7
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "{\"refinery_type\": \"analysis\", \"refinery_relationships\": [{\"category\":\"1-1\", \"set1\":\"tag file\", \"set2\":\"control file\"}]}",
|
|
4 "format-version": "0.1",
|
|
5 "name": "Test workflow: SPP analog",
|
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
|
9 "id": 0,
|
|
10 "input_connections": {},
|
|
11 "inputs": [
|
|
12 {
|
|
13 "description": "",
|
|
14 "name": "tag file"
|
|
15 }
|
|
16 ],
|
|
17 "name": "Input dataset",
|
|
18 "outputs": [],
|
|
19 "position": {
|
|
20 "left": 200,
|
|
21 "top": 254
|
|
22 },
|
|
23 "tool_errors": null,
|
|
24 "tool_id": null,
|
|
25 "tool_state": "{\"name\": \"tag file\"}",
|
|
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": "control file"
|
|
38 }
|
|
39 ],
|
|
40 "name": "Input dataset",
|
|
41 "outputs": [],
|
|
42 "position": {
|
|
43 "left": 202,
|
|
44 "top": 368
|
|
45 },
|
|
46 "tool_errors": null,
|
|
47 "tool_id": null,
|
|
48 "tool_state": "{\"name\": \"control file\"}",
|
|
49 "tool_version": null,
|
|
50 "type": "data_input",
|
|
51 "user_outputs": []
|
|
52 },
|
|
53 "2": {
|
|
54 "annotation": "",
|
|
55 "id": 2,
|
|
56 "input_connections": {
|
|
57 "input_file": {
|
|
58 "id": 0,
|
|
59 "output_name": "output"
|
|
60 }
|
|
61 },
|
|
62 "inputs": [],
|
|
63 "name": "Refinery test tool 1-1",
|
|
64 "outputs": [
|
|
65 {
|
|
66 "name": "output_file",
|
|
67 "type": "txt"
|
|
68 }
|
|
69 ],
|
|
70 "position": {
|
|
71 "left": 412,
|
|
72 "top": 242
|
|
73 },
|
|
74 "post_job_actions": {},
|
|
75 "tool_errors": null,
|
|
76 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
77 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
78 "tool_version": "0.1",
|
|
79 "type": "tool",
|
|
80 "user_outputs": []
|
|
81 },
|
|
82 "3": {
|
|
83 "annotation": "",
|
|
84 "id": 3,
|
|
85 "input_connections": {
|
|
86 "input_file": {
|
|
87 "id": 1,
|
|
88 "output_name": "output"
|
|
89 }
|
|
90 },
|
|
91 "inputs": [],
|
|
92 "name": "Refinery test tool 1-1",
|
|
93 "outputs": [
|
|
94 {
|
|
95 "name": "output_file",
|
|
96 "type": "txt"
|
|
97 }
|
|
98 ],
|
|
99 "position": {
|
|
100 "left": 414,
|
|
101 "top": 362
|
|
102 },
|
|
103 "post_job_actions": {},
|
|
104 "tool_errors": null,
|
|
105 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
106 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
107 "tool_version": "0.1",
|
|
108 "type": "tool",
|
|
109 "user_outputs": []
|
|
110 },
|
|
111 "4": {
|
|
112 "annotation": "",
|
|
113 "id": 4,
|
|
114 "input_connections": {
|
|
115 "input_file": {
|
|
116 "id": 2,
|
|
117 "output_name": "output_file"
|
|
118 }
|
|
119 },
|
|
120 "inputs": [],
|
|
121 "name": "Refinery test tool 1-1",
|
|
122 "outputs": [
|
|
123 {
|
|
124 "name": "output_file",
|
|
125 "type": "txt"
|
|
126 }
|
|
127 ],
|
|
128 "position": {
|
|
129 "left": 629,
|
|
130 "top": 246
|
|
131 },
|
|
132 "post_job_actions": {},
|
|
133 "tool_errors": null,
|
|
134 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
135 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
136 "tool_version": "0.1",
|
|
137 "type": "tool",
|
|
138 "user_outputs": []
|
|
139 },
|
|
140 "5": {
|
|
141 "annotation": "",
|
|
142 "id": 5,
|
|
143 "input_connections": {
|
|
144 "input_file": {
|
|
145 "id": 3,
|
|
146 "output_name": "output_file"
|
|
147 }
|
|
148 },
|
|
149 "inputs": [],
|
|
150 "name": "Refinery test tool 1-1",
|
|
151 "outputs": [
|
|
152 {
|
|
153 "name": "output_file",
|
|
154 "type": "txt"
|
|
155 }
|
|
156 ],
|
|
157 "position": {
|
|
158 "left": 629,
|
|
159 "top": 368
|
|
160 },
|
|
161 "post_job_actions": {},
|
|
162 "tool_errors": null,
|
|
163 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
164 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
165 "tool_version": "0.1",
|
|
166 "type": "tool",
|
|
167 "user_outputs": []
|
|
168 },
|
|
169 "6": {
|
|
170 "annotation": "",
|
|
171 "id": 6,
|
|
172 "input_connections": {
|
|
173 "input_file": {
|
|
174 "id": 4,
|
|
175 "output_name": "output_file"
|
|
176 }
|
|
177 },
|
|
178 "inputs": [],
|
|
179 "name": "Refinery test tool 1-1",
|
|
180 "outputs": [
|
|
181 {
|
|
182 "name": "output_file",
|
|
183 "type": "txt"
|
|
184 }
|
|
185 ],
|
|
186 "position": {
|
|
187 "left": 847,
|
|
188 "top": 251
|
|
189 },
|
|
190 "post_job_actions": {},
|
|
191 "tool_errors": null,
|
|
192 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
193 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
194 "tool_version": "0.1",
|
|
195 "type": "tool",
|
|
196 "user_outputs": []
|
|
197 },
|
|
198 "7": {
|
|
199 "annotation": "",
|
|
200 "id": 7,
|
|
201 "input_connections": {
|
|
202 "input_file": {
|
|
203 "id": 5,
|
|
204 "output_name": "output_file"
|
|
205 }
|
|
206 },
|
|
207 "inputs": [],
|
|
208 "name": "Refinery test tool 1-1",
|
|
209 "outputs": [
|
|
210 {
|
|
211 "name": "output_file",
|
|
212 "type": "txt"
|
|
213 }
|
|
214 ],
|
|
215 "position": {
|
|
216 "left": 847,
|
|
217 "top": 370
|
|
218 },
|
|
219 "post_job_actions": {},
|
|
220 "tool_errors": null,
|
|
221 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
222 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
223 "tool_version": "0.1",
|
|
224 "type": "tool",
|
|
225 "user_outputs": []
|
|
226 },
|
|
227 "8": {
|
|
228 "annotation": "{\"output_file\": {\"name\":\"test_01\", \"description\":\"\", \"type\":\"txt\"}}",
|
|
229 "id": 8,
|
|
230 "input_connections": {
|
|
231 "input_file": {
|
|
232 "id": 6,
|
|
233 "output_name": "output_file"
|
|
234 }
|
|
235 },
|
|
236 "inputs": [],
|
|
237 "name": "Refinery test tool 1-1",
|
|
238 "outputs": [
|
|
239 {
|
|
240 "name": "output_file",
|
|
241 "type": "txt"
|
|
242 }
|
|
243 ],
|
|
244 "position": {
|
|
245 "left": 1088,
|
|
246 "top": 212
|
|
247 },
|
|
248 "post_job_actions": {},
|
|
249 "tool_errors": null,
|
|
250 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
251 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
252 "tool_version": "0.1",
|
|
253 "type": "tool",
|
|
254 "user_outputs": []
|
|
255 },
|
|
256 "9": {
|
|
257 "annotation": "",
|
|
258 "id": 9,
|
|
259 "input_connections": {
|
|
260 "input_file1": {
|
|
261 "id": 6,
|
|
262 "output_name": "output_file"
|
|
263 },
|
|
264 "input_file2": {
|
|
265 "id": 7,
|
|
266 "output_name": "output_file"
|
|
267 }
|
|
268 },
|
|
269 "inputs": [],
|
|
270 "name": "Refinery test tool 2-6",
|
|
271 "outputs": [
|
|
272 {
|
|
273 "name": "output_file1",
|
|
274 "type": "txt"
|
|
275 },
|
|
276 {
|
|
277 "name": "output_file2",
|
|
278 "type": "txt"
|
|
279 },
|
|
280 {
|
|
281 "name": "output_file3",
|
|
282 "type": "txt"
|
|
283 },
|
|
284 {
|
|
285 "name": "output_file4",
|
|
286 "type": "txt"
|
|
287 },
|
|
288 {
|
|
289 "name": "output_file5",
|
|
290 "type": "txt"
|
|
291 },
|
|
292 {
|
|
293 "name": "output_file6",
|
|
294 "type": "txt"
|
|
295 }
|
|
296 ],
|
|
297 "position": {
|
|
298 "left": 1083,
|
|
299 "top": 330
|
|
300 },
|
|
301 "post_job_actions": {},
|
|
302 "tool_errors": null,
|
|
303 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_2-6/0.1",
|
|
304 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"sleep_time\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"input_file1\": \"null\", \"input_file2\": \"null\"}",
|
|
305 "tool_version": "0.1",
|
|
306 "type": "tool",
|
|
307 "user_outputs": []
|
|
308 },
|
|
309 "10": {
|
|
310 "annotation": "{\"output_file\": {\"name\":\"test_02\", \"description\":\"\", \"type\":\"txt\"}}",
|
|
311 "id": 10,
|
|
312 "input_connections": {
|
|
313 "input_file": {
|
|
314 "id": 7,
|
|
315 "output_name": "output_file"
|
|
316 }
|
|
317 },
|
|
318 "inputs": [],
|
|
319 "name": "Refinery test tool 1-1",
|
|
320 "outputs": [
|
|
321 {
|
|
322 "name": "output_file",
|
|
323 "type": "txt"
|
|
324 }
|
|
325 ],
|
|
326 "position": {
|
|
327 "left": 1088,
|
|
328 "top": 611
|
|
329 },
|
|
330 "post_job_actions": {},
|
|
331 "tool_errors": null,
|
|
332 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
333 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
334 "tool_version": "0.1",
|
|
335 "type": "tool",
|
|
336 "user_outputs": []
|
|
337 },
|
|
338 "11": {
|
|
339 "annotation": "",
|
|
340 "id": 11,
|
|
341 "input_connections": {
|
|
342 "input_file": {
|
|
343 "id": 9,
|
|
344 "output_name": "output_file2"
|
|
345 }
|
|
346 },
|
|
347 "inputs": [],
|
|
348 "name": "Refinery test tool 1-1",
|
|
349 "outputs": [
|
|
350 {
|
|
351 "name": "output_file",
|
|
352 "type": "txt"
|
|
353 }
|
|
354 ],
|
|
355 "position": {
|
|
356 "left": 1299,
|
|
357 "top": 371
|
|
358 },
|
|
359 "post_job_actions": {},
|
|
360 "tool_errors": null,
|
|
361 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
362 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
363 "tool_version": "0.1",
|
|
364 "type": "tool",
|
|
365 "user_outputs": []
|
|
366 },
|
|
367 "12": {
|
|
368 "annotation": "",
|
|
369 "id": 12,
|
|
370 "input_connections": {
|
|
371 "input_file": {
|
|
372 "id": 9,
|
|
373 "output_name": "output_file4"
|
|
374 }
|
|
375 },
|
|
376 "inputs": [],
|
|
377 "name": "Refinery test tool 1-1",
|
|
378 "outputs": [
|
|
379 {
|
|
380 "name": "output_file",
|
|
381 "type": "txt"
|
|
382 }
|
|
383 ],
|
|
384 "position": {
|
|
385 "left": 1301,
|
|
386 "top": 493
|
|
387 },
|
|
388 "post_job_actions": {},
|
|
389 "tool_errors": null,
|
|
390 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
391 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
392 "tool_version": "0.1",
|
|
393 "type": "tool",
|
|
394 "user_outputs": []
|
|
395 },
|
|
396 "13": {
|
|
397 "annotation": "",
|
|
398 "id": 13,
|
|
399 "input_connections": {
|
|
400 "input_file": {
|
|
401 "id": 11,
|
|
402 "output_name": "output_file"
|
|
403 }
|
|
404 },
|
|
405 "inputs": [],
|
|
406 "name": "Refinery test tool 1-1",
|
|
407 "outputs": [
|
|
408 {
|
|
409 "name": "output_file",
|
|
410 "type": "txt"
|
|
411 }
|
|
412 ],
|
|
413 "position": {
|
|
414 "left": 1522,
|
|
415 "top": 373
|
|
416 },
|
|
417 "post_job_actions": {},
|
|
418 "tool_errors": null,
|
|
419 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
420 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
421 "tool_version": "0.1",
|
|
422 "type": "tool",
|
|
423 "user_outputs": []
|
|
424 },
|
|
425 "14": {
|
|
426 "annotation": "",
|
|
427 "id": 14,
|
|
428 "input_connections": {
|
|
429 "input_file": {
|
|
430 "id": 12,
|
|
431 "output_name": "output_file"
|
|
432 }
|
|
433 },
|
|
434 "inputs": [],
|
|
435 "name": "Refinery test tool 1-1",
|
|
436 "outputs": [
|
|
437 {
|
|
438 "name": "output_file",
|
|
439 "type": "txt"
|
|
440 }
|
|
441 ],
|
|
442 "position": {
|
|
443 "left": 1522,
|
|
444 "top": 496
|
|
445 },
|
|
446 "post_job_actions": {},
|
|
447 "tool_errors": null,
|
|
448 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
449 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
450 "tool_version": "0.1",
|
|
451 "type": "tool",
|
|
452 "user_outputs": []
|
|
453 },
|
|
454 "15": {
|
|
455 "annotation": "{\"output_file\": {\"name\":\"test_03\", \"description\":\"\", \"type\":\"txt\"}}",
|
|
456 "id": 15,
|
|
457 "input_connections": {
|
|
458 "input_file": {
|
|
459 "id": 13,
|
|
460 "output_name": "output_file"
|
|
461 }
|
|
462 },
|
|
463 "inputs": [],
|
|
464 "name": "Refinery test tool 1-1",
|
|
465 "outputs": [
|
|
466 {
|
|
467 "name": "output_file",
|
|
468 "type": "txt"
|
|
469 }
|
|
470 ],
|
|
471 "position": {
|
|
472 "left": 1747,
|
|
473 "top": 377
|
|
474 },
|
|
475 "post_job_actions": {},
|
|
476 "tool_errors": null,
|
|
477 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
478 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
479 "tool_version": "0.1",
|
|
480 "type": "tool",
|
|
481 "user_outputs": []
|
|
482 },
|
|
483 "16": {
|
|
484 "annotation": "{\"output_file\": {\"name\":\"test_04\", \"description\":\"\", \"type\":\"txt\"}}",
|
|
485 "id": 16,
|
|
486 "input_connections": {
|
|
487 "input_file": {
|
|
488 "id": 14,
|
|
489 "output_name": "output_file"
|
|
490 }
|
|
491 },
|
|
492 "inputs": [],
|
|
493 "name": "Refinery test tool 1-1",
|
|
494 "outputs": [
|
|
495 {
|
|
496 "name": "output_file",
|
|
497 "type": "txt"
|
|
498 }
|
|
499 ],
|
|
500 "position": {
|
|
501 "left": 1745,
|
|
502 "top": 499
|
|
503 },
|
|
504 "post_job_actions": {},
|
|
505 "tool_errors": null,
|
|
506 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1",
|
|
507 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
508 "tool_version": "0.1",
|
|
509 "type": "tool",
|
|
510 "user_outputs": []
|
|
511 }
|
|
512 }
|
|
513 } |