 "outputs": [],
|
|
65 "position": {
|
7
|
66 "left": 226.84724473953247,
|
|
67 "top": 597.6805882453918
|
0
|
68 },
|
|
69 "tool_errors": null,
|
|
70 "tool_id": null,
|
|
71 "tool_state": "{\"name\": \"father_1.fastq\"}",
|
|
72 "tool_version": null,
|
|
73 "type": "data_input",
|
|
74 "user_outputs": []
|
|
75 },
|
|
76 "3": {
|
|
77 "annotation": "",
|
|
78 "id": 3,
|
|
79 "input_connections": {},
|
|
80 "inputs": [
|
|
81 {
|
|
82 "description": "",
|
|
83 "name": "father_2.fastq"
|
|
84 }
|
|
85 ],
|
|
86 "name": "Input dataset",
|
|
87 "outputs": [],
|
|
88 "position": {
|
7
|
89 "left": 205.8576512336731,
|
|
90 "top": 687.6805882453918
|
0
|
91 },
|
|
92 "tool_errors": null,
|
|
93 "tool_id": null,
|
|
94 "tool_state": "{\"name\": \"father_2.fastq\"}",
|
|
95 "tool_version": null,
|
|
96 "type": "data_input",
|
|
97 "user_outputs": []
|
|
98 },
|
|
99 "4": {
|
|
100 "annotation": "",
|
|
101 "id": 4,
|
|
102 "input_connections": {},
|
|
103 "inputs": [
|
|
104 {
|
|
105 "description": "",
|
|
106 "name": "daughter_1.fastq"
|
|
107 }
|
|
108 ],
|
|
109 "name": "Input dataset",
|
|
110 "outputs": [],
|
|
111 "position": {
|
7
|
112 "left": 199.65971422195435,
|
|
113 "top": 847.0208592414856
|
0
|
114 },
|
|
115 "tool_errors": null,
|
|
116 "tool_id": null,
|
|
117 "tool_state": "{\"name\": \"daughter_1.fastq\"}",
|
|
118 "tool_version": null,
|
|
119 "type": "data_input",
|
|
120 "user_outputs": []
|
|
121 },
|
|
122 "5": {
|
|
123 "annotation": "",
|
|
124 "id": 5,
|
|
125 "input_connections": {},
|
|
126 "inputs": [
|
|
127 {
|
|
128 "description": "",
|
|
129 "name": "daughter_2.fastq"
|
|
130 }
|
|
131 ],
|
|
132 "name": "Input dataset",
|
|
133 "outputs": [],
|
|
134 "position": {
|
7
|
135 "left": 205.66667222976685,
|
|
136 "top": 966.0139012336731
|
0
|
137 },
|
|
138 "tool_errors": null,
|
|
139 "tool_id": null,
|
|
140 "tool_state": "{\"name\": \"daughter_2.fastq\"}",
|
|
141 "tool_version": null,
|
|
142 "type": "data_input",
|
|
143 "user_outputs": []
|
|
144 },
|
|
145 "6": {
|
|
146 "annotation": "",
|
|
147 "id": 6,
|
|
148 "input_connections": {},
|
|
149 "inputs": [
|
|
150 {
|
|
151 "description": "",
|
|
152 "name": "son_1.fastq"
|
|
153 }
|
|
154 ],
|
|
155 "name": "Input dataset",
|
|
156 "outputs": [],
|
|
157 "position": {
|
7
|
158 "left": 215.66667222976685,
|
|
159 "top": 1110.024399280548
|
0
|
160 },
|
|
161 "tool_errors": null,
|
|
162 "tool_id": null,
|
|
163 "tool_state": "{\"name\": \"son_1.fastq\"}",
|
|
164 "tool_version": null,
|
|
165 "type": "data_input",
|
|
166 "user_outputs": []
|
|
167 },
|
|
168 "7": {
|
|
169 "annotation": "",
|
|
170 "id": 7,
|
|
171 "input_connections": {},
|
|
172 "inputs": [
|
|
173 {
|
|
174 "description": "",
|
|
175 "name": "son_2.fastq"
|
|
176 }
|
|
177 ],
|
|
178 "name": "Input dataset",
|
|
179 "outputs": [],
|
|
180 "position": {
|
7
|
181 "left": 206.67363023757935,
|
|
182 "top": 1224.0174412727356
|
0
|
183 },
|
|
184 "tool_errors": null,
|
|
185 "tool_id": null,
|
|
186 "tool_state": "{\"name\": \"son_2.fastq\"}",
|
|
187 "tool_version": null,
|
|
188 "type": "data_input",
|
|
189 "user_outputs": []
|
|
190 },
|
|
191 "8": {
|
|
192 "annotation": "",
|
|
193 "id": 8,
|
|
194 "input_connections": {
|
|
195 "input_file": {
|
|
196 "id": 0,
|
|
197 "output_name": "output"
|
|
198 }
|
|
199 },
|
|
200 "inputs": [],
|
|
201 "name": "FASTQ Groomer",
|
|
202 "outputs": [
|
|
203 {
|
|
204 "name": "output_file",
|
|
205 "type": "fastqsanger"
|
|
206 }
|
|
207 ],
|
|
208 "position": {
|
7
|
209 "left": 437.85417222976685,
|
|
210 "top": 273.6875157356262
|
0
|
211 },
|
|
212 "post_job_actions": {
|
|
213 "HideDatasetActionoutput_file": {
|
|
214 "action_arguments": {},
|
|
215 "action_type": "HideDatasetAction",
|
|
216 "output_name": "output_file"
|
|
217 }
|
|
218 },
|
|
219 "tool_errors": null,
|
|
220 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
221 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
222 "tool_version": "1.0.4",
|
|
223 "type": "tool",
|
|
224 "user_outputs": []
|
|
225 },
|
|
226 "9": {
|
|
227 "annotation": "",
|
|
228 "id": 9,
|
|
229 "input_connections": {
|
|
230 "input_file": {
|
|
231 "id": 1,
|
|
232 "output_name": "output"
|
|
233 }
|
|
234 },
|
|
235 "inputs": [],
|
|
236 "name": "FASTQ Groomer",
|
|
237 "outputs": [
|
|
238 {
|
|
239 "name": "output_file",
|
|
240 "type": "fastqsanger"
|
|
241 }
|
|
242 ],
|
|
243 "position": {
|
7
|
244 "left": 423.86113023757935,
|
|
245 "top": 433.6875157356262
|
0
|
246 },
|
|
247 "post_job_actions": {
|
|
248 "HideDatasetActionoutput_file": {
|
|
249 "action_arguments": {},
|
|
250 "action_type": "HideDatasetAction",
|
|
251 "output_name": "output_file"
|
|
252 }
|
|
253 },
|
|
254 "tool_errors": null,
|
|
255 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
256 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
257 "tool_version": "1.0.4",
|
|
258 "type": "tool",
|
|
259 "user_outputs": []
|
|
260 },
|
|
261 "10": {
|
|
262 "annotation": "",
|
|
263 "id": 10,
|
|
264 "input_connections": {
|
|
265 "input_file": {
|
|
266 "id": 2,
|
|
267 "output_name": "output"
|
|
268 }
|
|
269 },
|
|
270 "inputs": [],
|
|
271 "name": "FASTQ Groomer",
|
|
272 "outputs": [
|
|
273 {
|
|
274 "name": "output_file",
|
|
275 "type": "fastqsanger"
|
|
276 }
|
|
277 ],
|
|
278 "position": {
|
7
|
279 "left": 430.8576512336731,
|
|
280 "top": 584.6945042610168
|
0
|
281 },
|
|
282 "post_job_actions": {
|
|
283 "HideDatasetActionoutput_file": {
|
|
284 "action_arguments": {},
|
|
285 "action_type": "HideDatasetAction",
|
|
286 "output_name": "output_file"
|
|
287 }
|
|
288 },
|
|
289 "tool_errors": null,
|
|
290 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
291 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
292 "tool_version": "1.0.4",
|
|
293 "type": "tool",
|
|
294 "user_outputs": []
|
|
295 },
|
|
296 "11": {
|
|
297 "annotation": "",
|
|
298 "id": 11,
|
|
299 "input_connections": {
|
|
300 "input_file": {
|
|
301 "id": 3,
|
|
302 "output_name": "output"
|
|
303 }
|
|
304 },
|
|
305 "inputs": [],
|
|
306 "name": "FASTQ Groomer",
|
|
307 "outputs": [
|
|
308 {
|
|
309 "name": "output_file",
|
|
310 "type": "fastqsanger"
|
|
311 }
|
|
312 ],
|
|
313 "position": {
|
7
|
314 "left": 430.8576512336731,
|
|
315 "top": 716.6910252571106
|
0
|
316 },
|
|
317 "post_job_actions": {
|
|
318 "HideDatasetActionoutput_file": {
|
|
319 "action_arguments": {},
|
|
320 "action_type": "HideDatasetAction",
|
|
321 "output_name": "output_file"
|
|
322 }
|
|
323 },
|
|
324 "tool_errors": null,
|
|
325 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
326 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
327 "tool_version": "1.0.4",
|
|
328 "type": "tool",
|
|
329 "user_outputs": []
|
|
330 },
|
|
331 "12": {
|
|
332 "annotation": "",
|
|
333 "id": 12,
|
|
334 "input_connections": {
|
|
335 "input_file": {
|
|
336 "id": 4,
|
|
337 "output_name": "output"
|
|
338 }
|
|
339 },
|
|
340 "inputs": [],
|
|
341 "name": "FASTQ Groomer",
|
|
342 "outputs": [
|
|
343 {
|
|
344 "name": "output_file",
|
|
345 "type": "fastqsanger"
|
|
346 }
|
|
347 ],
|
|
348 "position": {
|
7
|
349 "left": 426.69096422195435,
|
|
350 "top": 839.0173802375793
|
0
|
351 },
|
|
352 "post_job_actions": {
|
|
353 "HideDatasetActionoutput_file": {
|
|
354 "action_arguments": {},
|
|
355 "action_type": "HideDatasetAction",
|
|
356 "output_name": "output_file"
|
|
357 }
|
|
358 },
|
|
359 "tool_errors": null,
|
|
360 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
361 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
362 "tool_version": "1.0.4",
|
|
363 "type": "tool",
|
|
364 "user_outputs": []
|
|
365 },
|
|
366 "13": {
|
|
367 "annotation": "",
|
|
368 "id": 13,
|
|
369 "input_connections": {
|
|
370 "input_file": {
|
|
371 "id": 5,
|
|
372 "output_name": "output"
|
|
373 }
|
|
374 },
|
|
375 "inputs": [],
|
|
376 "name": "FASTQ Groomer",
|
|
377 "outputs": [
|
|
378 {
|
|
379 "name": "output_file",
|
|
380 "type": "fastqsanger"
|
|
381 }
|
|
382 ],
|
|
383 "position": {
|
7
|
384 "left": 426.69096422195435,
|
|
385 "top": 975.0243992805481
|
0
|
386 },
|
|
387 "post_job_actions": {
|
|
388 "HideDatasetActionoutput_file": {
|
|
389 "action_arguments": {},
|
|
390 "action_type": "HideDatasetAction",
|
|
391 "output_name": "output_file"
|
|
392 }
|
|
393 },
|
|
394 "tool_errors": null,
|
|
395 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
396 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
397 "tool_version": "1.0.4",
|
|
398 "type": "tool",
|
|
399 "user_outputs": []
|
|
400 },
|
|
401 "14": {
|
|
402 "annotation": "",
|
|
403 "id": 14,
|
|
404 "input_connections": {
|
|
405 "input_file": {
|
|
406 "id": 6,
|
|
407 "output_name": "output"
|
|
408 }
|
|
409 },
|
|
410 "inputs": [],
|
|
411 "name": "FASTQ Groomer",
|
|
412 "outputs": [
|
|
413 {
|
|
414 "name": "output_file",
|
|
415 "type": "fastqsanger"
|
|
416 }
|
|
417 ],
|
|
418 "position": {
|
7
|
419 "left": 429.6944432258606,
|
|
420 "top": 1096.013901233673
|
0
|
421 },
|
|
422 "post_job_actions": {
|
|
423 "HideDatasetActionoutput_file": {
|
|
424 "action_arguments": {},
|
|
425 "action_type": "HideDatasetAction",
|
|
426 "output_name": "output_file"
|
|
427 }
|
|
428 },
|
|
429 "tool_errors": null,
|
|
430 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
431 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
432 "tool_version": "1.0.4",
|
|
433 "type": "tool",
|
|
434 "user_outputs": []
|
|
435 },
|
|
436 "15": {
|
|
437 "annotation": "",
|
|
438 "id": 15,
|
|
439 "input_connections": {
|
|
440 "input_file": {
|
|
441 "id": 7,
|
|
442 "output_name": "output"
|
|
443 }
|
|
444 },
|
|
445 "inputs": [],
|
|
446 "name": "FASTQ Groomer",
|
|
447 "outputs": [
|
|
448 {
|
|
449 "name": "output_file",
|
|
450 "type": "fastqsanger"
|
|
451 }
|
|
452 ],
|
|
453 "position": {
|
7
|
454 "left": 439.6944432258606,
|
|
455 "top": 1235.024399280548
|
0
|
456 },
|
|
457 "post_job_actions": {
|
|
458 "HideDatasetActionoutput_file": {
|
|
459 "action_arguments": {},
|
|
460 "action_type": "HideDatasetAction",
|
|
461 "output_name": "output_file"
|
|
462 }
|
|
463 },
|
|
464 "tool_errors": null,
|
|
465 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
466 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
467 "tool_version": "1.0.4",
|
|
468 "type": "tool",
|
|
469 "user_outputs": []
|
|
470 },
|
|
471 "16": {
|
|
472 "annotation": "",
|
|
473 "id": 16,
|
|
474 "input_connections": {
|
|
475 "inputs|left_input": {
|
|
476 "id": 8,
|
|
477 "output_name": "output_file"
|
|
478 },
|
|
479 "inputs|right_input": {
|
|
480 "id": 9,
|
|
481 "output_name": "output_file"
|
|
482 }
|
|
483 },
|
|
484 "inputs": [],
|
|
485 "name": "Trinity",
|
|
486 "outputs": [
|
|
487 {
|
|
488 "name": "trinity_log",
|
|
489 "type": "txt"
|
|
490 },
|
|
491 {
|
|
492 "name": "assembled_transcripts",
|
|
493 "type": "fasta"
|
|
494 }
|
|
495 ],
|
|
496 "position": {
|
7
|
497 "left": 835.8576512336731,
|
|
498 "top": 132.33334398269653
|
0
|
499 },
|
|
500 "post_job_actions": {
|
7
|
501 "HideDatasetActionassembled_transcripts": {
|
|
502 "action_arguments": {},
|
|
503 "action_type": "HideDatasetAction",
|
0
|
504 "output_name": "assembled_transcripts"
|
|
505 }
|
|
506 },
|
|
507 "tool_errors": null,
|
7
|
508 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/trinityrnaseq/trinityrnaseq/0.0.1",
|
0
|
509 "tool_state": "{\"__page__\": 0, \"additional_params\": \"{\\\"use_additional\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"inputs\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"library_type\\\": \\\"None\\\", \\\"group_pairs_distance\\\": \\\"500\\\", \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"path_reinforcement_distance\\\": \\\"75\\\", \\\"right_input\\\": null}\", \"__rerun_remap_job_id__\": null, \"JM\": \"\\\"1G\\\"\", \"CPU\": \"\\\"2\\\"\"}",
|
|
510 "tool_version": "0.0.1",
|
|
511 "type": "tool",
|
|
512 "user_outputs": []
|
|
513 },
|
|
514 "17": {
|
|
515 "annotation": "",
|
|
516 "id": 17,
|
|
517 "input_connections": {
|
|
518 "input1": {
|
|
519 "id": 16,
|
|
520 "output_name": "assembled_transcripts"
|
|
521 }
|
|
522 },
|
|
523 "inputs": [],
|
|
524 "name": "reformat_trinity_header",
|
|
525 "outputs": [
|
|
526 {
|
|
527 "name": "output",
|
|
528 "type": "fasta"
|
|
529 }
|
|
530 ],
|
|
531 "position": {
|
7
|
532 "left": 1139.920151233673,
|
|
533 "top": 149.39930772781372
|
0
|
534 },
|
7
|
535 "post_job_actions": {},
|
0
|
536 "tool_errors": null,
|
7
|
537 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/linkyx/reformat_trinity_header/1.1",
|
0
|
538 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
7
|
539 "tool_version": "1.1",
|
0
|
540 "type": "tool",
|
|
541 "user_outputs": []
|
|
542 },
|
|
543 "18": {
|
|
544 "annotation": "",
|
|
545 "id": 18,
|
|
546 "input_connections": {
|
|
547 "genomeSource|ownFile": {
|
|
548 "id": 17,
|
|
549 "output_name": "output"
|
|
550 },
|
|
551 "paired|input1": {
|
|
552 "id": 8,
|
|
553 "output_name": "output_file"
|
|
554 },
|
|
555 "paired|input2": {
|
|
556 "id": 9,
|
|
557 "output_name": "output_file"
|
|
558 }
|
|
559 },
|
|
560 "inputs": [],
|
|
561 "name": "Map with BWA for Illumina",
|
|
562 "outputs": [
|
|
563 {
|
|
564 "name": "output",
|
|
565 "type": "sam"
|
|
566 }
|
|
567 ],
|
|
568 "position": {
|
7
|
569 "left": 789.6944432258606,
|
|
570 "top": 381.0139012336731
|
0
|
571 },
|
|
572 "post_job_actions": {
|
|
573 "RenameDatasetActionoutput": {
|
|
574 "action_arguments": {
|
|
575 "newname": "mother.sam"
|
|
576 },
|
|
577 "action_type": "RenameDatasetAction",
|
|
578 "output_name": "output"
|
|
579 }
|
|
580 },
|
|
581 "tool_errors": null,
|
|
582 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
583 "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\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
|
|
584 "tool_version": "1.2.3",
|
|
585 "type": "tool",
|
|
586 "user_outputs": []
|
|
587 },
|
|
588 "19": {
|
|
589 "annotation": "",
|
|
590 "id": 19,
|
|
591 "input_connections": {
|
|
592 "genomeSource|ownFile": {
|
|
593 "id": 17,
|
|
594 "output_name": "output"
|
|
595 },
|
|
596 "paired|input1": {
|
|
597 "id": 10,
|
|
598 "output_name": "output_file"
|
|
599 },
|
|
600 "paired|input2": {
|
|
601 "id": 11,
|
|
602 "output_name": "output_file"
|
|
603 }
|
|
604 },
|
|
605 "inputs": [],
|
|
606 "name": "Map with BWA for Illumina",
|
|
607 "outputs": [
|
|
608 {
|
|
609 "name": "output",
|
|
610 "type": "sam"
|
|
611 }
|
|
612 ],
|
|
613 "position": {
|
7
|
614 "left": 746.3611302375793,
|
|
615 "top": 627.6805882453918
|
0
|
616 },
|
|
617 "post_job_actions": {
|
|
618 "RenameDatasetActionoutput": {
|
|
619 "action_arguments": {
|
|
620 "newname": "father.sam"
|
|
621 },
|
|
622 "action_type": "RenameDatasetAction",
|
|
623 "output_name": "output"
|
|
624 }
|
|
625 },
|
|
626 "tool_errors": null,
|
|
627 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
628 "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\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
|
|
629 "tool_version": "1.2.3",
|
|
630 "type": "tool",
|
|
631 "user_outputs": []
|
|
632 },
|
|
633 "20": {
|
|
634 "annotation": "",
|
|
635 "id": 20,
|
|
636 "input_connections": {
|
|
637 "genomeSource|ownFile": {
|
|
638 "id": 17,
|
|
639 "output_name": "output"
|
|
640 },
|
|
641 "paired|input1": {
|
|
642 "id": 12,
|
|
643 "output_name": "output_file"
|
|
644 },
|
|
645 "paired|input2": {
|
|
646 "id": 13,
|
|
647 "output_name": "output_file"
|
|
648 }
|
|
649 },
|
|
650 "inputs": [],
|
|
651 "name": "Map with BWA for Illumina",
|
|
652 "outputs": [
|
|
653 {
|
|
654 "name": "output",
|
|
655 "type": "sam"
|
|
656 }
|
|
657 ],
|
|
658 "position": {
|
7
|
659 "left": 734.6945042610168,
|
|
660 "top": 852.0208592414856
|
0
|
661 },
|
|
662 "post_job_actions": {
|
|
663 "RenameDatasetActionoutput": {
|
|
664 "action_arguments": {
|
|
665 "newname": "daughter.sam"
|
|
666 },
|
|
667 "action_type": "RenameDatasetAction",
|
|
668 "output_name": "output"
|
|
669 }
|
|
670 },
|
|
671 "tool_errors": null,
|
|
672 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
673 "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\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
|
|
674 "tool_version": "1.2.3",
|
|
675 "type": "tool",
|
|
676 "user_outputs": []
|
|
677 },
|
|
678 "21": {
|
|
679 "annotation": "",
|
|
680 "id": 21,
|
|
681 "input_connections": {
|
|
682 "genomeSource|ownFile": {
|
|
683 "id": 17,
|
|
684 "output_name": "output"
|
|
685 },
|
|
686 "paired|input1": {
|
|
687 "id": 14,
|
|
688 "output_name": "output_file"
|
|
689 },
|
|
690 "paired|input2": {
|
|
691 "id": 15,
|
|
692 "output_name": "output_file"
|
|
693 }
|
|
694 },
|
|
695 "inputs": [],
|
|
696 "name": "Map with BWA for Illumina",
|
|
697 "outputs": [
|
|
698 {
|
|
699 "name": "output",
|
|
700 "type": "sam"
|
|
701 }
|
|
702 ],
|
|
703 "position": {
|
7
|
704 "left": 770.6840672492981,
|
|
705 "top": 1096.013901233673
|
0
|
706 },
|
|
707 "post_job_actions": {
|
|
708 "RenameDatasetActionoutput": {
|
|
709 "action_arguments": {
|
|
710 "newname": "son.sam"
|
|
711 },
|
|
712 "action_type": "RenameDatasetAction",
|
|
713 "output_name": "output"
|
|
714 }
|
|
715 },
|
|
716 "tool_errors": null,
|
|
717 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
718 "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\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
|
|
719 "tool_version": "1.2.3",
|
|
720 "type": "tool",
|
|
721 "user_outputs": []
|
|
722 },
|
|
723 "22": {
|
|
724 "annotation": "",
|
|
725 "id": 22,
|
|
726 "input_connections": {
|
|
727 "source|input1": {
|
|
728 "id": 18,
|
|
729 "output_name": "output"
|
|
730 },
|
|
731 "source|ref_file": {
|
|
732 "id": 17,
|
|
733 "output_name": "output"
|
|
734 }
|
|
735 },
|
|
736 "inputs": [],
|
|
737 "name": "SAM-to-BAM",
|
|
738 "outputs": [
|
|
739 {
|
|
740 "name": "output1",
|
|
741 "type": "bam"
|
|
742 }
|
|
743 ],
|
|
744 "position": {
|
7
|
745 "left": 998.6874852180481,
|
|
746 "top": 421.0139012336731
|
0
|
747 },
|
|
748 "post_job_actions": {
|
|
749 "HideDatasetActionoutput1": {
|
|
750 "action_arguments": {},
|
|
751 "action_type": "HideDatasetAction",
|
|
752 "output_name": "output1"
|
|
753 },
|
|
754 "RenameDatasetActionoutput1": {
|
|
755 "action_arguments": {
|
|
756 "newname": "mother.bam"
|
|
757 },
|
|
758 "action_type": "RenameDatasetAction",
|
|
759 "output_name": "output1"
|
|
760 }
|
|
761 },
|
|
762 "tool_errors": null,
|
|
763 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
764 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
765 "tool_version": "1.1.4",
|
|
766 "type": "tool",
|
|
767 "user_outputs": []
|
|
768 },
|
|
769 "23": {
|
|
770 "annotation": "",
|
|
771 "id": 23,
|
|
772 "input_connections": {
|
|
773 "source|input1": {
|
|
774 "id": 19,
|
|
775 "output_name": "output"
|
|
776 },
|
|
777 "source|ref_file": {
|
|
778 "id": 17,
|
|
779 "output_name": "output"
|
|
780 }
|
|
781 },
|
|
782 "inputs": [],
|
|
783 "name": "SAM-to-BAM",
|
|
784 "outputs": [
|
|
785 {
|
|
786 "name": "output1",
|
|
787 "type": "bam"
|
|
788 }
|
|
789 ],
|
|
790 "position": {
|
7
|
791 "left": 998.8611912727356,
|
|
792 "top": 670.6840672492981
|
0
|
793 },
|
|
794 "post_job_actions": {
|
|
795 "HideDatasetActionoutput1": {
|
|
796 "action_arguments": {},
|
|
797 "action_type": "HideDatasetAction",
|
|
798 "output_name": "output1"
|
|
799 },
|
|
800 "RenameDatasetActionoutput1": {
|
|
801 "action_arguments": {
|
|
802 "newname": "father.bam"
|
|
803 },
|
|
804 "action_type": "RenameDatasetAction",
|
|
805 "output_name": "output1"
|
|
806 }
|
|
807 },
|
|
808 "tool_errors": null,
|
|
809 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
810 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
811 "tool_version": "1.1.4",
|
|
812 "type": "tool",
|
|
813 "user_outputs": []
|
|
814 },
|
|
815 "24": {
|
|
816 "annotation": "",
|
|
817 "id": 24,
|
|
818 "input_connections": {
|
|
819 "source|input1": {
|
|
820 "id": 20,
|
|
821 "output_name": "output"
|
|
822 },
|
|
823 "source|ref_file": {
|
|
824 "id": 17,
|
|
825 "output_name": "output"
|
|
826 }
|
|
827 },
|
|
828 "inputs": [],
|
|
829 "name": "SAM-to-BAM",
|
|
830 "outputs": [
|
|
831 {
|
|
832 "name": "output1",
|
|
833 "type": "bam"
|
|
834 }
|
|
835 ],
|
|
836 "position": {
|
7
|
837 "left": 982.6806492805481,
|
|
838 "top": 891.0139622688293
|
0
|
839 },
|
|
840 "post_job_actions": {
|
|
841 "HideDatasetActionoutput1": {
|
|
842 "action_arguments": {},
|
|
843 "action_type": "HideDatasetAction",
|
|
844 "output_name": "output1"
|
|
845 },
|
|
846 "RenameDatasetActionoutput1": {
|
|
847 "action_arguments": {
|
|
848 "newname": "daughter.bam"
|
|
849 },
|
|
850 "action_type": "RenameDatasetAction",
|
|
851 "output_name": "output1"
|
|
852 }
|
|
853 },
|
|
854 "tool_errors": null,
|
|
855 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
856 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
857 "tool_version": "1.1.4",
|
|
858 "type": "tool",
|
|
859 "user_outputs": []
|
|
860 },
|
|
861 "25": {
|
|
862 "annotation": "",
|
|
863 "id": 25,
|
|
864 "input_connections": {
|
|
865 "source|input1": {
|
|
866 "id": 21,
|
|
867 "output_name": "output"
|
|
868 },
|
|
869 "source|ref_file": {
|
|
870 "id": 17,
|
|
871 "output_name": "output"
|
|
872 }
|
|
873 },
|
|
874 "inputs": [],
|
|
875 "name": "SAM-to-BAM",
|
|
876 "outputs": [
|
|
877 {
|
|
878 "name": "output1",
|
|
879 "type": "bam"
|
|
880 }
|
|
881 ],
|
|
882 "position": {
|
7
|
883 "left": 993.6874852180481,
|
|
884 "top": 1144.0174412727356
|
0
|
885 },
|
|
886 "post_job_actions": {
|
|
887 "HideDatasetActionoutput1": {
|
|
888 "action_arguments": {},
|
|
889 "action_type": "HideDatasetAction",
|
|
890 "output_name": "output1"
|
|
891 },
|
|
892 "RenameDatasetActionoutput1": {
|
|
893 "action_arguments": {
|
|
894 "newname": "son.bam"
|
|
895 },
|
|
896 "action_type": "RenameDatasetAction",
|
|
897 "output_name": "output1"
|
|
898 }
|
|
899 },
|
|
900 "tool_errors": null,
|
|
901 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
902 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
903 "tool_version": "1.1.4",
|
|
904 "type": "tool",
|
|
905 "user_outputs": []
|
|
906 },
|
|
907 "26": {
|
|
908 "annotation": "",
|
|
909 "id": 26,
|
|
910 "input_connections": {
|
|
911 "input1": {
|
|
912 "id": 22,
|
|
913 "output_name": "output1"
|
|
914 }
|
|
915 },
|
|
916 "inputs": [],
|
|
917 "name": "sort",
|
|
918 "outputs": [
|
|
919 {
|
|
920 "name": "output1",
|
|
921 "type": "bam"
|
|
922 }
|
|
923 ],
|
|
924 "position": {
|
7
|
925 "left": 1170.684067249298,
|
|
926 "top": 440.02433824539185
|
0
|
927 },
|
|
928 "post_job_actions": {
|
|
929 "HideDatasetActionoutput1": {
|
|
930 "action_arguments": {},
|
|
931 "action_type": "HideDatasetAction",
|
|
932 "output_name": "output1"
|
|
933 },
|
|
934 "RenameDatasetActionoutput1": {
|
|
935 "action_arguments": {
|
|
936 "newname": "mother.sorted.bam"
|
|
937 },
|
|
938 "action_type": "RenameDatasetAction",
|
|
939 "output_name": "output1"
|
|
940 }
|
|
941 },
|
|
942 "tool_errors": null,
|
|
943 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
944 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
945 "tool_version": "1.0.2",
|
|
946 "type": "tool",
|
|
947 "user_outputs": []
|
|
948 },
|
|
949 "27": {
|
|
950 "annotation": "",
|
|
951 "id": 27,
|
|
952 "input_connections": {
|
|
953 "input1": {
|
|
954 "id": 23,
|
|
955 "output_name": "output1"
|
|
956 }
|
|
957 },
|
|
958 "inputs": [],
|
|
959 "name": "sort",
|
|
960 "outputs": [
|
|
961 {
|
|
962 "name": "output1",
|
|
963 "type": "bam"
|
|
964 }
|
|
965 ],
|
|
966 "position": {
|
7
|
967 "left": 1165.857651233673,
|
|
968 "top": 672.6805882453918
|
0
|
969 },
|
|
970 "post_job_actions": {
|
|
971 "HideDatasetActionoutput1": {
|
|
972 "action_arguments": {},
|
|
973 "action_type": "HideDatasetAction",
|
|
974 "output_name": "output1"
|
|
975 },
|
|
976 "RenameDatasetActionoutput1": {
|
|
977 "action_arguments": {
|
|
978 "newname": "father.sorted.bam"
|
|
979 },
|
|
980 "action_type": "RenameDatasetAction",
|
|
981 "output_name": "output1"
|
|
982 }
|
|
983 },
|
|
984 "tool_errors": null,
|
|
985 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
986 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
987 "tool_version": "1.0.2",
|
|
988 "type": "tool",
|
|
989 "user_outputs": []
|
|
990 },
|
|
991 "28": {
|
|
992 "annotation": "",
|
|
993 "id": 28,
|
|
994 "input_connections": {
|
|
995 "input1": {
|
|
996 "id": 24,
|
|
997 "output_name": "output1"
|
|
998 }
|
|
999 },
|
|
1000 "inputs": [],
|
|
1001 "name": "sort",
|
|
1002 "outputs": [
|
|
1003 {
|
|
1004 "name": "output1",
|
|
1005 "type": "bam"
|
|
1006 }
|
|
1007 ],
|
|
1008 "position": {
|
7
|
1009 "left": 1147.680649280548,
|
|
1010 "top": 903.0278172492981
|
0
|
1011 },
|
|
1012 "post_job_actions": {
|
|
1013 "HideDatasetActionoutput1": {
|
|
1014 "action_arguments": {},
|
|
1015 "action_type": "HideDatasetAction",
|
|
1016 "output_name": "output1"
|
|
1017 },
|
|
1018 "RenameDatasetActionoutput1": {
|
|
1019 "action_arguments": {
|
|
1020 "newname": "daughter.sorted.bam"
|
|
1021 },
|
|
1022 "action_type": "RenameDatasetAction",
|
|
1023 "output_name": "output1"
|
|
1024 }
|
|
1025 },
|
|
1026 "tool_errors": null,
|
|
1027 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
1028 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
1029 "tool_version": "1.0.2",
|
|
1030 "type": "tool",
|
|
1031 "user_outputs": []
|
|
1032 },
|
|
1033 "29": {
|
|
1034 "annotation": "",
|
|
1035 "id": 29,
|
|
1036 "input_connections": {
|
|
1037 "input1": {
|
|
1038 "id": 25,
|
|
1039 "output_name": "output1"
|
|
1040 }
|
|
1041 },
|
|
1042 "inputs": [],
|
|
1043 "name": "sort",
|
|
1044 "outputs": [
|
|
1045 {
|
|
1046 "name": "output1",
|
|
1047 "type": "bam"
|
|
1048 }
|
|
1049 ],
|
|
1050 "position": {
|
7
|
1051 "left": 1158.6876072883606,
|
|
1052 "top": 1123.027817249298
|
0
|
1053 },
|
|
1054 "post_job_actions": {
|
|
1055 "HideDatasetActionoutput1": {
|
|
1056 "action_arguments": {},
|
|
1057 "action_type": "HideDatasetAction",
|
|
1058 "output_name": "output1"
|
|
1059 },
|
|
1060 "RenameDatasetActionoutput1": {
|
|
1061 "action_arguments": {
|
|
1062 "newname": "son.sorted.bam"
|
|
1063 },
|
|
1064 "action_type": "RenameDatasetAction",
|
|
1065 "output_name": "output1"
|
|
1066 }
|
|
1067 },
|
|
1068 "tool_errors": null,
|
|
1069 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
1070 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
1071 "tool_version": "1.0.2",
|
|
1072 "type": "tool",
|
|
1073 "user_outputs": []
|
|
1074 },
|
|
1075 "30": {
|
|
1076 "annotation": "",
|
|
1077 "id": 30,
|
|
1078 "input_connections": {
|
|
1079 "input_file": {
|
|
1080 "id": 26,
|
|
1081 "output_name": "output1"
|
|
1082 }
|
|
1083 },
|
|
1084 "inputs": [],
|
|
1085 "name": "Mark Duplicate reads",
|
|
1086 "outputs": [
|
|
1087 {
|
|
1088 "name": "out_file",
|
|
1089 "type": "bam"
|
|
1090 },
|
|
1091 {
|
|
1092 "name": "html_file",
|
|
1093 "type": "html"
|
|
1094 }
|
|
1095 ],
|
|
1096 "position": {
|
7
|
1097 "left": 1365.684067249298,
|
|
1098 "top": 454.01738023757935
|
0
|
1099 },
|
|
1100 "post_job_actions": {
|
|
1101 "RenameDatasetActionhtml_file": {
|
|
1102 "action_arguments": {
|
|
1103 "newname": "mother.deduplicated.html"
|
|
1104 },
|
|
1105 "action_type": "RenameDatasetAction",
|
|
1106 "output_name": "html_file"
|
|
1107 },
|
|
1108 "RenameDatasetActionout_file": {
|
|
1109 "action_arguments": {
|
|
1110 "newname": "mother.deduplicated.bam"
|
|
1111 },
|
|
1112 "action_type": "RenameDatasetAction",
|
|
1113 "output_name": "out_file"
|
|
1114 }
|
|
1115 },
|
|
1116 "tool_errors": null,
|
|
1117 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
1118 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\"}",
|
|
1119 "tool_version": "1.56.0",
|
|
1120 "type": "tool",
|
|
1121 "user_outputs": []
|
|
1122 },
|
|
1123 "31": {
|
|
1124 "annotation": "",
|
|
1125 "id": 31,
|
|
1126 "input_connections": {
|
|
1127 "input_file": {
|
|
1128 "id": 27,
|
|
1129 "output_name": "output1"
|
|
1130 }
|
|
1131 },
|
|
1132 "inputs": [],
|
|
1133 "name": "Mark Duplicate reads",
|
|
1134 "outputs": [
|
|
1135 {
|
|
1136 "name": "out_file",
|
|
1137 "type": "bam"
|
|
1138 },
|
|
1139 {
|
|
1140 "name": "html_file",
|
|
1141 "type": "html"
|
|
1142 }
|
|
1143 ],
|
|
1144 "position": {
|
7
|
1145 "left": 1328.357651233673,
|
|
1146 "top": 646.6910252571106
|
0
|
1147 },
|
|
1148 "post_job_actions": {
|
|
1149 "RenameDatasetActionhtml_file": {
|
|
1150 "action_arguments": {
|
|
1151 "newname": "father.deduplicated.html"
|
|
1152 },
|
|
1153 "action_type": "RenameDatasetAction",
|
|
1154 "output_name": "html_file"
|
|
1155 },
|
|
1156 "RenameDatasetActionout_file": {
|
|
1157 "action_arguments": {
|
|
1158 "newname": "father.deduplicated.bam"
|
|
1159 },
|
|
1160 "action_type": "RenameDatasetAction",
|
|
1161 "output_name": "out_file"
|
|
1162 }
|
|
1163 },
|
|
1164 "tool_errors": null,
|
|
1165 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
1166 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\"}",
|
|
1167 "tool_version": "1.56.0",
|
|
1168 "type": "tool",
|
|
1169 "user_outputs": []
|
|
1170 },
|
|
1171 "32": {
|
|
1172 "annotation": "",
|
|
1173 "id": 32,
|
|
1174 "input_connections": {
|
|
1175 "input_file": {
|
|
1176 "id": 28,
|
|
1177 "output_name": "output1"
|
|
1178 }
|
|
1179 },
|
|
1180 "inputs": [],
|
|
1181 "name": "Mark Duplicate reads",
|
|
1182 "outputs": [
|
|
1183 {
|
|
1184 "name": "out_file",
|
|
1185 "type": "bam"
|
|
1186 },
|
|
1187 {
|
|
1188 "name": "html_file",
|
|
1189 "type": "html"
|
|
1190 }
|
|
1191 ],
|
|
1192 "position": {
|
7
|
1193 "left": 1338.6876072883606,
|
|
1194 "top": 873.0278172492981
|
0
|
1195 },
|
|
1196 "post_job_actions": {
|
|
1197 "RenameDatasetActionhtml_file": {
|
|
1198 "action_arguments": {
|
|
1199 "newname": "daughter.deduplicated.html"
|
|
1200 },
|
|
1201 "action_type": "RenameDatasetAction",
|
|
1202 "output_name": "html_file"
|
|
1203 },
|
|
1204 "RenameDatasetActionout_file": {
|
|
1205 "action_arguments": {
|
|
1206 "newname": "daughter.deduplicated.bam"
|
|
1207 },
|
|
1208 "action_type": "RenameDatasetAction",
|
|
1209 "output_name": "out_file"
|
|
1210 }
|
|
1211 },
|
|
1212 "tool_errors": null,
|
|
1213 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
1214 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\"}",
|
|
1215 "tool_version": "1.56.0",
|
|
1216 "type": "tool",
|
|
1217 "user_outputs": []
|
|
1218 },
|
|
1219 "33": {
|
|
1220 "annotation": "",
|
|
1221 "id": 33,
|
|
1222 "input_connections": {
|
|
1223 "input_file": {
|
|
1224 "id": 29,
|
|
1225 "output_name": "output1"
|
|
1226 }
|
|
1227 },
|
|
1228 "inputs": [],
|
|
1229 "name": "Mark Duplicate reads",
|
|
1230 "outputs": [
|
|
1231 {
|
|
1232 "name": "out_file",
|
|
1233 "type": "bam"
|
|
1234 },
|
|
1235 {
|
|
1236 "name": "html_file",
|
|
1237 "type": "html"
|
|
1238 }
|
|
1239 ],
|
|
1240 "position": {
|
7
|
1241 "left": 1354.694565296173,
|
|
1242 "top": 1102.0208592414856
|
0
|
1243 },
|
|
1244 "post_job_actions": {
|
|
1245 "RenameDatasetActionhtml_file": {
|
|
1246 "action_arguments": {
|
|
1247 "newname": "son.deduplicated.html"
|
|
1248 },
|
|
1249 "action_type": "RenameDatasetAction",
|
|
1250 "output_name": "html_file"
|
|
1251 },
|
|
1252 "RenameDatasetActionout_file": {
|
|
1253 "action_arguments": {
|
|
1254 "newname": "son.deduplicated.bam"
|
|
1255 },
|
|
1256 "action_type": "RenameDatasetAction",
|
|
1257 "output_name": "out_file"
|
|
1258 }
|
|
1259 },
|
|
1260 "tool_errors": null,
|
|
1261 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
1262 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\"}",
|
|
1263 "tool_version": "1.56.0",
|
|
1264 "type": "tool",
|
|
1265 "user_outputs": []
|
|
1266 },
|
|
1267 "34": {
|
|
1268 "annotation": "",
|
|
1269 "id": 34,
|
|
1270 "input_connections": {
|
|
1271 "input1": {
|
|
1272 "id": 30,
|
|
1273 "output_name": "out_file"
|
|
1274 },
|
|
1275 "input2": {
|
|
1276 "id": 17,
|
|
1277 "output_name": "output"
|
|
1278 }
|
|
1279 },
|
|
1280 "inputs": [],
|
|
1281 "name": "LINKYX_mpileup",
|
|
1282 "outputs": [
|
|
1283 {
|
|
1284 "name": "output",
|
|
1285 "type": "vcf"
|
|
1286 }
|
|
1287 ],
|
|
1288 "position": {
|
7
|
1289 "left": 1643.6876072883606,
|
|
1290 "top": 465.02433824539185
|
0
|
1291 },
|
|
1292 "post_job_actions": {
|
|
1293 "RenameDatasetActionoutput": {
|
|
1294 "action_arguments": {
|
|
1295 "newname": "mother.vcf"
|
|
1296 },
|
|
1297 "action_type": "RenameDatasetAction",
|
|
1298 "output_name": "output"
|
|
1299 }
|
|
1300 },
|
|
1301 "tool_errors": null,
|
7
|
1302 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/linkyx/LINKYX_mpileup/1.1",
|
0
|
1303 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
7
|
1304 "tool_version": "1.1",
|
0
|
1305 "type": "tool",
|
|
1306 "user_outputs": []
|
|
1307 },
|
|
1308 "35": {
|
|
1309 "annotation": "",
|
|
1310 "id": 35,
|
|
1311 "input_connections": {
|
|
1312 "input1": {
|
|
1313 "id": 31,
|
|
1314 "output_name": "out_file"
|
|
1315 },
|
|
1316 "input2": {
|
|
1317 "id": 17,
|
|
1318 "output_name": "output"
|
|
1319 }
|
|
1320 },
|
|
1321 "inputs": [],
|
|
1322 "name": "LINKYX_mpileup",
|
|
1323 "outputs": [
|
|
1324 {
|
|
1325 "name": "output",
|
|
1326 "type": "vcf"
|
|
1327 }
|
|
1328 ],
|
|
1329 "position": {
|
7
|
1330 "left": 1653.3577733039856,
|
|
1331 "top": 656.1875462532043
|
0
|
1332 },
|
|
1333 "post_job_actions": {
|
|
1334 "RenameDatasetActionoutput": {
|
|
1335 "action_arguments": {
|
|
1336 "newname": "father.vcf"
|
|
1337 },
|
|
1338 "action_type": "RenameDatasetAction",
|
|
1339 "output_name": "output"
|
|
1340 }
|
|
1341 },
|
|
1342 "tool_errors": null,
|
7
|
1343 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/linkyx/LINKYX_mpileup/1.1",
|
0
|
1344 "tool_state": "{\"input2\": \"null\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}",
|
7
|
1345 "tool_version": "1.1",
|
0
|
1346 "type": "tool",
|
|
1347 "user_outputs": []
|
|
1348 },
|
|
1349 "36": {
|
|
1350 "annotation": "",
|
|
1351 "id": 36,
|
|
1352 "input_connections": {
|
|
1353 "input1": {
|
|
1354 "id": 32,
|
|
1355 "output_name": "out_file"
|
|
1356 },
|
|
1357 "input2": {
|
|
1358 "id": 17,
|
|
1359 "output_name": "output"
|
|
1360 }
|
|
1361 },
|
|
1362 "inputs": [],
|
|
1363 "name": "LINKYX_mpileup",
|
|
1364 "outputs": [
|
|
1365 {
|
|
1366 "name": "output",
|
|
1367 "type": "vcf"
|
|
1368 }
|
|
1369 ],
|
|
1370 "position": {
|
7
|
1371 "left": 1652.680649280548,
|
|
1372 "top": 873.0278172492981
|
0
|
1373 },
|
|
1374 "post_job_actions": {
|
|
1375 "RenameDatasetActionoutput": {
|
|
1376 "action_arguments": {
|
|
1377 "newname": "daughter.vcf"
|
|
1378 },
|
|
1379 "action_type": "RenameDatasetAction",
|
|
1380 "output_name": "output"
|
|
1381 }
|
|
1382 },
|
|
1383 "tool_errors": null,
|
7
|
1384 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/linkyx/LINKYX_mpileup/1.1",
|
0
|
1385 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
7
|
1386 "tool_version": "1.1",
|
0
|
1387 "type": "tool",
|
|
1388 "user_outputs": []
|
|
1389 },
|
|
1390 "37": {
|
|
1391 "annotation": "",
|
|
1392 "id": 37,
|
|
1393 "input_connections": {
|
|
1394 "input1": {
|
|
1395 "id": 33,
|
|
1396 "output_name": "out_file"
|
|
1397 },
|
|
1398 "input2": {
|
|
1399 "id": 17,
|
|
1400 "output_name": "output"
|
|
1401 }
|
|
1402 },
|
|
1403 "inputs": [],
|
|
1404 "name": "LINKYX_mpileup",
|
|
1405 "outputs": [
|
|
1406 {
|
|
1407 "name": "output",
|
|
1408 "type": "vcf"
|
|
1409 }
|
|
1410 ],
|
|
1411 "position": {
|
7
|
1412 "left": 1670.684067249298,
|
|
1413 "top": 1104.0174412727356
|
0
|
1414 },
|
|
1415 "post_job_actions": {
|
|
1416 "RenameDatasetActionoutput": {
|
|
1417 "action_arguments": {
|
|
1418 "newname": "son.vcf"
|
|
1419 },
|
|
1420 "action_type": "RenameDatasetAction",
|
|
1421 "output_name": "output"
|
|
1422 }
|
|
1423 },
|
|
1424 "tool_errors": null,
|
7
|
1425 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/linkyx/LINKYX_mpileup/1.1",
|
0
|
1426 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
7
|
1427 "tool_version": "1.1",
|
0
|
1428 "type": "tool",
|
|
1429 "user_outputs": []
|
|
1430 },
|
|
1431 "38": {
|
|
1432 "annotation": "",
|
|
1433 "id": 38,
|
|
1434 "input_connections": {
|
|
1435 "input1": {
|
|
1436 "id": 17,
|
|
1437 "output_name": "output"
|
|
1438 },
|
|
1439 "input2": {
|
|
1440 "id": 30,
|
|
1441 "output_name": "out_file"
|
|
1442 },
|
|
1443 "input3": {
|
|
1444 "id": 34,
|
|
1445 "output_name": "output"
|
|
1446 },
|
|
1447 "input4": {
|
|
1448 "id": 31,
|
|
1449 "output_name": "out_file"
|
|
1450 },
|
|
1451 "input5": {
|
|
1452 "id": 35,
|
|
1453 "output_name": "output"
|
|
1454 },
|
|
1455 "input6": {
|
|
1456 "id": 32,
|
|
1457 "output_name": "out_file"
|
|
1458 },
|
|
1459 "input7": {
|
|
1460 "id": 36,
|
|
1461 "output_name": "output"
|
|
1462 },
|
|
1463 "input8": {
|
|
1464 "id": 33,
|
|
1465 "output_name": "out_file"
|
|
1466 },
|
|
1467 "input9": {
|
|
1468 "id": 37,
|
|
1469 "output_name": "output"
|
|
1470 }
|
|
1471 },
|
|
1472 "inputs": [],
|
|
1473 "name": "LINKYX_X",
|
|
1474 "outputs": [
|
|
1475 {
|
|
1476 "name": "output",
|
|
1477 "type": "txt"
|
|
1478 },
|
|
1479 {
|
|
1480 "name": "output1",
|
|
1481 "type": "fasta"
|
|
1482 },
|
|
1483 {
|
|
1484 "name": "output2",
|
|
1485 "type": "bam"
|
|
1486 },
|
|
1487 {
|
|
1488 "name": "output3",
|
|
1489 "type": "bam"
|
|
1490 },
|
|
1491 {
|
|
1492 "name": "output4",
|
|
1493 "type": "bam"
|
|
1494 },
|
|
1495 {
|
|
1496 "name": "output5",
|
|
1497 "type": "bam"
|
|
1498 }
|
|
1499 ],
|
|
1500 "position": {
|
7
|
1501 "left": 1921.517563343048,
|
|
1502 "top": 602.0208592414856
|
0
|
1503 },
|
|
1504 "post_job_actions": {},
|
|
1505 "tool_errors": null,
|
7
|
1506 "tool_id": "toolshed.g2.bx.psu.edu/repos/biomonika/linkyx/LINKYX_X/1.1",
|
0
|
1507 "tool_state": "{\"input2\": \"null\", \"input3\": \"null\", \"input1\": \"null\", \"input6\": \"null\", \"input7\": \"null\", \"input4\": \"null\", \"input5\": \"null\", \"__page__\": 0, \"input8\": \"null\", \"input9\": \"null\", \"__rerun_remap_job_id__\": null}",
|
7
|
1508 "tool_version": "1.1",
|
0
|
1509 "type": "tool",
|
|
1510 "user_outputs": []
|
|
1511 }
|
7
|
1512 },
|
|
1513 "uuid": "72f03b6e-5cd7-498c-81f0-5bdf30fc0c36"
|
0
|
1514 } |