|
0
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "linkX",
|
|
|
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": {
|
|
|
20 "left": 244.16668701171875,
|
|
|
21 "top": 295
|
|
|
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": {
|
|
|
43 "left": 230.16668701171875,
|
|
|
44 "top": 443
|
|
|
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": {
|
|
|
66 "left": 227.16668701171875,
|
|
|
67 "top": 598
|
|
|
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": {
|
|
|
89 "left": 206.16668701171875,
|
|
|
90 "top": 688
|
|
|
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": {
|
|
|
112 "left": 199.97918701171875,
|
|
|
113 "top": 847.3333740234375
|
|
|
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": {
|
|
|
135 "left": 205.97918701171875,
|
|
|
136 "top": 966.3333740234375
|
|
|
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": {
|
|
|
158 "left": 215.97918701171875,
|
|
|
159 "top": 1110.3333740234375
|
|
|
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": {
|
|
|
181 "left": 206.97918701171875,
|
|
|
182 "top": 1224.3333740234375
|
|
|
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": {
|
|
|
209 "left": 438.16668701171875,
|
|
|
210 "top": 274
|
|
|
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": {
|
|
|
244 "left": 424.16668701171875,
|
|
|
245 "top": 434
|
|
|
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": {
|
|
|
279 "left": 431.16668701171875,
|
|
|
280 "top": 585
|
|
|
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": {
|
|
|
314 "left": 431.16668701171875,
|
|
|
315 "top": 717
|
|
|
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": {
|
|
|
349 "left": 427,
|
|
|
350 "top": 839.3333740234375
|
|
|
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": {
|
|
|
384 "left": 427,
|
|
|
385 "top": 975.3333740234375
|
|
|
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": {
|
|
|
419 "left": 430,
|
|
|
420 "top": 1096.3333740234375
|
|
|
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": {
|
|
|
454 "left": 440,
|
|
|
455 "top": 1235.3333740234375
|
|
|
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": {
|
|
|
497 "left": 810.166748046875,
|
|
|
498 "top": 106
|
|
|
499 },
|
|
|
500 "post_job_actions": {
|
|
|
501 "RenameDatasetActionassembled_transcripts": {
|
|
|
502 "action_arguments": {
|
|
|
503 "newname": "Trinity.fasta"
|
|
|
504 },
|
|
|
505 "action_type": "RenameDatasetAction",
|
|
|
506 "output_name": "assembled_transcripts"
|
|
|
507 }
|
|
|
508 },
|
|
|
509 "tool_errors": null,
|
|
|
510 "tool_id": "toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1",
|
|
|
511 "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\\\"\"}",
|
|
|
512 "tool_version": "0.0.1",
|
|
|
513 "type": "tool",
|
|
|
514 "user_outputs": []
|
|
|
515 },
|
|
|
516 "17": {
|
|
|
517 "annotation": "",
|
|
|
518 "id": 17,
|
|
|
519 "input_connections": {
|
|
|
520 "input1": {
|
|
|
521 "id": 16,
|
|
|
522 "output_name": "assembled_transcripts"
|
|
|
523 }
|
|
|
524 },
|
|
|
525 "inputs": [],
|
|
|
526 "name": "reformat_trinity_header",
|
|
|
527 "outputs": [
|
|
|
528 {
|
|
|
529 "name": "output",
|
|
|
530 "type": "fasta"
|
|
|
531 }
|
|
|
532 ],
|
|
|
533 "position": {
|
|
|
534 "left": 1153.166748046875,
|
|
|
535 "top": 151.5
|
|
|
536 },
|
|
|
537 "post_job_actions": {
|
|
|
538 "RenameDatasetActionoutput": {
|
|
|
539 "action_arguments": {
|
|
|
540 "newname": "Trinity_reformatted.fasta"
|
|
|
541 },
|
|
|
542 "action_type": "RenameDatasetAction",
|
|
|
543 "output_name": "output"
|
|
|
544 }
|
|
|
545 },
|
|
|
546 "tool_errors": null,
|
|
|
547 "tool_id": "reformat_trinity_header",
|
|
|
548 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
|
|
549 "tool_version": "1.0.0",
|
|
|
550 "type": "tool",
|
|
|
551 "user_outputs": []
|
|
|
552 },
|
|
|
553 "18": {
|
|
|
554 "annotation": "",
|
|
|
555 "id": 18,
|
|
|
556 "input_connections": {
|
|
|
557 "genomeSource|ownFile": {
|
|
|
558 "id": 17,
|
|
|
559 "output_name": "output"
|
|
|
560 },
|
|
|
561 "paired|input1": {
|
|
|
562 "id": 8,
|
|
|
563 "output_name": "output_file"
|
|
|
564 },
|
|
|
565 "paired|input2": {
|
|
|
566 "id": 9,
|
|
|
567 "output_name": "output_file"
|
|
|
568 }
|
|
|
569 },
|
|
|
570 "inputs": [],
|
|
|
571 "name": "Map with BWA for Illumina",
|
|
|
572 "outputs": [
|
|
|
573 {
|
|
|
574 "name": "output",
|
|
|
575 "type": "sam"
|
|
|
576 }
|
|
|
577 ],
|
|
|
578 "position": {
|
|
|
579 "left": 790,
|
|
|
580 "top": 381.3333435058594
|
|
|
581 },
|
|
|
582 "post_job_actions": {
|
|
|
583 "RenameDatasetActionoutput": {
|
|
|
584 "action_arguments": {
|
|
|
585 "newname": "mother.sam"
|
|
|
586 },
|
|
|
587 "action_type": "RenameDatasetAction",
|
|
|
588 "output_name": "output"
|
|
|
589 }
|
|
|
590 },
|
|
|
591 "tool_errors": null,
|
|
|
592 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
593 "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\\\"\"}",
|
|
|
594 "tool_version": "1.2.3",
|
|
|
595 "type": "tool",
|
|
|
596 "user_outputs": []
|
|
|
597 },
|
|
|
598 "19": {
|
|
|
599 "annotation": "",
|
|
|
600 "id": 19,
|
|
|
601 "input_connections": {
|
|
|
602 "genomeSource|ownFile": {
|
|
|
603 "id": 17,
|
|
|
604 "output_name": "output"
|
|
|
605 },
|
|
|
606 "paired|input1": {
|
|
|
607 "id": 10,
|
|
|
608 "output_name": "output_file"
|
|
|
609 },
|
|
|
610 "paired|input2": {
|
|
|
611 "id": 11,
|
|
|
612 "output_name": "output_file"
|
|
|
613 }
|
|
|
614 },
|
|
|
615 "inputs": [],
|
|
|
616 "name": "Map with BWA for Illumina",
|
|
|
617 "outputs": [
|
|
|
618 {
|
|
|
619 "name": "output",
|
|
|
620 "type": "sam"
|
|
|
621 }
|
|
|
622 ],
|
|
|
623 "position": {
|
|
|
624 "left": 746.6666870117188,
|
|
|
625 "top": 628
|
|
|
626 },
|
|
|
627 "post_job_actions": {
|
|
|
628 "RenameDatasetActionoutput": {
|
|
|
629 "action_arguments": {
|
|
|
630 "newname": "father.sam"
|
|
|
631 },
|
|
|
632 "action_type": "RenameDatasetAction",
|
|
|
633 "output_name": "output"
|
|
|
634 }
|
|
|
635 },
|
|
|
636 "tool_errors": null,
|
|
|
637 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
638 "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\\\"\"}",
|
|
|
639 "tool_version": "1.2.3",
|
|
|
640 "type": "tool",
|
|
|
641 "user_outputs": []
|
|
|
642 },
|
|
|
643 "20": {
|
|
|
644 "annotation": "",
|
|
|
645 "id": 20,
|
|
|
646 "input_connections": {
|
|
|
647 "genomeSource|ownFile": {
|
|
|
648 "id": 17,
|
|
|
649 "output_name": "output"
|
|
|
650 },
|
|
|
651 "paired|input1": {
|
|
|
652 "id": 12,
|
|
|
653 "output_name": "output_file"
|
|
|
654 },
|
|
|
655 "paired|input2": {
|
|
|
656 "id": 13,
|
|
|
657 "output_name": "output_file"
|
|
|
658 }
|
|
|
659 },
|
|
|
660 "inputs": [],
|
|
|
661 "name": "Map with BWA for Illumina",
|
|
|
662 "outputs": [
|
|
|
663 {
|
|
|
664 "name": "output",
|
|
|
665 "type": "sam"
|
|
|
666 }
|
|
|
667 ],
|
|
|
668 "position": {
|
|
|
669 "left": 735,
|
|
|
670 "top": 852.3333740234375
|
|
|
671 },
|
|
|
672 "post_job_actions": {
|
|
|
673 "RenameDatasetActionoutput": {
|
|
|
674 "action_arguments": {
|
|
|
675 "newname": "daughter.sam"
|
|
|
676 },
|
|
|
677 "action_type": "RenameDatasetAction",
|
|
|
678 "output_name": "output"
|
|
|
679 }
|
|
|
680 },
|
|
|
681 "tool_errors": null,
|
|
|
682 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
683 "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\\\"\"}",
|
|
|
684 "tool_version": "1.2.3",
|
|
|
685 "type": "tool",
|
|
|
686 "user_outputs": []
|
|
|
687 },
|
|
|
688 "21": {
|
|
|
689 "annotation": "",
|
|
|
690 "id": 21,
|
|
|
691 "input_connections": {
|
|
|
692 "genomeSource|ownFile": {
|
|
|
693 "id": 17,
|
|
|
694 "output_name": "output"
|
|
|
695 },
|
|
|
696 "paired|input1": {
|
|
|
697 "id": 14,
|
|
|
698 "output_name": "output_file"
|
|
|
699 },
|
|
|
700 "paired|input2": {
|
|
|
701 "id": 15,
|
|
|
702 "output_name": "output_file"
|
|
|
703 }
|
|
|
704 },
|
|
|
705 "inputs": [],
|
|
|
706 "name": "Map with BWA for Illumina",
|
|
|
707 "outputs": [
|
|
|
708 {
|
|
|
709 "name": "output",
|
|
|
710 "type": "sam"
|
|
|
711 }
|
|
|
712 ],
|
|
|
713 "position": {
|
|
|
714 "left": 771,
|
|
|
715 "top": 1096.3333740234375
|
|
|
716 },
|
|
|
717 "post_job_actions": {
|
|
|
718 "RenameDatasetActionoutput": {
|
|
|
719 "action_arguments": {
|
|
|
720 "newname": "son.sam"
|
|
|
721 },
|
|
|
722 "action_type": "RenameDatasetAction",
|
|
|
723 "output_name": "output"
|
|
|
724 }
|
|
|
725 },
|
|
|
726 "tool_errors": null,
|
|
|
727 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
728 "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\\\"\"}",
|
|
|
729 "tool_version": "1.2.3",
|
|
|
730 "type": "tool",
|
|
|
731 "user_outputs": []
|
|
|
732 },
|
|
|
733 "22": {
|
|
|
734 "annotation": "",
|
|
|
735 "id": 22,
|
|
|
736 "input_connections": {
|
|
|
737 "source|input1": {
|
|
|
738 "id": 18,
|
|
|
739 "output_name": "output"
|
|
|
740 },
|
|
|
741 "source|ref_file": {
|
|
|
742 "id": 17,
|
|
|
743 "output_name": "output"
|
|
|
744 }
|
|
|
745 },
|
|
|
746 "inputs": [],
|
|
|
747 "name": "SAM-to-BAM",
|
|
|
748 "outputs": [
|
|
|
749 {
|
|
|
750 "name": "output1",
|
|
|
751 "type": "bam"
|
|
|
752 }
|
|
|
753 ],
|
|
|
754 "position": {
|
|
|
755 "left": 999,
|
|
|
756 "top": 421.3333435058594
|
|
|
757 },
|
|
|
758 "post_job_actions": {
|
|
|
759 "HideDatasetActionoutput1": {
|
|
|
760 "action_arguments": {},
|
|
|
761 "action_type": "HideDatasetAction",
|
|
|
762 "output_name": "output1"
|
|
|
763 },
|
|
|
764 "RenameDatasetActionoutput1": {
|
|
|
765 "action_arguments": {
|
|
|
766 "newname": "mother.bam"
|
|
|
767 },
|
|
|
768 "action_type": "RenameDatasetAction",
|
|
|
769 "output_name": "output1"
|
|
|
770 }
|
|
|
771 },
|
|
|
772 "tool_errors": null,
|
|
|
773 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
774 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
775 "tool_version": "1.1.4",
|
|
|
776 "type": "tool",
|
|
|
777 "user_outputs": []
|
|
|
778 },
|
|
|
779 "23": {
|
|
|
780 "annotation": "",
|
|
|
781 "id": 23,
|
|
|
782 "input_connections": {
|
|
|
783 "source|input1": {
|
|
|
784 "id": 19,
|
|
|
785 "output_name": "output"
|
|
|
786 },
|
|
|
787 "source|ref_file": {
|
|
|
788 "id": 17,
|
|
|
789 "output_name": "output"
|
|
|
790 }
|
|
|
791 },
|
|
|
792 "inputs": [],
|
|
|
793 "name": "SAM-to-BAM",
|
|
|
794 "outputs": [
|
|
|
795 {
|
|
|
796 "name": "output1",
|
|
|
797 "type": "bam"
|
|
|
798 }
|
|
|
799 ],
|
|
|
800 "position": {
|
|
|
801 "left": 999.166748046875,
|
|
|
802 "top": 671
|
|
|
803 },
|
|
|
804 "post_job_actions": {
|
|
|
805 "HideDatasetActionoutput1": {
|
|
|
806 "action_arguments": {},
|
|
|
807 "action_type": "HideDatasetAction",
|
|
|
808 "output_name": "output1"
|
|
|
809 },
|
|
|
810 "RenameDatasetActionoutput1": {
|
|
|
811 "action_arguments": {
|
|
|
812 "newname": "father.bam"
|
|
|
813 },
|
|
|
814 "action_type": "RenameDatasetAction",
|
|
|
815 "output_name": "output1"
|
|
|
816 }
|
|
|
817 },
|
|
|
818 "tool_errors": null,
|
|
|
819 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
820 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
821 "tool_version": "1.1.4",
|
|
|
822 "type": "tool",
|
|
|
823 "user_outputs": []
|
|
|
824 },
|
|
|
825 "24": {
|
|
|
826 "annotation": "",
|
|
|
827 "id": 24,
|
|
|
828 "input_connections": {
|
|
|
829 "source|input1": {
|
|
|
830 "id": 20,
|
|
|
831 "output_name": "output"
|
|
|
832 },
|
|
|
833 "source|ref_file": {
|
|
|
834 "id": 17,
|
|
|
835 "output_name": "output"
|
|
|
836 }
|
|
|
837 },
|
|
|
838 "inputs": [],
|
|
|
839 "name": "SAM-to-BAM",
|
|
|
840 "outputs": [
|
|
|
841 {
|
|
|
842 "name": "output1",
|
|
|
843 "type": "bam"
|
|
|
844 }
|
|
|
845 ],
|
|
|
846 "position": {
|
|
|
847 "left": 983,
|
|
|
848 "top": 891.3333740234375
|
|
|
849 },
|
|
|
850 "post_job_actions": {
|
|
|
851 "HideDatasetActionoutput1": {
|
|
|
852 "action_arguments": {},
|
|
|
853 "action_type": "HideDatasetAction",
|
|
|
854 "output_name": "output1"
|
|
|
855 },
|
|
|
856 "RenameDatasetActionoutput1": {
|
|
|
857 "action_arguments": {
|
|
|
858 "newname": "daughter.bam"
|
|
|
859 },
|
|
|
860 "action_type": "RenameDatasetAction",
|
|
|
861 "output_name": "output1"
|
|
|
862 }
|
|
|
863 },
|
|
|
864 "tool_errors": null,
|
|
|
865 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
866 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
867 "tool_version": "1.1.4",
|
|
|
868 "type": "tool",
|
|
|
869 "user_outputs": []
|
|
|
870 },
|
|
|
871 "25": {
|
|
|
872 "annotation": "",
|
|
|
873 "id": 25,
|
|
|
874 "input_connections": {
|
|
|
875 "source|input1": {
|
|
|
876 "id": 21,
|
|
|
877 "output_name": "output"
|
|
|
878 },
|
|
|
879 "source|ref_file": {
|
|
|
880 "id": 17,
|
|
|
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": 994,
|
|
|
894 "top": 1144.3333740234375
|
|
|
895 },
|
|
|
896 "post_job_actions": {
|
|
|
897 "HideDatasetActionoutput1": {
|
|
|
898 "action_arguments": {},
|
|
|
899 "action_type": "HideDatasetAction",
|
|
|
900 "output_name": "output1"
|
|
|
901 },
|
|
|
902 "RenameDatasetActionoutput1": {
|
|
|
903 "action_arguments": {
|
|
|
904 "newname": "son.bam"
|
|
|
905 },
|
|
|
906 "action_type": "RenameDatasetAction",
|
|
|
907 "output_name": "output1"
|
|
|
908 }
|
|
|
909 },
|
|
|
910 "tool_errors": null,
|
|
|
911 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
912 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
913 "tool_version": "1.1.4",
|
|
|
914 "type": "tool",
|
|
|
915 "user_outputs": []
|
|
|
916 },
|
|
|
917 "26": {
|
|
|
918 "annotation": "",
|
|
|
919 "id": 26,
|
|
|
920 "input_connections": {
|
|
|
921 "input1": {
|
|
|
922 "id": 22,
|
|
|
923 "output_name": "output1"
|
|
|
924 }
|
|
|
925 },
|
|
|
926 "inputs": [],
|
|
|
927 "name": "sort",
|
|
|
928 "outputs": [
|
|
|
929 {
|
|
|
930 "name": "output1",
|
|
|
931 "type": "bam"
|
|
|
932 }
|
|
|
933 ],
|
|
|
934 "position": {
|
|
|
935 "left": 1171,
|
|
|
936 "top": 440.3333435058594
|
|
|
937 },
|
|
|
938 "post_job_actions": {
|
|
|
939 "HideDatasetActionoutput1": {
|
|
|
940 "action_arguments": {},
|
|
|
941 "action_type": "HideDatasetAction",
|
|
|
942 "output_name": "output1"
|
|
|
943 },
|
|
|
944 "RenameDatasetActionoutput1": {
|
|
|
945 "action_arguments": {
|
|
|
946 "newname": "mother.sorted.bam"
|
|
|
947 },
|
|
|
948 "action_type": "RenameDatasetAction",
|
|
|
949 "output_name": "output1"
|
|
|
950 }
|
|
|
951 },
|
|
|
952 "tool_errors": null,
|
|
|
953 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
954 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
955 "tool_version": "1.0.2",
|
|
|
956 "type": "tool",
|
|
|
957 "user_outputs": []
|
|
|
958 },
|
|
|
959 "27": {
|
|
|
960 "annotation": "",
|
|
|
961 "id": 27,
|
|
|
962 "input_connections": {
|
|
|
963 "input1": {
|
|
|
964 "id": 23,
|
|
|
965 "output_name": "output1"
|
|
|
966 }
|
|
|
967 },
|
|
|
968 "inputs": [],
|
|
|
969 "name": "sort",
|
|
|
970 "outputs": [
|
|
|
971 {
|
|
|
972 "name": "output1",
|
|
|
973 "type": "bam"
|
|
|
974 }
|
|
|
975 ],
|
|
|
976 "position": {
|
|
|
977 "left": 1166.166748046875,
|
|
|
978 "top": 673
|
|
|
979 },
|
|
|
980 "post_job_actions": {
|
|
|
981 "HideDatasetActionoutput1": {
|
|
|
982 "action_arguments": {},
|
|
|
983 "action_type": "HideDatasetAction",
|
|
|
984 "output_name": "output1"
|
|
|
985 },
|
|
|
986 "RenameDatasetActionoutput1": {
|
|
|
987 "action_arguments": {
|
|
|
988 "newname": "father.sorted.bam"
|
|
|
989 },
|
|
|
990 "action_type": "RenameDatasetAction",
|
|
|
991 "output_name": "output1"
|
|
|
992 }
|
|
|
993 },
|
|
|
994 "tool_errors": null,
|
|
|
995 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
996 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
997 "tool_version": "1.0.2",
|
|
|
998 "type": "tool",
|
|
|
999 "user_outputs": []
|
|
|
1000 },
|
|
|
1001 "28": {
|
|
|
1002 "annotation": "",
|
|
|
1003 "id": 28,
|
|
|
1004 "input_connections": {
|
|
|
1005 "input1": {
|
|
|
1006 "id": 24,
|
|
|
1007 "output_name": "output1"
|
|
|
1008 }
|
|
|
1009 },
|
|
|
1010 "inputs": [],
|
|
|
1011 "name": "sort",
|
|
|
1012 "outputs": [
|
|
|
1013 {
|
|
|
1014 "name": "output1",
|
|
|
1015 "type": "bam"
|
|
|
1016 }
|
|
|
1017 ],
|
|
|
1018 "position": {
|
|
|
1019 "left": 1148,
|
|
|
1020 "top": 903.3333740234375
|
|
|
1021 },
|
|
|
1022 "post_job_actions": {
|
|
|
1023 "HideDatasetActionoutput1": {
|
|
|
1024 "action_arguments": {},
|
|
|
1025 "action_type": "HideDatasetAction",
|
|
|
1026 "output_name": "output1"
|
|
|
1027 },
|
|
|
1028 "RenameDatasetActionoutput1": {
|
|
|
1029 "action_arguments": {
|
|
|
1030 "newname": "daughter.sorted.bam"
|
|
|
1031 },
|
|
|
1032 "action_type": "RenameDatasetAction",
|
|
|
1033 "output_name": "output1"
|
|
|
1034 }
|
|
|
1035 },
|
|
|
1036 "tool_errors": null,
|
|
|
1037 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
1038 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
1039 "tool_version": "1.0.2",
|
|
|
1040 "type": "tool",
|
|
|
1041 "user_outputs": []
|
|
|
1042 },
|
|
|
1043 "29": {
|
|
|
1044 "annotation": "",
|
|
|
1045 "id": 29,
|
|
|
1046 "input_connections": {
|
|
|
1047 "input1": {
|
|
|
1048 "id": 25,
|
|
|
1049 "output_name": "output1"
|
|
|
1050 }
|
|
|
1051 },
|
|
|
1052 "inputs": [],
|
|
|
1053 "name": "sort",
|
|
|
1054 "outputs": [
|
|
|
1055 {
|
|
|
1056 "name": "output1",
|
|
|
1057 "type": "bam"
|
|
|
1058 }
|
|
|
1059 ],
|
|
|
1060 "position": {
|
|
|
1061 "left": 1159,
|
|
|
1062 "top": 1123.3333740234375
|
|
|
1063 },
|
|
|
1064 "post_job_actions": {
|
|
|
1065 "HideDatasetActionoutput1": {
|
|
|
1066 "action_arguments": {},
|
|
|
1067 "action_type": "HideDatasetAction",
|
|
|
1068 "output_name": "output1"
|
|
|
1069 },
|
|
|
1070 "RenameDatasetActionoutput1": {
|
|
|
1071 "action_arguments": {
|
|
|
1072 "newname": "son.sorted.bam"
|
|
|
1073 },
|
|
|
1074 "action_type": "RenameDatasetAction",
|
|
|
1075 "output_name": "output1"
|
|
|
1076 }
|
|
|
1077 },
|
|
|
1078 "tool_errors": null,
|
|
|
1079 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2",
|
|
|
1080 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"sort_mode\": \"\\\"\\\"\"}",
|
|
|
1081 "tool_version": "1.0.2",
|
|
|
1082 "type": "tool",
|
|
|
1083 "user_outputs": []
|
|
|
1084 },
|
|
|
1085 "30": {
|
|
|
1086 "annotation": "",
|
|
|
1087 "id": 30,
|
|
|
1088 "input_connections": {
|
|
|
1089 "input_file": {
|
|
|
1090 "id": 26,
|
|
|
1091 "output_name": "output1"
|
|
|
1092 }
|
|
|
1093 },
|
|
|
1094 "inputs": [],
|
|
|
1095 "name": "Mark Duplicate reads",
|
|
|
1096 "outputs": [
|
|
|
1097 {
|
|
|
1098 "name": "out_file",
|
|
|
1099 "type": "bam"
|
|
|
1100 },
|
|
|
1101 {
|
|
|
1102 "name": "html_file",
|
|
|
1103 "type": "html"
|
|
|
1104 }
|
|
|
1105 ],
|
|
|
1106 "position": {
|
|
|
1107 "left": 1366,
|
|
|
1108 "top": 454.3333435058594
|
|
|
1109 },
|
|
|
1110 "post_job_actions": {
|
|
|
1111 "RenameDatasetActionhtml_file": {
|
|
|
1112 "action_arguments": {
|
|
|
1113 "newname": "mother.deduplicated.html"
|
|
|
1114 },
|
|
|
1115 "action_type": "RenameDatasetAction",
|
|
|
1116 "output_name": "html_file"
|
|
|
1117 },
|
|
|
1118 "RenameDatasetActionout_file": {
|
|
|
1119 "action_arguments": {
|
|
|
1120 "newname": "mother.deduplicated.bam"
|
|
|
1121 },
|
|
|
1122 "action_type": "RenameDatasetAction",
|
|
|
1123 "output_name": "out_file"
|
|
|
1124 }
|
|
|
1125 },
|
|
|
1126 "tool_errors": null,
|
|
|
1127 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1128 "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\\\"\"}",
|
|
|
1129 "tool_version": "1.56.0",
|
|
|
1130 "type": "tool",
|
|
|
1131 "user_outputs": []
|
|
|
1132 },
|
|
|
1133 "31": {
|
|
|
1134 "annotation": "",
|
|
|
1135 "id": 31,
|
|
|
1136 "input_connections": {
|
|
|
1137 "input_file": {
|
|
|
1138 "id": 27,
|
|
|
1139 "output_name": "output1"
|
|
|
1140 }
|
|
|
1141 },
|
|
|
1142 "inputs": [],
|
|
|
1143 "name": "Mark Duplicate reads",
|
|
|
1144 "outputs": [
|
|
|
1145 {
|
|
|
1146 "name": "out_file",
|
|
|
1147 "type": "bam"
|
|
|
1148 },
|
|
|
1149 {
|
|
|
1150 "name": "html_file",
|
|
|
1151 "type": "html"
|
|
|
1152 }
|
|
|
1153 ],
|
|
|
1154 "position": {
|
|
|
1155 "left": 1328.666748046875,
|
|
|
1156 "top": 647
|
|
|
1157 },
|
|
|
1158 "post_job_actions": {
|
|
|
1159 "RenameDatasetActionhtml_file": {
|
|
|
1160 "action_arguments": {
|
|
|
1161 "newname": "father.deduplicated.html"
|
|
|
1162 },
|
|
|
1163 "action_type": "RenameDatasetAction",
|
|
|
1164 "output_name": "html_file"
|
|
|
1165 },
|
|
|
1166 "RenameDatasetActionout_file": {
|
|
|
1167 "action_arguments": {
|
|
|
1168 "newname": "father.deduplicated.bam"
|
|
|
1169 },
|
|
|
1170 "action_type": "RenameDatasetAction",
|
|
|
1171 "output_name": "out_file"
|
|
|
1172 }
|
|
|
1173 },
|
|
|
1174 "tool_errors": null,
|
|
|
1175 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1176 "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\\\"\"}",
|
|
|
1177 "tool_version": "1.56.0",
|
|
|
1178 "type": "tool",
|
|
|
1179 "user_outputs": []
|
|
|
1180 },
|
|
|
1181 "32": {
|
|
|
1182 "annotation": "",
|
|
|
1183 "id": 32,
|
|
|
1184 "input_connections": {
|
|
|
1185 "input_file": {
|
|
|
1186 "id": 28,
|
|
|
1187 "output_name": "output1"
|
|
|
1188 }
|
|
|
1189 },
|
|
|
1190 "inputs": [],
|
|
|
1191 "name": "Mark Duplicate reads",
|
|
|
1192 "outputs": [
|
|
|
1193 {
|
|
|
1194 "name": "out_file",
|
|
|
1195 "type": "bam"
|
|
|
1196 },
|
|
|
1197 {
|
|
|
1198 "name": "html_file",
|
|
|
1199 "type": "html"
|
|
|
1200 }
|
|
|
1201 ],
|
|
|
1202 "position": {
|
|
|
1203 "left": 1339,
|
|
|
1204 "top": 873.3333740234375
|
|
|
1205 },
|
|
|
1206 "post_job_actions": {
|
|
|
1207 "RenameDatasetActionhtml_file": {
|
|
|
1208 "action_arguments": {
|
|
|
1209 "newname": "daughter.deduplicated.html"
|
|
|
1210 },
|
|
|
1211 "action_type": "RenameDatasetAction",
|
|
|
1212 "output_name": "html_file"
|
|
|
1213 },
|
|
|
1214 "RenameDatasetActionout_file": {
|
|
|
1215 "action_arguments": {
|
|
|
1216 "newname": "daughter.deduplicated.bam"
|
|
|
1217 },
|
|
|
1218 "action_type": "RenameDatasetAction",
|
|
|
1219 "output_name": "out_file"
|
|
|
1220 }
|
|
|
1221 },
|
|
|
1222 "tool_errors": null,
|
|
|
1223 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1224 "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\\\"\"}",
|
|
|
1225 "tool_version": "1.56.0",
|
|
|
1226 "type": "tool",
|
|
|
1227 "user_outputs": []
|
|
|
1228 },
|
|
|
1229 "33": {
|
|
|
1230 "annotation": "",
|
|
|
1231 "id": 33,
|
|
|
1232 "input_connections": {
|
|
|
1233 "input_file": {
|
|
|
1234 "id": 29,
|
|
|
1235 "output_name": "output1"
|
|
|
1236 }
|
|
|
1237 },
|
|
|
1238 "inputs": [],
|
|
|
1239 "name": "Mark Duplicate reads",
|
|
|
1240 "outputs": [
|
|
|
1241 {
|
|
|
1242 "name": "out_file",
|
|
|
1243 "type": "bam"
|
|
|
1244 },
|
|
|
1245 {
|
|
|
1246 "name": "html_file",
|
|
|
1247 "type": "html"
|
|
|
1248 }
|
|
|
1249 ],
|
|
|
1250 "position": {
|
|
|
1251 "left": 1355,
|
|
|
1252 "top": 1102.3333740234375
|
|
|
1253 },
|
|
|
1254 "post_job_actions": {
|
|
|
1255 "RenameDatasetActionhtml_file": {
|
|
|
1256 "action_arguments": {
|
|
|
1257 "newname": "son.deduplicated.html"
|
|
|
1258 },
|
|
|
1259 "action_type": "RenameDatasetAction",
|
|
|
1260 "output_name": "html_file"
|
|
|
1261 },
|
|
|
1262 "RenameDatasetActionout_file": {
|
|
|
1263 "action_arguments": {
|
|
|
1264 "newname": "son.deduplicated.bam"
|
|
|
1265 },
|
|
|
1266 "action_type": "RenameDatasetAction",
|
|
|
1267 "output_name": "out_file"
|
|
|
1268 }
|
|
|
1269 },
|
|
|
1270 "tool_errors": null,
|
|
|
1271 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0",
|
|
|
1272 "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\\\"\"}",
|
|
|
1273 "tool_version": "1.56.0",
|
|
|
1274 "type": "tool",
|
|
|
1275 "user_outputs": []
|
|
|
1276 },
|
|
|
1277 "34": {
|
|
|
1278 "annotation": "",
|
|
|
1279 "id": 34,
|
|
|
1280 "input_connections": {
|
|
|
1281 "input1": {
|
|
|
1282 "id": 30,
|
|
|
1283 "output_name": "out_file"
|
|
|
1284 },
|
|
|
1285 "input2": {
|
|
|
1286 "id": 17,
|
|
|
1287 "output_name": "output"
|
|
|
1288 }
|
|
|
1289 },
|
|
|
1290 "inputs": [],
|
|
|
1291 "name": "LINKYX_mpileup",
|
|
|
1292 "outputs": [
|
|
|
1293 {
|
|
|
1294 "name": "output",
|
|
|
1295 "type": "vcf"
|
|
|
1296 }
|
|
|
1297 ],
|
|
|
1298 "position": {
|
|
|
1299 "left": 1644,
|
|
|
1300 "top": 465.3333435058594
|
|
|
1301 },
|
|
|
1302 "post_job_actions": {
|
|
|
1303 "RenameDatasetActionoutput": {
|
|
|
1304 "action_arguments": {
|
|
|
1305 "newname": "mother.vcf"
|
|
|
1306 },
|
|
|
1307 "action_type": "RenameDatasetAction",
|
|
|
1308 "output_name": "output"
|
|
|
1309 }
|
|
|
1310 },
|
|
|
1311 "tool_errors": null,
|
|
|
1312 "tool_id": "LINKYX_mpileup",
|
|
|
1313 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
|
|
1314 "tool_version": "1.0.0",
|
|
|
1315 "type": "tool",
|
|
|
1316 "user_outputs": []
|
|
|
1317 },
|
|
|
1318 "35": {
|
|
|
1319 "annotation": "",
|
|
|
1320 "id": 35,
|
|
|
1321 "input_connections": {
|
|
|
1322 "input1": {
|
|
|
1323 "id": 31,
|
|
|
1324 "output_name": "out_file"
|
|
|
1325 },
|
|
|
1326 "input2": {
|
|
|
1327 "id": 17,
|
|
|
1328 "output_name": "output"
|
|
|
1329 }
|
|
|
1330 },
|
|
|
1331 "inputs": [],
|
|
|
1332 "name": "LINKYX_mpileup",
|
|
|
1333 "outputs": [
|
|
|
1334 {
|
|
|
1335 "name": "output",
|
|
|
1336 "type": "vcf"
|
|
|
1337 }
|
|
|
1338 ],
|
|
|
1339 "position": {
|
|
|
1340 "left": 1653.666748046875,
|
|
|
1341 "top": 656.5
|
|
|
1342 },
|
|
|
1343 "post_job_actions": {
|
|
|
1344 "RenameDatasetActionoutput": {
|
|
|
1345 "action_arguments": {
|
|
|
1346 "newname": "father.vcf"
|
|
|
1347 },
|
|
|
1348 "action_type": "RenameDatasetAction",
|
|
|
1349 "output_name": "output"
|
|
|
1350 }
|
|
|
1351 },
|
|
|
1352 "tool_errors": null,
|
|
|
1353 "tool_id": "LINKYX_mpileup",
|
|
|
1354 "tool_state": "{\"input2\": \"null\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}",
|
|
|
1355 "tool_version": "1.0.0",
|
|
|
1356 "type": "tool",
|
|
|
1357 "user_outputs": []
|
|
|
1358 },
|
|
|
1359 "36": {
|
|
|
1360 "annotation": "",
|
|
|
1361 "id": 36,
|
|
|
1362 "input_connections": {
|
|
|
1363 "input1": {
|
|
|
1364 "id": 32,
|
|
|
1365 "output_name": "out_file"
|
|
|
1366 },
|
|
|
1367 "input2": {
|
|
|
1368 "id": 17,
|
|
|
1369 "output_name": "output"
|
|
|
1370 }
|
|
|
1371 },
|
|
|
1372 "inputs": [],
|
|
|
1373 "name": "LINKYX_mpileup",
|
|
|
1374 "outputs": [
|
|
|
1375 {
|
|
|
1376 "name": "output",
|
|
|
1377 "type": "vcf"
|
|
|
1378 }
|
|
|
1379 ],
|
|
|
1380 "position": {
|
|
|
1381 "left": 1653,
|
|
|
1382 "top": 873.3333740234375
|
|
|
1383 },
|
|
|
1384 "post_job_actions": {
|
|
|
1385 "RenameDatasetActionoutput": {
|
|
|
1386 "action_arguments": {
|
|
|
1387 "newname": "daughter.vcf"
|
|
|
1388 },
|
|
|
1389 "action_type": "RenameDatasetAction",
|
|
|
1390 "output_name": "output"
|
|
|
1391 }
|
|
|
1392 },
|
|
|
1393 "tool_errors": null,
|
|
|
1394 "tool_id": "LINKYX_mpileup",
|
|
|
1395 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
|
|
1396 "tool_version": "1.0.0",
|
|
|
1397 "type": "tool",
|
|
|
1398 "user_outputs": []
|
|
|
1399 },
|
|
|
1400 "37": {
|
|
|
1401 "annotation": "",
|
|
|
1402 "id": 37,
|
|
|
1403 "input_connections": {
|
|
|
1404 "input1": {
|
|
|
1405 "id": 33,
|
|
|
1406 "output_name": "out_file"
|
|
|
1407 },
|
|
|
1408 "input2": {
|
|
|
1409 "id": 17,
|
|
|
1410 "output_name": "output"
|
|
|
1411 }
|
|
|
1412 },
|
|
|
1413 "inputs": [],
|
|
|
1414 "name": "LINKYX_mpileup",
|
|
|
1415 "outputs": [
|
|
|
1416 {
|
|
|
1417 "name": "output",
|
|
|
1418 "type": "vcf"
|
|
|
1419 }
|
|
|
1420 ],
|
|
|
1421 "position": {
|
|
|
1422 "left": 1671,
|
|
|
1423 "top": 1104.3333740234375
|
|
|
1424 },
|
|
|
1425 "post_job_actions": {
|
|
|
1426 "RenameDatasetActionoutput": {
|
|
|
1427 "action_arguments": {
|
|
|
1428 "newname": "son.vcf"
|
|
|
1429 },
|
|
|
1430 "action_type": "RenameDatasetAction",
|
|
|
1431 "output_name": "output"
|
|
|
1432 }
|
|
|
1433 },
|
|
|
1434 "tool_errors": null,
|
|
|
1435 "tool_id": "LINKYX_mpileup",
|
|
|
1436 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
|
|
|
1437 "tool_version": "1.0.0",
|
|
|
1438 "type": "tool",
|
|
|
1439 "user_outputs": []
|
|
|
1440 },
|
|
|
1441 "38": {
|
|
|
1442 "annotation": "",
|
|
|
1443 "id": 38,
|
|
|
1444 "input_connections": {
|
|
|
1445 "input1": {
|
|
|
1446 "id": 17,
|
|
|
1447 "output_name": "output"
|
|
|
1448 },
|
|
|
1449 "input2": {
|
|
|
1450 "id": 30,
|
|
|
1451 "output_name": "out_file"
|
|
|
1452 },
|
|
|
1453 "input3": {
|
|
|
1454 "id": 34,
|
|
|
1455 "output_name": "output"
|
|
|
1456 },
|
|
|
1457 "input4": {
|
|
|
1458 "id": 31,
|
|
|
1459 "output_name": "out_file"
|
|
|
1460 },
|
|
|
1461 "input5": {
|
|
|
1462 "id": 35,
|
|
|
1463 "output_name": "output"
|
|
|
1464 },
|
|
|
1465 "input6": {
|
|
|
1466 "id": 32,
|
|
|
1467 "output_name": "out_file"
|
|
|
1468 },
|
|
|
1469 "input7": {
|
|
|
1470 "id": 36,
|
|
|
1471 "output_name": "output"
|
|
|
1472 },
|
|
|
1473 "input8": {
|
|
|
1474 "id": 33,
|
|
|
1475 "output_name": "out_file"
|
|
|
1476 },
|
|
|
1477 "input9": {
|
|
|
1478 "id": 37,
|
|
|
1479 "output_name": "output"
|
|
|
1480 }
|
|
|
1481 },
|
|
|
1482 "inputs": [],
|
|
|
1483 "name": "LINKYX_X",
|
|
|
1484 "outputs": [
|
|
|
1485 {
|
|
|
1486 "name": "output",
|
|
|
1487 "type": "txt"
|
|
|
1488 },
|
|
|
1489 {
|
|
|
1490 "name": "output1",
|
|
|
1491 "type": "fasta"
|
|
|
1492 },
|
|
|
1493 {
|
|
|
1494 "name": "output2",
|
|
|
1495 "type": "bam"
|
|
|
1496 },
|
|
|
1497 {
|
|
|
1498 "name": "output3",
|
|
|
1499 "type": "bam"
|
|
|
1500 },
|
|
|
1501 {
|
|
|
1502 "name": "output4",
|
|
|
1503 "type": "bam"
|
|
|
1504 },
|
|
|
1505 {
|
|
|
1506 "name": "output5",
|
|
|
1507 "type": "bam"
|
|
|
1508 }
|
|
|
1509 ],
|
|
|
1510 "position": {
|
|
|
1511 "left": 1921.83349609375,
|
|
|
1512 "top": 602.3333740234375
|
|
|
1513 },
|
|
|
1514 "post_job_actions": {},
|
|
|
1515 "tool_errors": null,
|
|
|
1516 "tool_id": "LINKYX_X",
|
|
|
1517 "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}",
|
|
|
1518 "tool_version": "1.0.0",
|
|
|
1519 "type": "tool",
|
|
|
1520 "user_outputs": []
|
|
|
1521 }
|
|
|
1522 }
|
|
|
1523 } |
