|
0
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "linkY",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "id": 0,
|
|
|
10 "input_connections": {},
|
|
|
11 "inputs": [
|
|
|
12 {
|
|
|
13 "description": "",
|
|
|
14 "name": "Mother_reads_1"
|
|
|
15 }
|
|
|
16 ],
|
|
|
17 "name": "Input dataset",
|
|
|
18 "outputs": [],
|
|
|
19 "position": {
|
|
|
20 "left": 195.70834350585938,
|
|
|
21 "top": 304.9375
|
|
|
22 },
|
|
|
23 "tool_errors": null,
|
|
|
24 "tool_id": null,
|
|
|
25 "tool_state": "{\"name\": \"Mother_reads_1\"}",
|
|
|
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_reads_2"
|
|
|
38 }
|
|
|
39 ],
|
|
|
40 "name": "Input dataset",
|
|
|
41 "outputs": [],
|
|
|
42 "position": {
|
|
|
43 "left": 190.70834350585938,
|
|
|
44 "top": 428.9375
|
|
|
45 },
|
|
|
46 "tool_errors": null,
|
|
|
47 "tool_id": null,
|
|
|
48 "tool_state": "{\"name\": \"Mother_reads_2\"}",
|
|
|
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_reads_1"
|
|
|
61 }
|
|
|
62 ],
|
|
|
63 "name": "Input dataset",
|
|
|
64 "outputs": [],
|
|
|
65 "position": {
|
|
|
66 "left": 194.6875,
|
|
|
67 "top": 555.9375
|
|
|
68 },
|
|
|
69 "tool_errors": null,
|
|
|
70 "tool_id": null,
|
|
|
71 "tool_state": "{\"name\": \"Father_reads_1\"}",
|
|
|
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_reads_2"
|
|
|
84 }
|
|
|
85 ],
|
|
|
86 "name": "Input dataset",
|
|
|
87 "outputs": [],
|
|
|
88 "position": {
|
|
|
89 "left": 195.70834350585938,
|
|
|
90 "top": 677.9375
|
|
|
91 },
|
|
|
92 "tool_errors": null,
|
|
|
93 "tool_id": null,
|
|
|
94 "tool_state": "{\"name\": \"Father_reads_2\"}",
|
|
|
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_reads_1"
|
|
|
107 }
|
|
|
108 ],
|
|
|
109 "name": "Input dataset",
|
|
|
110 "outputs": [],
|
|
|
111 "position": {
|
|
|
112 "left": 204.6875,
|
|
|
113 "top": 812.9375
|
|
|
114 },
|
|
|
115 "tool_errors": null,
|
|
|
116 "tool_id": null,
|
|
|
117 "tool_state": "{\"name\": \"Daughter_reads_1\"}",
|
|
|
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_reads_2"
|
|
|
130 }
|
|
|
131 ],
|
|
|
132 "name": "Input dataset",
|
|
|
133 "outputs": [],
|
|
|
134 "position": {
|
|
|
135 "left": 200.70834350585938,
|
|
|
136 "top": 913.9375
|
|
|
137 },
|
|
|
138 "tool_errors": null,
|
|
|
139 "tool_id": null,
|
|
|
140 "tool_state": "{\"name\": \"Daughter_reads_2\"}",
|
|
|
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_reads_1"
|
|
|
153 }
|
|
|
154 ],
|
|
|
155 "name": "Input dataset",
|
|
|
156 "outputs": [],
|
|
|
157 "position": {
|
|
|
158 "left": 208.70834350585938,
|
|
|
159 "top": 1030.9375
|
|
|
160 },
|
|
|
161 "tool_errors": null,
|
|
|
162 "tool_id": null,
|
|
|
163 "tool_state": "{\"name\": \"Son_reads_1\"}",
|
|
|
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_reads_2"
|
|
|
176 }
|
|
|
177 ],
|
|
|
178 "name": "Input dataset",
|
|
|
179 "outputs": [],
|
|
|
180 "position": {
|
|
|
181 "left": 216.6875,
|
|
|
182 "top": 1159.9375
|
|
|
183 },
|
|
|
184 "tool_errors": null,
|
|
|
185 "tool_id": null,
|
|
|
186 "tool_state": "{\"name\": \"Son_reads_2\"}",
|
|
|
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": {
|
|
|
209 "left": 384.6875,
|
|
|
210 "top": 279.4375
|
|
|
211 },
|
|
|
212 "post_job_actions": {
|
|
|
213 "HideDatasetActionoutput_file": {
|
|
|
214 "action_arguments": {},
|
|
|
215 "action_type": "HideDatasetAction",
|
|
|
216 "output_name": "output_file"
|
|
|
217 },
|
|
|
218 "RenameDatasetActionoutput_file": {
|
|
|
219 "action_arguments": {
|
|
|
220 "newname": "Mother_reads_1_groomed"
|
|
|
221 },
|
|
|
222 "action_type": "RenameDatasetAction",
|
|
|
223 "output_name": "output_file"
|
|
|
224 }
|
|
|
225 },
|
|
|
226 "tool_errors": null,
|
|
|
227 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
228 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
229 "tool_version": "1.0.4",
|
|
|
230 "type": "tool",
|
|
|
231 "user_outputs": []
|
|
|
232 },
|
|
|
233 "9": {
|
|
|
234 "annotation": "",
|
|
|
235 "id": 9,
|
|
|
236 "input_connections": {
|
|
|
237 "input_file": {
|
|
|
238 "id": 1,
|
|
|
239 "output_name": "output"
|
|
|
240 }
|
|
|
241 },
|
|
|
242 "inputs": [],
|
|
|
243 "name": "FASTQ Groomer",
|
|
|
244 "outputs": [
|
|
|
245 {
|
|
|
246 "name": "output_file",
|
|
|
247 "type": "fastqsanger"
|
|
|
248 }
|
|
|
249 ],
|
|
|
250 "position": {
|
|
|
251 "left": 394.6875,
|
|
|
252 "top": 414.4375
|
|
|
253 },
|
|
|
254 "post_job_actions": {
|
|
|
255 "HideDatasetActionoutput_file": {
|
|
|
256 "action_arguments": {},
|
|
|
257 "action_type": "HideDatasetAction",
|
|
|
258 "output_name": "output_file"
|
|
|
259 },
|
|
|
260 "RenameDatasetActionoutput_file": {
|
|
|
261 "action_arguments": {
|
|
|
262 "newname": "Mother_reads_2_groomed"
|
|
|
263 },
|
|
|
264 "action_type": "RenameDatasetAction",
|
|
|
265 "output_name": "output_file"
|
|
|
266 }
|
|
|
267 },
|
|
|
268 "tool_errors": null,
|
|
|
269 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
270 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
271 "tool_version": "1.0.4",
|
|
|
272 "type": "tool",
|
|
|
273 "user_outputs": []
|
|
|
274 },
|
|
|
275 "10": {
|
|
|
276 "annotation": "",
|
|
|
277 "id": 10,
|
|
|
278 "input_connections": {
|
|
|
279 "input_file": {
|
|
|
280 "id": 2,
|
|
|
281 "output_name": "output"
|
|
|
282 }
|
|
|
283 },
|
|
|
284 "inputs": [],
|
|
|
285 "name": "FASTQ Groomer",
|
|
|
286 "outputs": [
|
|
|
287 {
|
|
|
288 "name": "output_file",
|
|
|
289 "type": "fastqsanger"
|
|
|
290 }
|
|
|
291 ],
|
|
|
292 "position": {
|
|
|
293 "left": 392.6875,
|
|
|
294 "top": 536.4375
|
|
|
295 },
|
|
|
296 "post_job_actions": {
|
|
|
297 "HideDatasetActionoutput_file": {
|
|
|
298 "action_arguments": {},
|
|
|
299 "action_type": "HideDatasetAction",
|
|
|
300 "output_name": "output_file"
|
|
|
301 },
|
|
|
302 "RenameDatasetActionoutput_file": {
|
|
|
303 "action_arguments": {
|
|
|
304 "newname": "Father_reads_1_groomed"
|
|
|
305 },
|
|
|
306 "action_type": "RenameDatasetAction",
|
|
|
307 "output_name": "output_file"
|
|
|
308 }
|
|
|
309 },
|
|
|
310 "tool_errors": null,
|
|
|
311 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
312 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
313 "tool_version": "1.0.4",
|
|
|
314 "type": "tool",
|
|
|
315 "user_outputs": []
|
|
|
316 },
|
|
|
317 "11": {
|
|
|
318 "annotation": "",
|
|
|
319 "id": 11,
|
|
|
320 "input_connections": {
|
|
|
321 "input_file": {
|
|
|
322 "id": 3,
|
|
|
323 "output_name": "output"
|
|
|
324 }
|
|
|
325 },
|
|
|
326 "inputs": [],
|
|
|
327 "name": "FASTQ Groomer",
|
|
|
328 "outputs": [
|
|
|
329 {
|
|
|
330 "name": "output_file",
|
|
|
331 "type": "fastqsanger"
|
|
|
332 }
|
|
|
333 ],
|
|
|
334 "position": {
|
|
|
335 "left": 400.7083740234375,
|
|
|
336 "top": 668.4375
|
|
|
337 },
|
|
|
338 "post_job_actions": {
|
|
|
339 "HideDatasetActionoutput_file": {
|
|
|
340 "action_arguments": {},
|
|
|
341 "action_type": "HideDatasetAction",
|
|
|
342 "output_name": "output_file"
|
|
|
343 },
|
|
|
344 "RenameDatasetActionoutput_file": {
|
|
|
345 "action_arguments": {
|
|
|
346 "newname": "Father_reads_2_groomed"
|
|
|
347 },
|
|
|
348 "action_type": "RenameDatasetAction",
|
|
|
349 "output_name": "output_file"
|
|
|
350 }
|
|
|
351 },
|
|
|
352 "tool_errors": null,
|
|
|
353 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
354 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
355 "tool_version": "1.0.4",
|
|
|
356 "type": "tool",
|
|
|
357 "user_outputs": []
|
|
|
358 },
|
|
|
359 "12": {
|
|
|
360 "annotation": "",
|
|
|
361 "id": 12,
|
|
|
362 "input_connections": {
|
|
|
363 "input_file": {
|
|
|
364 "id": 4,
|
|
|
365 "output_name": "output"
|
|
|
366 }
|
|
|
367 },
|
|
|
368 "inputs": [],
|
|
|
369 "name": "FASTQ Groomer",
|
|
|
370 "outputs": [
|
|
|
371 {
|
|
|
372 "name": "output_file",
|
|
|
373 "type": "fastqsanger"
|
|
|
374 }
|
|
|
375 ],
|
|
|
376 "position": {
|
|
|
377 "left": 397.6875,
|
|
|
378 "top": 790.4375
|
|
|
379 },
|
|
|
380 "post_job_actions": {
|
|
|
381 "HideDatasetActionoutput_file": {
|
|
|
382 "action_arguments": {},
|
|
|
383 "action_type": "HideDatasetAction",
|
|
|
384 "output_name": "output_file"
|
|
|
385 },
|
|
|
386 "RenameDatasetActionoutput_file": {
|
|
|
387 "action_arguments": {
|
|
|
388 "newname": "Daughter_reads_1_groomed"
|
|
|
389 },
|
|
|
390 "action_type": "RenameDatasetAction",
|
|
|
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\": \"\\\"illumina\\\"\", \"__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 "13": {
|
|
|
402 "annotation": "",
|
|
|
403 "id": 13,
|
|
|
404 "input_connections": {
|
|
|
405 "input_file": {
|
|
|
406 "id": 5,
|
|
|
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": {
|
|
|
419 "left": 404.6875,
|
|
|
420 "top": 910.4375
|
|
|
421 },
|
|
|
422 "post_job_actions": {
|
|
|
423 "HideDatasetActionoutput_file": {
|
|
|
424 "action_arguments": {},
|
|
|
425 "action_type": "HideDatasetAction",
|
|
|
426 "output_name": "output_file"
|
|
|
427 },
|
|
|
428 "RenameDatasetActionoutput_file": {
|
|
|
429 "action_arguments": {
|
|
|
430 "newname": "Daughter_reads_2_groomed"
|
|
|
431 },
|
|
|
432 "action_type": "RenameDatasetAction",
|
|
|
433 "output_name": "output_file"
|
|
|
434 }
|
|
|
435 },
|
|
|
436 "tool_errors": null,
|
|
|
437 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
438 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
439 "tool_version": "1.0.4",
|
|
|
440 "type": "tool",
|
|
|
441 "user_outputs": []
|
|
|
442 },
|
|
|
443 "14": {
|
|
|
444 "annotation": "",
|
|
|
445 "id": 14,
|
|
|
446 "input_connections": {
|
|
|
447 "input_file": {
|
|
|
448 "id": 6,
|
|
|
449 "output_name": "output"
|
|
|
450 }
|
|
|
451 },
|
|
|
452 "inputs": [],
|
|
|
453 "name": "FASTQ Groomer",
|
|
|
454 "outputs": [
|
|
|
455 {
|
|
|
456 "name": "output_file",
|
|
|
457 "type": "fastqsanger"
|
|
|
458 }
|
|
|
459 ],
|
|
|
460 "position": {
|
|
|
461 "left": 394.6875,
|
|
|
462 "top": 1032.4375
|
|
|
463 },
|
|
|
464 "post_job_actions": {
|
|
|
465 "HideDatasetActionoutput_file": {
|
|
|
466 "action_arguments": {},
|
|
|
467 "action_type": "HideDatasetAction",
|
|
|
468 "output_name": "output_file"
|
|
|
469 },
|
|
|
470 "RenameDatasetActionoutput_file": {
|
|
|
471 "action_arguments": {
|
|
|
472 "newname": "Son_reads_1_groomed"
|
|
|
473 },
|
|
|
474 "action_type": "RenameDatasetAction",
|
|
|
475 "output_name": "output_file"
|
|
|
476 }
|
|
|
477 },
|
|
|
478 "tool_errors": null,
|
|
|
479 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
480 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
481 "tool_version": "1.0.4",
|
|
|
482 "type": "tool",
|
|
|
483 "user_outputs": []
|
|
|
484 },
|
|
|
485 "15": {
|
|
|
486 "annotation": "",
|
|
|
487 "id": 15,
|
|
|
488 "input_connections": {
|
|
|
489 "input_file": {
|
|
|
490 "id": 7,
|
|
|
491 "output_name": "output"
|
|
|
492 }
|
|
|
493 },
|
|
|
494 "inputs": [],
|
|
|
495 "name": "FASTQ Groomer",
|
|
|
496 "outputs": [
|
|
|
497 {
|
|
|
498 "name": "output_file",
|
|
|
499 "type": "fastqsanger"
|
|
|
500 }
|
|
|
501 ],
|
|
|
502 "position": {
|
|
|
503 "left": 404.6875,
|
|
|
504 "top": 1162.4375
|
|
|
505 },
|
|
|
506 "post_job_actions": {
|
|
|
507 "HideDatasetActionoutput_file": {
|
|
|
508 "action_arguments": {},
|
|
|
509 "action_type": "HideDatasetAction",
|
|
|
510 "output_name": "output_file"
|
|
|
511 },
|
|
|
512 "RenameDatasetActionoutput_file": {
|
|
|
513 "action_arguments": {
|
|
|
514 "newname": "Son_reads_2_groomed"
|
|
|
515 },
|
|
|
516 "action_type": "RenameDatasetAction",
|
|
|
517 "output_name": "output_file"
|
|
|
518 }
|
|
|
519 },
|
|
|
520 "tool_errors": null,
|
|
|
521 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4",
|
|
|
522 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"illumina\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}",
|
|
|
523 "tool_version": "1.0.4",
|
|
|
524 "type": "tool",
|
|
|
525 "user_outputs": []
|
|
|
526 },
|
|
|
527 "16": {
|
|
|
528 "annotation": "",
|
|
|
529 "id": 16,
|
|
|
530 "input_connections": {
|
|
|
531 "input1": {
|
|
|
532 "id": 10,
|
|
|
533 "output_name": "output_file"
|
|
|
534 },
|
|
|
535 "queries_0|input2": {
|
|
|
536 "id": 14,
|
|
|
537 "output_name": "output_file"
|
|
|
538 }
|
|
|
539 },
|
|
|
540 "inputs": [],
|
|
|
541 "name": "Concatenate datasets",
|
|
|
542 "outputs": [
|
|
|
543 {
|
|
|
544 "name": "out_file1",
|
|
|
545 "type": "input"
|
|
|
546 }
|
|
|
547 ],
|
|
|
548 "position": {
|
|
|
549 "left": 894.166748046875,
|
|
|
550 "top": 205
|
|
|
551 },
|
|
|
552 "post_job_actions": {
|
|
|
553 "RenameDatasetActionout_file1": {
|
|
|
554 "action_arguments": {
|
|
|
555 "newname": "male_1.fastq"
|
|
|
556 },
|
|
|
557 "action_type": "RenameDatasetAction",
|
|
|
558 "output_name": "out_file1"
|
|
|
559 }
|
|
|
560 },
|
|
|
561 "tool_errors": null,
|
|
|
562 "tool_id": "cat1",
|
|
|
563 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
|
|
|
564 "tool_version": "1.0.0",
|
|
|
565 "type": "tool",
|
|
|
566 "user_outputs": []
|
|
|
567 },
|
|
|
568 "17": {
|
|
|
569 "annotation": "",
|
|
|
570 "id": 17,
|
|
|
571 "input_connections": {
|
|
|
572 "input1": {
|
|
|
573 "id": 11,
|
|
|
574 "output_name": "output_file"
|
|
|
575 },
|
|
|
576 "queries_0|input2": {
|
|
|
577 "id": 15,
|
|
|
578 "output_name": "output_file"
|
|
|
579 }
|
|
|
580 },
|
|
|
581 "inputs": [],
|
|
|
582 "name": "Concatenate datasets",
|
|
|
583 "outputs": [
|
|
|
584 {
|
|
|
585 "name": "out_file1",
|
|
|
586 "type": "input"
|
|
|
587 }
|
|
|
588 ],
|
|
|
589 "position": {
|
|
|
590 "left": 895.1875,
|
|
|
591 "top": 337.0208435058594
|
|
|
592 },
|
|
|
593 "post_job_actions": {
|
|
|
594 "RenameDatasetActionout_file1": {
|
|
|
595 "action_arguments": {
|
|
|
596 "newname": "male_2.fastq"
|
|
|
597 },
|
|
|
598 "action_type": "RenameDatasetAction",
|
|
|
599 "output_name": "out_file1"
|
|
|
600 }
|
|
|
601 },
|
|
|
602 "tool_errors": null,
|
|
|
603 "tool_id": "cat1",
|
|
|
604 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
|
|
|
605 "tool_version": "1.0.0",
|
|
|
606 "type": "tool",
|
|
|
607 "user_outputs": []
|
|
|
608 },
|
|
|
609 "18": {
|
|
|
610 "annotation": "",
|
|
|
611 "id": 18,
|
|
|
612 "input_connections": {
|
|
|
613 "inputs|left_input": {
|
|
|
614 "id": 16,
|
|
|
615 "output_name": "out_file1"
|
|
|
616 },
|
|
|
617 "inputs|right_input": {
|
|
|
618 "id": 17,
|
|
|
619 "output_name": "out_file1"
|
|
|
620 }
|
|
|
621 },
|
|
|
622 "inputs": [],
|
|
|
623 "name": "Trinity",
|
|
|
624 "outputs": [
|
|
|
625 {
|
|
|
626 "name": "trinity_log",
|
|
|
627 "type": "txt"
|
|
|
628 },
|
|
|
629 {
|
|
|
630 "name": "assembled_transcripts",
|
|
|
631 "type": "fasta"
|
|
|
632 }
|
|
|
633 ],
|
|
|
634 "position": {
|
|
|
635 "left": 1187.5,
|
|
|
636 "top": 233.875
|
|
|
637 },
|
|
|
638 "post_job_actions": {
|
|
|
639 "RenameDatasetActionassembled_transcripts": {
|
|
|
640 "action_arguments": {
|
|
|
641 "newname": "Trinity.fasta"
|
|
|
642 },
|
|
|
643 "action_type": "RenameDatasetAction",
|
|
|
644 "output_name": "assembled_transcripts"
|
|
|
645 }
|
|
|
646 },
|
|
|
647 "tool_errors": null,
|
|
|
648 "tool_id": "toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1",
|
|
|
649 "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\\\"\"}",
|
|
|
650 "tool_version": "0.0.1",
|
|
|
651 "type": "tool",
|
|
|
652 "user_outputs": []
|
|
|
653 },
|
|
|
654 "19": {
|
|
|
655 "annotation": "",
|
|
|
656 "id": 19,
|
|
|
657 "input_connections": {
|
|
|
658 "input1": {
|
|
|
659 "id": 18,
|
|
|
660 "output_name": "assembled_transcripts"
|
|
|
661 }
|
|
|
662 },
|
|
|
663 "inputs": [],
|
|
|
664 "name": "reformat_trinity_header",
|
|
|
665 "outputs": [
|
|
|
666 {
|
|
|
667 "name": "output",
|
|
|
668 "type": "fasta"
|
|
|
669 }
|
|
|
670 ],
|
|
|
671 "position": {
|
|
|
672 "left": 1448,
|
|
|
673 "top": 235.875
|
|
|
674 },
|
|
|
675 "post_job_actions": {
|
|
|
676 "RenameDatasetActionoutput": {
|
|
|
677 "action_arguments": {
|
|
|
678 "newname": "Trinity_reformatted.fasta"
|
|
|
679 },
|
|
|
680 "action_type": "RenameDatasetAction",
|
|
|
681 "output_name": "output"
|
|
|
682 }
|
|
|
683 },
|
|
|
684 "tool_errors": null,
|
|
|
685 "tool_id": "reformat_trinity_header",
|
|
|
686 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
|
|
687 "tool_version": "1.0.0",
|
|
|
688 "type": "tool",
|
|
|
689 "user_outputs": []
|
|
|
690 },
|
|
|
691 "20": {
|
|
|
692 "annotation": "",
|
|
|
693 "id": 20,
|
|
|
694 "input_connections": {
|
|
|
695 "genomeSource|ownFile": {
|
|
|
696 "id": 19,
|
|
|
697 "output_name": "output"
|
|
|
698 },
|
|
|
699 "paired|input1": {
|
|
|
700 "id": 8,
|
|
|
701 "output_name": "output_file"
|
|
|
702 },
|
|
|
703 "paired|input2": {
|
|
|
704 "id": 9,
|
|
|
705 "output_name": "output_file"
|
|
|
706 }
|
|
|
707 },
|
|
|
708 "inputs": [],
|
|
|
709 "name": "Map with BWA for Illumina",
|
|
|
710 "outputs": [
|
|
|
711 {
|
|
|
712 "name": "output",
|
|
|
713 "type": "sam"
|
|
|
714 }
|
|
|
715 ],
|
|
|
716 "position": {
|
|
|
717 "left": 906.1875,
|
|
|
718 "top": 514.9375
|
|
|
719 },
|
|
|
720 "post_job_actions": {
|
|
|
721 "RenameDatasetActionoutput": {
|
|
|
722 "action_arguments": {
|
|
|
723 "newname": "mother_male.sam"
|
|
|
724 },
|
|
|
725 "action_type": "RenameDatasetAction",
|
|
|
726 "output_name": "output"
|
|
|
727 }
|
|
|
728 },
|
|
|
729 "tool_errors": null,
|
|
|
730 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
731 "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\\\"\"}",
|
|
|
732 "tool_version": "1.2.3",
|
|
|
733 "type": "tool",
|
|
|
734 "user_outputs": []
|
|
|
735 },
|
|
|
736 "21": {
|
|
|
737 "annotation": "",
|
|
|
738 "id": 21,
|
|
|
739 "input_connections": {
|
|
|
740 "genomeSource|ownFile": {
|
|
|
741 "id": 19,
|
|
|
742 "output_name": "output"
|
|
|
743 },
|
|
|
744 "paired|input1": {
|
|
|
745 "id": 10,
|
|
|
746 "output_name": "output_file"
|
|
|
747 },
|
|
|
748 "paired|input2": {
|
|
|
749 "id": 11,
|
|
|
750 "output_name": "output_file"
|
|
|
751 }
|
|
|
752 },
|
|
|
753 "inputs": [],
|
|
|
754 "name": "Map with BWA for Illumina",
|
|
|
755 "outputs": [
|
|
|
756 {
|
|
|
757 "name": "output",
|
|
|
758 "type": "sam"
|
|
|
759 }
|
|
|
760 ],
|
|
|
761 "position": {
|
|
|
762 "left": 916.1875,
|
|
|
763 "top": 684.9375
|
|
|
764 },
|
|
|
765 "post_job_actions": {
|
|
|
766 "RenameDatasetActionoutput": {
|
|
|
767 "action_arguments": {
|
|
|
768 "newname": "father_male.sam"
|
|
|
769 },
|
|
|
770 "action_type": "RenameDatasetAction",
|
|
|
771 "output_name": "output"
|
|
|
772 }
|
|
|
773 },
|
|
|
774 "tool_errors": null,
|
|
|
775 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
776 "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\\\"\"}",
|
|
|
777 "tool_version": "1.2.3",
|
|
|
778 "type": "tool",
|
|
|
779 "user_outputs": []
|
|
|
780 },
|
|
|
781 "22": {
|
|
|
782 "annotation": "",
|
|
|
783 "id": 22,
|
|
|
784 "input_connections": {
|
|
|
785 "genomeSource|ownFile": {
|
|
|
786 "id": 19,
|
|
|
787 "output_name": "output"
|
|
|
788 },
|
|
|
789 "paired|input1": {
|
|
|
790 "id": 12,
|
|
|
791 "output_name": "output_file"
|
|
|
792 },
|
|
|
793 "paired|input2": {
|
|
|
794 "id": 13,
|
|
|
795 "output_name": "output_file"
|
|
|
796 }
|
|
|
797 },
|
|
|
798 "inputs": [],
|
|
|
799 "name": "Map with BWA for Illumina",
|
|
|
800 "outputs": [
|
|
|
801 {
|
|
|
802 "name": "output",
|
|
|
803 "type": "sam"
|
|
|
804 }
|
|
|
805 ],
|
|
|
806 "position": {
|
|
|
807 "left": 911.1875,
|
|
|
808 "top": 847.875
|
|
|
809 },
|
|
|
810 "post_job_actions": {
|
|
|
811 "RenameDatasetActionoutput": {
|
|
|
812 "action_arguments": {
|
|
|
813 "newname": "daughter_male.sam"
|
|
|
814 },
|
|
|
815 "action_type": "RenameDatasetAction",
|
|
|
816 "output_name": "output"
|
|
|
817 }
|
|
|
818 },
|
|
|
819 "tool_errors": null,
|
|
|
820 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
821 "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\\\"\"}",
|
|
|
822 "tool_version": "1.2.3",
|
|
|
823 "type": "tool",
|
|
|
824 "user_outputs": []
|
|
|
825 },
|
|
|
826 "23": {
|
|
|
827 "annotation": "",
|
|
|
828 "id": 23,
|
|
|
829 "input_connections": {
|
|
|
830 "genomeSource|ownFile": {
|
|
|
831 "id": 19,
|
|
|
832 "output_name": "output"
|
|
|
833 },
|
|
|
834 "paired|input1": {
|
|
|
835 "id": 14,
|
|
|
836 "output_name": "output_file"
|
|
|
837 },
|
|
|
838 "paired|input2": {
|
|
|
839 "id": 15,
|
|
|
840 "output_name": "output_file"
|
|
|
841 }
|
|
|
842 },
|
|
|
843 "inputs": [],
|
|
|
844 "name": "Map with BWA for Illumina",
|
|
|
845 "outputs": [
|
|
|
846 {
|
|
|
847 "name": "output",
|
|
|
848 "type": "sam"
|
|
|
849 }
|
|
|
850 ],
|
|
|
851 "position": {
|
|
|
852 "left": 918.1875,
|
|
|
853 "top": 1024.916748046875
|
|
|
854 },
|
|
|
855 "post_job_actions": {
|
|
|
856 "RenameDatasetActionoutput": {
|
|
|
857 "action_arguments": {
|
|
|
858 "newname": "son_male.sam"
|
|
|
859 },
|
|
|
860 "action_type": "RenameDatasetAction",
|
|
|
861 "output_name": "output"
|
|
|
862 }
|
|
|
863 },
|
|
|
864 "tool_errors": null,
|
|
|
865 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
866 "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\\\"\"}",
|
|
|
867 "tool_version": "1.2.3",
|
|
|
868 "type": "tool",
|
|
|
869 "user_outputs": []
|
|
|
870 },
|
|
|
871 "24": {
|
|
|
872 "annotation": "",
|
|
|
873 "id": 24,
|
|
|
874 "input_connections": {
|
|
|
875 "source|input1": {
|
|
|
876 "id": 20,
|
|
|
877 "output_name": "output"
|
|
|
878 },
|
|
|
879 "source|ref_file": {
|
|
|
880 "id": 19,
|
|
|
881 "output_name": "output"
|
|
|
882 }
|
|
|
883 },
|
|
|
884 "inputs": [],
|
|
|
885 "name": "SAM-to-BAM",
|
|
|
886 "outputs": [
|
|
|
887 {
|
|
|
888 "name": "output1",
|
|
|
889 "type": "bam"
|
|
|
890 }
|
|
|
891 ],
|
|
|
892 "position": {
|
|
|
893 "left": 1179.6875,
|
|
|
894 "top": 503.9375
|
|
|
895 },
|
|
|
896 "post_job_actions": {
|
|
|
897 "RenameDatasetActionoutput1": {
|
|
|
898 "action_arguments": {
|
|
|
899 "newname": "mother_male.bam"
|
|
|
900 },
|
|
|
901 "action_type": "RenameDatasetAction",
|
|
|
902 "output_name": "output1"
|
|
|
903 }
|
|
|
904 },
|
|
|
905 "tool_errors": null,
|
|
|
906 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
907 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
908 "tool_version": "1.1.4",
|
|
|
909 "type": "tool",
|
|
|
910 "user_outputs": []
|
|
|
911 },
|
|
|
912 "25": {
|
|
|
913 "annotation": "",
|
|
|
914 "id": 25,
|
|
|
915 "input_connections": {
|
|
|
916 "source|input1": {
|
|
|
917 "id": 21,
|
|
|
918 "output_name": "output"
|
|
|
919 },
|
|
|
920 "source|ref_file": {
|
|
|
921 "id": 19,
|
|
|
922 "output_name": "output"
|
|
|
923 }
|
|
|
924 },
|
|
|
925 "inputs": [],
|
|
|
926 "name": "SAM-to-BAM",
|
|
|
927 "outputs": [
|
|
|
928 {
|
|
|
929 "name": "output1",
|
|
|
930 "type": "bam"
|
|
|
931 }
|
|
|
932 ],
|
|
|
933 "position": {
|
|
|
934 "left": 1172.6875,
|
|
|
935 "top": 682.9375
|
|
|
936 },
|
|
|
937 "post_job_actions": {
|
|
|
938 "RenameDatasetActionoutput1": {
|
|
|
939 "action_arguments": {
|
|
|
940 "newname": "father_male.bam"
|
|
|
941 },
|
|
|
942 "action_type": "RenameDatasetAction",
|
|
|
943 "output_name": "output1"
|
|
|
944 }
|
|
|
945 },
|
|
|
946 "tool_errors": null,
|
|
|
947 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
948 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
949 "tool_version": "1.1.4",
|
|
|
950 "type": "tool",
|
|
|
951 "user_outputs": []
|
|
|
952 },
|
|
|
953 "26": {
|
|
|
954 "annotation": "",
|
|
|
955 "id": 26,
|
|
|
956 "input_connections": {
|
|
|
957 "source|input1": {
|
|
|
958 "id": 22,
|
|
|
959 "output_name": "output"
|
|
|
960 },
|
|
|
961 "source|ref_file": {
|
|
|
962 "id": 19,
|
|
|
963 "output_name": "output"
|
|
|
964 }
|
|
|
965 },
|
|
|
966 "inputs": [],
|
|
|
967 "name": "SAM-to-BAM",
|
|
|
968 "outputs": [
|
|
|
969 {
|
|
|
970 "name": "output1",
|
|
|
971 "type": "bam"
|
|
|
972 }
|
|
|
973 ],
|
|
|
974 "position": {
|
|
|
975 "left": 1186.6875,
|
|
|
976 "top": 854.9375
|
|
|
977 },
|
|
|
978 "post_job_actions": {
|
|
|
979 "RenameDatasetActionoutput1": {
|
|
|
980 "action_arguments": {
|
|
|
981 "newname": "daughter_male.bam"
|
|
|
982 },
|
|
|
983 "action_type": "RenameDatasetAction",
|
|
|
984 "output_name": "output1"
|
|
|
985 }
|
|
|
986 },
|
|
|
987 "tool_errors": null,
|
|
|
988 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
989 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
990 "tool_version": "1.1.4",
|
|
|
991 "type": "tool",
|
|
|
992 "user_outputs": []
|
|
|
993 },
|
|
|
994 "27": {
|
|
|
995 "annotation": "",
|
|
|
996 "id": 27,
|
|
|
997 "input_connections": {
|
|
|
998 "source|input1": {
|
|
|
999 "id": 23,
|
|
|
1000 "output_name": "output"
|
|
|
1001 },
|
|
|
1002 "source|ref_file": {
|
|
|
1003 "id": 19,
|
|
|
1004 "output_name": "output"
|
|
|
1005 }
|
|
|
1006 },
|
|
|
1007 "inputs": [],
|
|
|
1008 "name": "SAM-to-BAM",
|
|
|
1009 "outputs": [
|
|
|
1010 {
|
|
|
1011 "name": "output1",
|
|
|
1012 "type": "bam"
|
|
|
1013 }
|
|
|
1014 ],
|
|
|
1015 "position": {
|
|
|
1016 "left": 1197.6875,
|
|
|
1017 "top": 1022.9375
|
|
|
1018 },
|
|
|
1019 "post_job_actions": {
|
|
|
1020 "RenameDatasetActionoutput1": {
|
|
|
1021 "action_arguments": {
|
|
|
1022 "newname": "son_male.bam"
|
|
|
1023 },
|
|
|
1024 "action_type": "RenameDatasetAction",
|
|
|
1025 "output_name": "output1"
|
|
|
1026 }
|
|
|
1027 },
|
|
|
1028 "tool_errors": null,
|
|
|
1029 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
1030 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
1031 "tool_version": "1.1.4",
|
|
|
1032 "type": "tool",
|
|
|
1033 "user_outputs": []
|
|
|
1034 },
|
|
|
1035 "28": {
|
|
|
1036 "annotation": "",
|
|
|
1037 "id": 28,
|
|
|
1038 "input_connections": {
|
|
|
1039 "input1": {
|
|
|
1040 "id": 24,
|
|
|
1041 "output_name": "output1"
|
|
|
1042 }
|
|
|
1043 },
|
|
|
1044 "inputs": [],
|
|
|
1045 "name": "sort",
|
|
|
1046 "outputs": [
|
|
|
1047 {
|
|
|
1048 "name": "output1",
|
|
|
1049 "type": "bam"
|
|
|
1050 }
|
|
|
1051 ],
|
|
|
1052 "position": {
|
|
|
1053 "left": 1388.8333740234375,
|
|
|
1054 "top": 511.3333740234375
|
|
|
1055 },
|
|
|
1056 "post_job_actions": {
|
|
|
1057 "RenameDatasetActionoutput1": {
|
|
|
1058 "action_arguments": {
|
|
|
1059 "newname": "mother_male.sorted.bam"
|
|
|
1060 },
|
|
|
1061 "action_type": "RenameDatasetAction",
|
|
|
1062 "output_name": "output1"
|
|
|
1063 }
|
|
|
1064 },
|
|
|
1065 "tool_errors": null,
|
|
|
1066 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
1067 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
1068 "tool_version": "1.0.2",
|
|
|
1069 "type": "tool",
|
|
|
1070 "user_outputs": []
|
|
|
1071 },
|
|
|
1072 "29": {
|
|
|
1073 "annotation": "",
|
|
|
1074 "id": 29,
|
|
|
1075 "input_connections": {
|
|
|
1076 "input1": {
|
|
|
1077 "id": 25,
|
|
|
1078 "output_name": "output1"
|
|
|
1079 }
|
|
|
1080 },
|
|
|
1081 "inputs": [],
|
|
|
1082 "name": "sort",
|
|
|
1083 "outputs": [
|
|
|
1084 {
|
|
|
1085 "name": "output1",
|
|
|
1086 "type": "bam"
|
|
|
1087 }
|
|
|
1088 ],
|
|
|
1089 "position": {
|
|
|
1090 "left": 1384.8333740234375,
|
|
|
1091 "top": 678.3333740234375
|
|
|
1092 },
|
|
|
1093 "post_job_actions": {
|
|
|
1094 "RenameDatasetActionoutput1": {
|
|
|
1095 "action_arguments": {
|
|
|
1096 "newname": "father_male.sorted.bam"
|
|
|
1097 },
|
|
|
1098 "action_type": "RenameDatasetAction",
|
|
|
1099 "output_name": "output1"
|
|
|
1100 }
|
|
|
1101 },
|
|
|
1102 "tool_errors": null,
|
|
|
1103 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
1104 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
1105 "tool_version": "1.0.2",
|
|
|
1106 "type": "tool",
|
|
|
1107 "user_outputs": []
|
|
|
1108 },
|
|
|
1109 "30": {
|
|
|
1110 "annotation": "",
|
|
|
1111 "id": 30,
|
|
|
1112 "input_connections": {
|
|
|
1113 "input1": {
|
|
|
1114 "id": 26,
|
|
|
1115 "output_name": "output1"
|
|
|
1116 }
|
|
|
1117 },
|
|
|
1118 "inputs": [],
|
|
|
1119 "name": "sort",
|
|
|
1120 "outputs": [
|
|
|
1121 {
|
|
|
1122 "name": "output1",
|
|
|
1123 "type": "bam"
|
|
|
1124 }
|
|
|
1125 ],
|
|
|
1126 "position": {
|
|
|
1127 "left": 1401.8333740234375,
|
|
|
1128 "top": 854.3333740234375
|
|
|
1129 },
|
|
|
1130 "post_job_actions": {
|
|
|
1131 "RenameDatasetActionoutput1": {
|
|
|
1132 "action_arguments": {
|
|
|
1133 "newname": "daughter_male.sorted.bam"
|
|
|
1134 },
|
|
|
1135 "action_type": "RenameDatasetAction",
|
|
|
1136 "output_name": "output1"
|
|
|
1137 }
|
|
|
1138 },
|
|
|
1139 "tool_errors": null,
|
|
|
1140 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
1141 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
1142 "tool_version": "1.0.2",
|
|
|
1143 "type": "tool",
|
|
|
1144 "user_outputs": []
|
|
|
1145 },
|
|
|
1146 "31": {
|
|
|
1147 "annotation": "",
|
|
|
1148 "id": 31,
|
|
|
1149 "input_connections": {
|
|
|
1150 "input1": {
|
|
|
1151 "id": 27,
|
|
|
1152 "output_name": "output1"
|
|
|
1153 }
|
|
|
1154 },
|
|
|
1155 "inputs": [],
|
|
|
1156 "name": "sort",
|
|
|
1157 "outputs": [
|
|
|
1158 {
|
|
|
1159 "name": "output1",
|
|
|
1160 "type": "bam"
|
|
|
1161 }
|
|
|
1162 ],
|
|
|
1163 "position": {
|
|
|
1164 "left": 1399.8333740234375,
|
|
|
1165 "top": 1022.3333740234375
|
|
|
1166 },
|
|
|
1167 "post_job_actions": {
|
|
|
1168 "RenameDatasetActionoutput1": {
|
|
|
1169 "action_arguments": {
|
|
|
1170 "newname": "son_male.sorted.bam"
|
|
|
1171 },
|
|
|
1172 "action_type": "RenameDatasetAction",
|
|
|
1173 "output_name": "output1"
|
|
|
1174 }
|
|
|
1175 },
|
|
|
1176 "tool_errors": null,
|
|
|
1177 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
1178 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
1179 "tool_version": "1.0.2",
|
|
|
1180 "type": "tool",
|
|
|
1181 "user_outputs": []
|
|
|
1182 },
|
|
|
1183 "32": {
|
|
|
1184 "annotation": "",
|
|
|
1185 "id": 32,
|
|
|
1186 "input_connections": {
|
|
|
1187 "input_file": {
|
|
|
1188 "id": 28,
|
|
|
1189 "output_name": "output1"
|
|
|
1190 }
|
|
|
1191 },
|
|
|
1192 "inputs": [],
|
|
|
1193 "name": "Mark Duplicate reads",
|
|
|
1194 "outputs": [
|
|
|
1195 {
|
|
|
1196 "name": "out_file",
|
|
|
1197 "type": "bam"
|
|
|
1198 },
|
|
|
1199 {
|
|
|
1200 "name": "html_file",
|
|
|
1201 "type": "html"
|
|
|
1202 }
|
|
|
1203 ],
|
|
|
1204 "position": {
|
|
|
1205 "left": 1572.8333740234375,
|
|
|
1206 "top": 514.3333740234375
|
|
|
1207 },
|
|
|
1208 "post_job_actions": {
|
|
|
1209 "RenameDatasetActionhtml_file": {
|
|
|
1210 "action_arguments": {
|
|
|
1211 "newname": "mother_male.deduplicated.html"
|
|
|
1212 },
|
|
|
1213 "action_type": "RenameDatasetAction",
|
|
|
1214 "output_name": "html_file"
|
|
|
1215 },
|
|
|
1216 "RenameDatasetActionout_file": {
|
|
|
1217 "action_arguments": {
|
|
|
1218 "newname": "mother_male.deduplicated.bam"
|
|
|
1219 },
|
|
|
1220 "action_type": "RenameDatasetAction",
|
|
|
1221 "output_name": "out_file"
|
|
|
1222 }
|
|
|
1223 },
|
|
|
1224 "tool_errors": null,
|
|
|
1225 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1226 "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\\\"\"}",
|
|
|
1227 "tool_version": "1.56.0",
|
|
|
1228 "type": "tool",
|
|
|
1229 "user_outputs": []
|
|
|
1230 },
|
|
|
1231 "33": {
|
|
|
1232 "annotation": "",
|
|
|
1233 "id": 33,
|
|
|
1234 "input_connections": {
|
|
|
1235 "input_file": {
|
|
|
1236 "id": 29,
|
|
|
1237 "output_name": "output1"
|
|
|
1238 }
|
|
|
1239 },
|
|
|
1240 "inputs": [],
|
|
|
1241 "name": "Mark Duplicate reads",
|
|
|
1242 "outputs": [
|
|
|
1243 {
|
|
|
1244 "name": "out_file",
|
|
|
1245 "type": "bam"
|
|
|
1246 },
|
|
|
1247 {
|
|
|
1248 "name": "html_file",
|
|
|
1249 "type": "html"
|
|
|
1250 }
|
|
|
1251 ],
|
|
|
1252 "position": {
|
|
|
1253 "left": 1577.8333740234375,
|
|
|
1254 "top": 684.3333740234375
|
|
|
1255 },
|
|
|
1256 "post_job_actions": {
|
|
|
1257 "RenameDatasetActionhtml_file": {
|
|
|
1258 "action_arguments": {
|
|
|
1259 "newname": "father_male.deduplicated.html"
|
|
|
1260 },
|
|
|
1261 "action_type": "RenameDatasetAction",
|
|
|
1262 "output_name": "html_file"
|
|
|
1263 },
|
|
|
1264 "RenameDatasetActionout_file": {
|
|
|
1265 "action_arguments": {
|
|
|
1266 "newname": "father_male.deduplicated.bam"
|
|
|
1267 },
|
|
|
1268 "action_type": "RenameDatasetAction",
|
|
|
1269 "output_name": "out_file"
|
|
|
1270 }
|
|
|
1271 },
|
|
|
1272 "tool_errors": null,
|
|
|
1273 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1274 "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\\\"\"}",
|
|
|
1275 "tool_version": "1.56.0",
|
|
|
1276 "type": "tool",
|
|
|
1277 "user_outputs": []
|
|
|
1278 },
|
|
|
1279 "34": {
|
|
|
1280 "annotation": "",
|
|
|
1281 "id": 34,
|
|
|
1282 "input_connections": {
|
|
|
1283 "input_file": {
|
|
|
1284 "id": 30,
|
|
|
1285 "output_name": "output1"
|
|
|
1286 }
|
|
|
1287 },
|
|
|
1288 "inputs": [],
|
|
|
1289 "name": "Mark Duplicate reads",
|
|
|
1290 "outputs": [
|
|
|
1291 {
|
|
|
1292 "name": "out_file",
|
|
|
1293 "type": "bam"
|
|
|
1294 },
|
|
|
1295 {
|
|
|
1296 "name": "html_file",
|
|
|
1297 "type": "html"
|
|
|
1298 }
|
|
|
1299 ],
|
|
|
1300 "position": {
|
|
|
1301 "left": 1580.8333740234375,
|
|
|
1302 "top": 855.3333740234375
|
|
|
1303 },
|
|
|
1304 "post_job_actions": {
|
|
|
1305 "RenameDatasetActionhtml_file": {
|
|
|
1306 "action_arguments": {
|
|
|
1307 "newname": "daughter_male.deduplicated.html"
|
|
|
1308 },
|
|
|
1309 "action_type": "RenameDatasetAction",
|
|
|
1310 "output_name": "html_file"
|
|
|
1311 },
|
|
|
1312 "RenameDatasetActionout_file": {
|
|
|
1313 "action_arguments": {
|
|
|
1314 "newname": "daughter_male.deduplicated.bam"
|
|
|
1315 },
|
|
|
1316 "action_type": "RenameDatasetAction",
|
|
|
1317 "output_name": "out_file"
|
|
|
1318 }
|
|
|
1319 },
|
|
|
1320 "tool_errors": null,
|
|
|
1321 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1322 "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\\\"\"}",
|
|
|
1323 "tool_version": "1.56.0",
|
|
|
1324 "type": "tool",
|
|
|
1325 "user_outputs": []
|
|
|
1326 },
|
|
|
1327 "35": {
|
|
|
1328 "annotation": "",
|
|
|
1329 "id": 35,
|
|
|
1330 "input_connections": {
|
|
|
1331 "input_file": {
|
|
|
1332 "id": 31,
|
|
|
1333 "output_name": "output1"
|
|
|
1334 }
|
|
|
1335 },
|
|
|
1336 "inputs": [],
|
|
|
1337 "name": "Mark Duplicate reads",
|
|
|
1338 "outputs": [
|
|
|
1339 {
|
|
|
1340 "name": "out_file",
|
|
|
1341 "type": "bam"
|
|
|
1342 },
|
|
|
1343 {
|
|
|
1344 "name": "html_file",
|
|
|
1345 "type": "html"
|
|
|
1346 }
|
|
|
1347 ],
|
|
|
1348 "position": {
|
|
|
1349 "left": 1585.8333740234375,
|
|
|
1350 "top": 1027.3333740234375
|
|
|
1351 },
|
|
|
1352 "post_job_actions": {
|
|
|
1353 "RenameDatasetActionhtml_file": {
|
|
|
1354 "action_arguments": {
|
|
|
1355 "newname": "son_male.deduplicated.html"
|
|
|
1356 },
|
|
|
1357 "action_type": "RenameDatasetAction",
|
|
|
1358 "output_name": "html_file"
|
|
|
1359 },
|
|
|
1360 "RenameDatasetActionout_file": {
|
|
|
1361 "action_arguments": {
|
|
|
1362 "newname": "son_male.deduplicated.bam"
|
|
|
1363 },
|
|
|
1364 "action_type": "RenameDatasetAction",
|
|
|
1365 "output_name": "out_file"
|
|
|
1366 }
|
|
|
1367 },
|
|
|
1368 "tool_errors": null,
|
|
|
1369 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1370 "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\\\"\"}",
|
|
|
1371 "tool_version": "1.56.0",
|
|
|
1372 "type": "tool",
|
|
|
1373 "user_outputs": []
|
|
|
1374 },
|
|
|
1375 "36": {
|
|
|
1376 "annotation": "",
|
|
|
1377 "id": 36,
|
|
|
1378 "input_connections": {
|
|
|
1379 "input1": {
|
|
|
1380 "id": 19,
|
|
|
1381 "output_name": "output"
|
|
|
1382 },
|
|
|
1383 "input2": {
|
|
|
1384 "id": 32,
|
|
|
1385 "output_name": "out_file"
|
|
|
1386 },
|
|
|
1387 "input3": {
|
|
|
1388 "id": 33,
|
|
|
1389 "output_name": "out_file"
|
|
|
1390 },
|
|
|
1391 "input4": {
|
|
|
1392 "id": 34,
|
|
|
1393 "output_name": "out_file"
|
|
|
1394 },
|
|
|
1395 "input5": {
|
|
|
1396 "id": 35,
|
|
|
1397 "output_name": "out_file"
|
|
|
1398 }
|
|
|
1399 },
|
|
|
1400 "inputs": [],
|
|
|
1401 "name": "LINKYX_Y",
|
|
|
1402 "outputs": [
|
|
|
1403 {
|
|
|
1404 "name": "output",
|
|
|
1405 "type": "txt"
|
|
|
1406 },
|
|
|
1407 {
|
|
|
1408 "name": "output1",
|
|
|
1409 "type": "fasta"
|
|
|
1410 },
|
|
|
1411 {
|
|
|
1412 "name": "output2",
|
|
|
1413 "type": "bam"
|
|
|
1414 },
|
|
|
1415 {
|
|
|
1416 "name": "output3",
|
|
|
1417 "type": "bam"
|
|
|
1418 },
|
|
|
1419 {
|
|
|
1420 "name": "output4",
|
|
|
1421 "type": "bam"
|
|
|
1422 },
|
|
|
1423 {
|
|
|
1424 "name": "output5",
|
|
|
1425 "type": "bam"
|
|
|
1426 }
|
|
|
1427 ],
|
|
|
1428 "position": {
|
|
|
1429 "left": 1874.0625,
|
|
|
1430 "top": 379.3125
|
|
|
1431 },
|
|
|
1432 "post_job_actions": {},
|
|
|
1433 "tool_errors": null,
|
|
|
1434 "tool_id": "LINKYX_Y",
|
|
|
1435 "tool_state": "{\"input2\": \"null\", \"input3\": \"null\", \"input1\": \"null\", \"input4\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input5\": \"null\"}",
|
|
|
1436 "tool_version": "1.0.0",
|
|
|
1437 "type": "tool",
|
|
|
1438 "user_outputs": []
|
|
|
1439 }
|
|
|
1440 }
|
|
|
1441 } |
