1
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "{\n\t\"description\": \"Test workflow SPP analog\",\n\t\t\"file_relationship\": {\n\t\t \"value_type\": \"LIST\",\n\t\t \"name\": \"List of Paired Input files\",\n \"file_relationship\": {\n\t\t\t\"file_relationship\": {},\n\t\t\t\"value_type\": \"PAIR\",\n\t\t\t\"name\": \"Paired Input files\",\n\t\t\t\"input_files\": [{\n\t\t\t\t\t\"allowed_filetypes\": [{\"name\": \"TXT\"}],\n\t\t\t\t\t\"name\": \"Tag File\",\n\t\t\t\t\t\"description\": \"Input Tag File\"\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t\"allowed_filetypes\": [{\"name\": \"TXT\"}],\n\t\t\t\t\t\"name\": \"Control File\",\n\t\t\t\t\t\"description\": \"Input Control File\"\n\t\t\t\t}\n\t\t\t]\n\t\t}\n }\n}",
|
|
4 "format-version": "0.1",
|
|
5 "name": "Test workflow: SPP analog",
|
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
|
9 "content_id": null,
|
|
10 "errors": null,
|
|
11 "id": 0,
|
|
12 "input_connections": {},
|
|
13 "inputs": [],
|
|
14 "label": null,
|
|
15 "name": "Input dataset collection",
|
|
16 "outputs": [],
|
|
17 "position": {
|
|
18 "left": 179.5,
|
|
19 "top": 350.5
|
|
20 },
|
|
21 "tool_id": null,
|
|
22 "tool_state": "{\"collection_type\": \"paired\"}",
|
|
23 "tool_version": null,
|
|
24 "type": "data_collection_input",
|
|
25 "uuid": "91742ad7-8c63-4c6d-9eba-a06e49f0919a",
|
|
26 "workflow_outputs": [
|
|
27 {
|
|
28 "label": null,
|
|
29 "output_name": "output",
|
|
30 "uuid": "fb1d7e2e-169b-4992-9e0f-ef50bcdfb4df"
|
|
31 }
|
|
32 ]
|
|
33 },
|
|
34 "1": {
|
|
35 "annotation": "",
|
|
36 "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
|
|
37 "errors": null,
|
|
38 "id": 1,
|
|
39 "input_connections": {
|
|
40 "input_collection": {
|
|
41 "id": 0,
|
|
42 "output_name": "output"
|
|
43 }
|
|
44 },
|
|
45 "inputs": [
|
|
46 {
|
|
47 "description": "runtime parameter for tool Split Paired Collection",
|
|
48 "name": "input_collection"
|
|
49 }
|
|
50 ],
|
|
51 "label": null,
|
|
52 "name": "Split Paired Collection",
|
|
53 "outputs": [
|
|
54 {
|
|
55 "name": "forward_element",
|
|
56 "type": "data"
|
|
57 },
|
|
58 {
|
|
59 "name": "reverse_element",
|
|
60 "type": "data"
|
|
61 }
|
|
62 ],
|
|
63 "position": {
|
|
64 "left": 477.5,
|
|
65 "top": 346.5
|
|
66 },
|
|
67 "post_job_actions": {
|
|
68 "ChangeDatatypeActionforward_element": {
|
|
69 "action_arguments": {
|
|
70 "newtype": "txt"
|
|
71 },
|
|
72 "action_type": "ChangeDatatypeAction",
|
|
73 "output_name": "forward_element"
|
|
74 },
|
|
75 "ChangeDatatypeActionreverse_element": {
|
|
76 "action_arguments": {
|
|
77 "newtype": "txt"
|
|
78 },
|
|
79 "action_type": "ChangeDatatypeAction",
|
|
80 "output_name": "reverse_element"
|
|
81 },
|
|
82 "HideDatasetActionforward_element": {
|
|
83 "action_arguments": {},
|
|
84 "action_type": "HideDatasetAction",
|
|
85 "output_name": "forward_element"
|
|
86 },
|
|
87 "HideDatasetActionreverse_element": {
|
|
88 "action_arguments": {},
|
|
89 "action_type": "HideDatasetAction",
|
|
90 "output_name": "reverse_element"
|
|
91 }
|
|
92 },
|
|
93 "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2",
|
|
94 "tool_shed_repository": {
|
|
95 "changeset_revision": "3a60513b51a2",
|
|
96 "name": "split_paired_collection",
|
|
97 "owner": "refinery-platform",
|
|
98 "tool_shed": "toolshed.g2.bx.psu.edu"
|
|
99 },
|
|
100 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_collection\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
|
|
101 "tool_version": "0.2",
|
|
102 "type": "tool",
|
|
103 "uuid": "65d6b62c-9fcb-4779-a4a7-f0cfd2ece6a3",
|
|
104 "workflow_outputs": []
|
|
105 },
|
|
106 "2": {
|
|
107 "annotation": "",
|
|
108 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
109 "errors": null,
|
|
110 "id": 2,
|
|
111 "input_connections": {
|
|
112 "input_file": {
|
|
113 "id": 1,
|
|
114 "output_name": "forward_element"
|
|
115 }
|
|
116 },
|
|
117 "inputs": [
|
|
118 {
|
|
119 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
120 "name": "input_file"
|
|
121 }
|
|
122 ],
|
|
123 "label": null,
|
|
124 "name": "Refinery test tool 1-1",
|
|
125 "outputs": [
|
|
126 {
|
|
127 "name": "output_file",
|
|
128 "type": "txt"
|
|
129 }
|
|
130 ],
|
|
131 "position": {
|
|
132 "left": 763.5,
|
|
133 "top": 317
|
|
134 },
|
|
135 "post_job_actions": {
|
|
136 "HideDatasetActionoutput_file": {
|
|
137 "action_arguments": {},
|
|
138 "action_type": "HideDatasetAction",
|
|
139 "output_name": "output_file"
|
|
140 }
|
|
141 },
|
|
142 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
143 "tool_shed_repository": {
|
|
144 "changeset_revision": "b87749d7a24c",
|
|
145 "name": "refinery_test",
|
|
146 "owner": "refinery-platform",
|
|
147 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
148 },
|
|
149 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
150 "tool_version": "0.1",
|
|
151 "type": "tool",
|
|
152 "uuid": "bc924f87-d2a6-4477-89f7-0c0308e8f8a3",
|
|
153 "workflow_outputs": []
|
|
154 },
|
|
155 "3": {
|
|
156 "annotation": "",
|
|
157 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
158 "errors": null,
|
|
159 "id": 3,
|
|
160 "input_connections": {
|
|
161 "input_file": {
|
|
162 "id": 1,
|
|
163 "output_name": "reverse_element"
|
|
164 }
|
|
165 },
|
|
166 "inputs": [
|
|
167 {
|
|
168 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
169 "name": "input_file"
|
|
170 }
|
|
171 ],
|
|
172 "label": null,
|
|
173 "name": "Refinery test tool 1-1",
|
|
174 "outputs": [
|
|
175 {
|
|
176 "name": "output_file",
|
|
177 "type": "txt"
|
|
178 }
|
|
179 ],
|
|
180 "position": {
|
|
181 "left": 765.5,
|
|
182 "top": 437
|
|
183 },
|
|
184 "post_job_actions": {
|
|
185 "HideDatasetActionoutput_file": {
|
|
186 "action_arguments": {},
|
|
187 "action_type": "HideDatasetAction",
|
|
188 "output_name": "output_file"
|
|
189 }
|
|
190 },
|
|
191 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
192 "tool_shed_repository": {
|
|
193 "changeset_revision": "b87749d7a24c",
|
|
194 "name": "refinery_test",
|
|
195 "owner": "refinery-platform",
|
|
196 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
197 },
|
|
198 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
199 "tool_version": "0.1",
|
|
200 "type": "tool",
|
|
201 "uuid": "5f3c2623-fb89-4393-ba29-7ee3f2a00bca",
|
|
202 "workflow_outputs": []
|
|
203 },
|
|
204 "4": {
|
|
205 "annotation": "",
|
|
206 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
207 "errors": null,
|
|
208 "id": 4,
|
|
209 "input_connections": {
|
|
210 "input_file": {
|
|
211 "id": 2,
|
|
212 "output_name": "output_file"
|
|
213 }
|
|
214 },
|
|
215 "inputs": [
|
|
216 {
|
|
217 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
218 "name": "input_file"
|
|
219 }
|
|
220 ],
|
|
221 "label": null,
|
|
222 "name": "Refinery test tool 1-1",
|
|
223 "outputs": [
|
|
224 {
|
|
225 "name": "output_file",
|
|
226 "type": "txt"
|
|
227 }
|
|
228 ],
|
|
229 "position": {
|
|
230 "left": 980.5,
|
|
231 "top": 321
|
|
232 },
|
|
233 "post_job_actions": {
|
|
234 "HideDatasetActionoutput_file": {
|
|
235 "action_arguments": {},
|
|
236 "action_type": "HideDatasetAction",
|
|
237 "output_name": "output_file"
|
|
238 }
|
|
239 },
|
|
240 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
241 "tool_shed_repository": {
|
|
242 "changeset_revision": "b87749d7a24c",
|
|
243 "name": "refinery_test",
|
|
244 "owner": "refinery-platform",
|
|
245 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
246 },
|
|
247 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
248 "tool_version": "0.1",
|
|
249 "type": "tool",
|
|
250 "uuid": "24e512de-f882-40e5-bf65-2b2a3e945c00",
|
|
251 "workflow_outputs": []
|
|
252 },
|
|
253 "5": {
|
|
254 "annotation": "",
|
|
255 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
256 "errors": null,
|
|
257 "id": 5,
|
|
258 "input_connections": {
|
|
259 "input_file": {
|
|
260 "id": 3,
|
|
261 "output_name": "output_file"
|
|
262 }
|
|
263 },
|
|
264 "inputs": [
|
|
265 {
|
|
266 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
267 "name": "input_file"
|
|
268 }
|
|
269 ],
|
|
270 "label": null,
|
|
271 "name": "Refinery test tool 1-1",
|
|
272 "outputs": [
|
|
273 {
|
|
274 "name": "output_file",
|
|
275 "type": "txt"
|
|
276 }
|
|
277 ],
|
|
278 "position": {
|
|
279 "left": 980.5,
|
|
280 "top": 443
|
|
281 },
|
|
282 "post_job_actions": {
|
|
283 "HideDatasetActionoutput_file": {
|
|
284 "action_arguments": {},
|
|
285 "action_type": "HideDatasetAction",
|
|
286 "output_name": "output_file"
|
|
287 }
|
|
288 },
|
|
289 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
290 "tool_shed_repository": {
|
|
291 "changeset_revision": "b87749d7a24c",
|
|
292 "name": "refinery_test",
|
|
293 "owner": "refinery-platform",
|
|
294 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
295 },
|
|
296 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
297 "tool_version": "0.1",
|
|
298 "type": "tool",
|
|
299 "uuid": "4e354bed-9a38-45fa-a726-5d4da8b5e48b",
|
|
300 "workflow_outputs": []
|
|
301 },
|
|
302 "6": {
|
|
303 "annotation": "",
|
|
304 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
305 "errors": null,
|
|
306 "id": 6,
|
|
307 "input_connections": {
|
|
308 "input_file": {
|
|
309 "id": 4,
|
|
310 "output_name": "output_file"
|
|
311 }
|
|
312 },
|
|
313 "inputs": [
|
|
314 {
|
|
315 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
316 "name": "input_file"
|
|
317 }
|
|
318 ],
|
|
319 "label": null,
|
|
320 "name": "Refinery test tool 1-1",
|
|
321 "outputs": [
|
|
322 {
|
|
323 "name": "output_file",
|
|
324 "type": "txt"
|
|
325 }
|
|
326 ],
|
|
327 "position": {
|
|
328 "left": 1198.5,
|
|
329 "top": 326
|
|
330 },
|
|
331 "post_job_actions": {
|
|
332 "HideDatasetActionoutput_file": {
|
|
333 "action_arguments": {},
|
|
334 "action_type": "HideDatasetAction",
|
|
335 "output_name": "output_file"
|
|
336 }
|
|
337 },
|
|
338 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
339 "tool_shed_repository": {
|
|
340 "changeset_revision": "b87749d7a24c",
|
|
341 "name": "refinery_test",
|
|
342 "owner": "refinery-platform",
|
|
343 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
344 },
|
|
345 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
346 "tool_version": "0.1",
|
|
347 "type": "tool",
|
|
348 "uuid": "1f44b18f-cdef-4af9-872b-760e8664749a",
|
|
349 "workflow_outputs": []
|
|
350 },
|
|
351 "7": {
|
|
352 "annotation": "",
|
|
353 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
354 "errors": null,
|
|
355 "id": 7,
|
|
356 "input_connections": {
|
|
357 "input_file": {
|
|
358 "id": 5,
|
|
359 "output_name": "output_file"
|
|
360 }
|
|
361 },
|
|
362 "inputs": [
|
|
363 {
|
|
364 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
365 "name": "input_file"
|
|
366 }
|
|
367 ],
|
|
368 "label": null,
|
|
369 "name": "Refinery test tool 1-1",
|
|
370 "outputs": [
|
|
371 {
|
|
372 "name": "output_file",
|
|
373 "type": "txt"
|
|
374 }
|
|
375 ],
|
|
376 "position": {
|
|
377 "left": 1198.5,
|
|
378 "top": 445
|
|
379 },
|
|
380 "post_job_actions": {
|
|
381 "HideDatasetActionoutput_file": {
|
|
382 "action_arguments": {},
|
|
383 "action_type": "HideDatasetAction",
|
|
384 "output_name": "output_file"
|
|
385 }
|
|
386 },
|
|
387 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
388 "tool_shed_repository": {
|
|
389 "changeset_revision": "b87749d7a24c",
|
|
390 "name": "refinery_test",
|
|
391 "owner": "refinery-platform",
|
|
392 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
393 },
|
|
394 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
395 "tool_version": "0.1",
|
|
396 "type": "tool",
|
|
397 "uuid": "6b124c6d-9991-444c-b677-8a1e976dd0d3",
|
|
398 "workflow_outputs": []
|
|
399 },
|
|
400 "8": {
|
|
401 "annotation": "",
|
|
402 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
403 "errors": null,
|
|
404 "id": 8,
|
|
405 "input_connections": {
|
|
406 "input_file": {
|
|
407 "id": 6,
|
|
408 "output_name": "output_file"
|
|
409 }
|
|
410 },
|
|
411 "inputs": [
|
|
412 {
|
|
413 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
414 "name": "input_file"
|
|
415 }
|
|
416 ],
|
|
417 "label": null,
|
|
418 "name": "Refinery test tool 1-1",
|
|
419 "outputs": [
|
|
420 {
|
|
421 "name": "output_file",
|
|
422 "type": "txt"
|
|
423 }
|
|
424 ],
|
|
425 "position": {
|
|
426 "left": 1439.5,
|
|
427 "top": 287
|
|
428 },
|
|
429 "post_job_actions": {
|
|
430 "RenameDatasetActionoutput_file": {
|
|
431 "action_arguments": {
|
|
432 "newname": "test_01"
|
|
433 },
|
|
434 "action_type": "RenameDatasetAction",
|
|
435 "output_name": "output_file"
|
|
436 }
|
|
437 },
|
|
438 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
439 "tool_shed_repository": {
|
|
440 "changeset_revision": "b87749d7a24c",
|
|
441 "name": "refinery_test",
|
|
442 "owner": "refinery-platform",
|
|
443 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
444 },
|
|
445 "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
446 "tool_version": "0.1",
|
|
447 "type": "tool",
|
|
448 "uuid": "6c12fe60-10fb-4b89-aca1-8168684f75a9",
|
|
449 "workflow_outputs": [
|
|
450 {
|
|
451 "label": null,
|
|
452 "output_name": "output_file",
|
|
453 "uuid": "b1cdfb67-73b9-4638-87cf-5b32040243ac"
|
|
454 }
|
|
455 ]
|
|
456 },
|
|
457 "9": {
|
|
458 "annotation": "",
|
|
459 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_2-6/0.1",
|
|
460 "errors": null,
|
|
461 "id": 9,
|
|
462 "input_connections": {
|
|
463 "input_file1": {
|
|
464 "id": 6,
|
|
465 "output_name": "output_file"
|
|
466 },
|
|
467 "input_file2": {
|
|
468 "id": 7,
|
|
469 "output_name": "output_file"
|
|
470 }
|
|
471 },
|
|
472 "inputs": [
|
|
473 {
|
|
474 "description": "runtime parameter for tool Refinery test tool 2-6",
|
|
475 "name": "input_file1"
|
|
476 },
|
|
477 {
|
|
478 "description": "runtime parameter for tool Refinery test tool 2-6",
|
|
479 "name": "input_file2"
|
|
480 }
|
|
481 ],
|
|
482 "label": null,
|
|
483 "name": "Refinery test tool 2-6",
|
|
484 "outputs": [
|
|
485 {
|
|
486 "name": "output_file1",
|
|
487 "type": "txt"
|
|
488 },
|
|
489 {
|
|
490 "name": "output_file2",
|
|
491 "type": "txt"
|
|
492 },
|
|
493 {
|
|
494 "name": "output_file3",
|
|
495 "type": "txt"
|
|
496 },
|
|
497 {
|
|
498 "name": "output_file4",
|
|
499 "type": "txt"
|
|
500 },
|
|
501 {
|
|
502 "name": "output_file5",
|
|
503 "type": "txt"
|
|
504 },
|
|
505 {
|
|
506 "name": "output_file6",
|
|
507 "type": "txt"
|
|
508 }
|
|
509 ],
|
|
510 "position": {
|
|
511 "left": 1434.5,
|
|
512 "top": 405
|
|
513 },
|
|
514 "post_job_actions": {
|
|
515 "HideDatasetActionoutput_file1": {
|
|
516 "action_arguments": {},
|
|
517 "action_type": "HideDatasetAction",
|
|
518 "output_name": "output_file1"
|
|
519 },
|
|
520 "HideDatasetActionoutput_file2": {
|
|
521 "action_arguments": {},
|
|
522 "action_type": "HideDatasetAction",
|
|
523 "output_name": "output_file2"
|
|
524 },
|
|
525 "HideDatasetActionoutput_file3": {
|
|
526 "action_arguments": {},
|
|
527 "action_type": "HideDatasetAction",
|
|
528 "output_name": "output_file3"
|
|
529 },
|
|
530 "HideDatasetActionoutput_file4": {
|
|
531 "action_arguments": {},
|
|
532 "action_type": "HideDatasetAction",
|
|
533 "output_name": "output_file4"
|
|
534 },
|
|
535 "HideDatasetActionoutput_file5": {
|
|
536 "action_arguments": {},
|
|
537 "action_type": "HideDatasetAction",
|
|
538 "output_name": "output_file5"
|
|
539 },
|
|
540 "HideDatasetActionoutput_file6": {
|
|
541 "action_arguments": {},
|
|
542 "action_type": "HideDatasetAction",
|
|
543 "output_name": "output_file6"
|
|
544 }
|
|
545 },
|
|
546 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_2-6/0.1",
|
|
547 "tool_shed_repository": {
|
|
548 "changeset_revision": "b87749d7a24c",
|
|
549 "name": "refinery_test",
|
|
550 "owner": "refinery-platform",
|
|
551 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
552 },
|
|
553 "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"exit_code\": \"\\\"0\\\"\", \"sleep_time\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"input_file1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
|
|
554 "tool_version": "0.1",
|
|
555 "type": "tool",
|
|
556 "uuid": "60e1e5d6-e3b3-47c4-b1bf-6e8302380d29",
|
|
557 "workflow_outputs": []
|
|
558 },
|
|
559 "10": {
|
|
560 "annotation": "",
|
|
561 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
562 "errors": null,
|
|
563 "id": 10,
|
|
564 "input_connections": {
|
|
565 "input_file": {
|
|
566 "id": 7,
|
|
567 "output_name": "output_file"
|
|
568 }
|
|
569 },
|
|
570 "inputs": [
|
|
571 {
|
|
572 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
573 "name": "input_file"
|
|
574 }
|
|
575 ],
|
|
576 "label": null,
|
|
577 "name": "Refinery test tool 1-1",
|
|
578 "outputs": [
|
|
579 {
|
|
580 "name": "output_file",
|
|
581 "type": "txt"
|
|
582 }
|
|
583 ],
|
|
584 "position": {
|
|
585 "left": 1439.5,
|
|
586 "top": 686
|
|
587 },
|
|
588 "post_job_actions": {
|
|
589 "RenameDatasetActionoutput_file": {
|
|
590 "action_arguments": {
|
|
591 "newname": "test_02"
|
|
592 },
|
|
593 "action_type": "RenameDatasetAction",
|
|
594 "output_name": "output_file"
|
|
595 }
|
|
596 },
|
|
597 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
598 "tool_shed_repository": {
|
|
599 "changeset_revision": "b87749d7a24c",
|
|
600 "name": "refinery_test",
|
|
601 "owner": "refinery-platform",
|
|
602 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
603 },
|
|
604 "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
605 "tool_version": "0.1",
|
|
606 "type": "tool",
|
|
607 "uuid": "ed365790-6058-4781-b793-d10fb502c501",
|
|
608 "workflow_outputs": [
|
|
609 {
|
|
610 "label": null,
|
|
611 "output_name": "output_file",
|
|
612 "uuid": "21b744f7-912d-4e94-aa2b-cae246eb48f0"
|
|
613 }
|
|
614 ]
|
|
615 },
|
|
616 "11": {
|
|
617 "annotation": "",
|
|
618 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
619 "errors": null,
|
|
620 "id": 11,
|
|
621 "input_connections": {
|
|
622 "input_file": {
|
|
623 "id": 9,
|
|
624 "output_name": "output_file2"
|
|
625 }
|
|
626 },
|
|
627 "inputs": [
|
|
628 {
|
|
629 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
630 "name": "input_file"
|
|
631 }
|
|
632 ],
|
|
633 "label": null,
|
|
634 "name": "Refinery test tool 1-1",
|
|
635 "outputs": [
|
|
636 {
|
|
637 "name": "output_file",
|
|
638 "type": "txt"
|
|
639 }
|
|
640 ],
|
|
641 "position": {
|
|
642 "left": 1650.5,
|
|
643 "top": 446
|
|
644 },
|
|
645 "post_job_actions": {
|
|
646 "HideDatasetActionoutput_file": {
|
|
647 "action_arguments": {},
|
|
648 "action_type": "HideDatasetAction",
|
|
649 "output_name": "output_file"
|
|
650 }
|
|
651 },
|
|
652 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
653 "tool_shed_repository": {
|
|
654 "changeset_revision": "b87749d7a24c",
|
|
655 "name": "refinery_test",
|
|
656 "owner": "refinery-platform",
|
|
657 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
658 },
|
|
659 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
660 "tool_version": "0.1",
|
|
661 "type": "tool",
|
|
662 "uuid": "d972e887-d691-452b-afe0-3feaa6e8e2ad",
|
|
663 "workflow_outputs": []
|
|
664 },
|
|
665 "12": {
|
|
666 "annotation": "",
|
|
667 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
668 "errors": null,
|
|
669 "id": 12,
|
|
670 "input_connections": {
|
|
671 "input_file": {
|
|
672 "id": 9,
|
|
673 "output_name": "output_file4"
|
|
674 }
|
|
675 },
|
|
676 "inputs": [
|
|
677 {
|
|
678 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
679 "name": "input_file"
|
|
680 }
|
|
681 ],
|
|
682 "label": null,
|
|
683 "name": "Refinery test tool 1-1",
|
|
684 "outputs": [
|
|
685 {
|
|
686 "name": "output_file",
|
|
687 "type": "txt"
|
|
688 }
|
|
689 ],
|
|
690 "position": {
|
|
691 "left": 1652.5,
|
|
692 "top": 568
|
|
693 },
|
|
694 "post_job_actions": {
|
|
695 "HideDatasetActionoutput_file": {
|
|
696 "action_arguments": {},
|
|
697 "action_type": "HideDatasetAction",
|
|
698 "output_name": "output_file"
|
|
699 }
|
|
700 },
|
|
701 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
702 "tool_shed_repository": {
|
|
703 "changeset_revision": "b87749d7a24c",
|
|
704 "name": "refinery_test",
|
|
705 "owner": "refinery-platform",
|
|
706 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
707 },
|
|
708 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
709 "tool_version": "0.1",
|
|
710 "type": "tool",
|
|
711 "uuid": "d04c9fd7-0718-4a62-821a-3ccc297f253b",
|
|
712 "workflow_outputs": []
|
|
713 },
|
|
714 "13": {
|
|
715 "annotation": "",
|
|
716 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
717 "errors": null,
|
|
718 "id": 13,
|
|
719 "input_connections": {
|
|
720 "input_file": {
|
|
721 "id": 11,
|
|
722 "output_name": "output_file"
|
|
723 }
|
|
724 },
|
|
725 "inputs": [
|
|
726 {
|
|
727 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
728 "name": "input_file"
|
|
729 }
|
|
730 ],
|
|
731 "label": null,
|
|
732 "name": "Refinery test tool 1-1",
|
|
733 "outputs": [
|
|
734 {
|
|
735 "name": "output_file",
|
|
736 "type": "txt"
|
|
737 }
|
|
738 ],
|
|
739 "position": {
|
|
740 "left": 1873.5,
|
|
741 "top": 448
|
|
742 },
|
|
743 "post_job_actions": {
|
|
744 "HideDatasetActionoutput_file": {
|
|
745 "action_arguments": {},
|
|
746 "action_type": "HideDatasetAction",
|
|
747 "output_name": "output_file"
|
|
748 }
|
|
749 },
|
|
750 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
751 "tool_shed_repository": {
|
|
752 "changeset_revision": "b87749d7a24c",
|
|
753 "name": "refinery_test",
|
|
754 "owner": "refinery-platform",
|
|
755 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
756 },
|
|
757 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
758 "tool_version": "0.1",
|
|
759 "type": "tool",
|
|
760 "uuid": "00639c4a-aaf6-44cd-a8fe-48b628ccd1be",
|
|
761 "workflow_outputs": []
|
|
762 },
|
|
763 "14": {
|
|
764 "annotation": "",
|
|
765 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
766 "errors": null,
|
|
767 "id": 14,
|
|
768 "input_connections": {
|
|
769 "input_file": {
|
|
770 "id": 12,
|
|
771 "output_name": "output_file"
|
|
772 }
|
|
773 },
|
|
774 "inputs": [
|
|
775 {
|
|
776 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
777 "name": "input_file"
|
|
778 }
|
|
779 ],
|
|
780 "label": null,
|
|
781 "name": "Refinery test tool 1-1",
|
|
782 "outputs": [
|
|
783 {
|
|
784 "name": "output_file",
|
|
785 "type": "txt"
|
|
786 }
|
|
787 ],
|
|
788 "position": {
|
|
789 "left": 1873.5,
|
|
790 "top": 571
|
|
791 },
|
|
792 "post_job_actions": {
|
|
793 "HideDatasetActionoutput_file": {
|
|
794 "action_arguments": {},
|
|
795 "action_type": "HideDatasetAction",
|
|
796 "output_name": "output_file"
|
|
797 }
|
|
798 },
|
|
799 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
800 "tool_shed_repository": {
|
|
801 "changeset_revision": "b87749d7a24c",
|
|
802 "name": "refinery_test",
|
|
803 "owner": "refinery-platform",
|
|
804 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
805 },
|
|
806 "tool_state": "{\"__page__\": 0, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
807 "tool_version": "0.1",
|
|
808 "type": "tool",
|
|
809 "uuid": "433002cf-6ff4-4ab5-ace0-798f1bfffdb0",
|
|
810 "workflow_outputs": []
|
|
811 },
|
|
812 "15": {
|
|
813 "annotation": "{\n \"parameters\": [\n {\n \"name\": \"exit_code\",\n \"description\": \"Exit code for the final Refinery Test Tool 1-1 in the workflow\",\n \"value_type\": \"INTEGER\",\n \"default_value\": 0\n },\n {\n \"name\": \"p_fail\",\n \"description\": \"Probability of failure for the final Refinery Test Tool 1-1 in the workflow\",\n \"value_type\": \"FLOAT\",\n \"default_value\": 0.0\n },\n {\n \"name\": \"empty_outfile\",\n \"description\": \"Whether or not the final Refinery Test Tool 1-1 in the workflow will produce an empty output file\",\n \"value_type\": \"BOOLEAN\",\n \"default_value\": false\n }\n ]\n}",
|
|
814 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
815 "errors": null,
|
|
816 "id": 15,
|
|
817 "input_connections": {
|
|
818 "input_file": {
|
|
819 "id": 13,
|
|
820 "output_name": "output_file"
|
|
821 }
|
|
822 },
|
|
823 "inputs": [
|
|
824 {
|
|
825 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
826 "name": "input_file"
|
|
827 }
|
|
828 ],
|
|
829 "label": null,
|
|
830 "name": "Refinery test tool 1-1",
|
|
831 "outputs": [
|
|
832 {
|
|
833 "name": "output_file",
|
|
834 "type": "txt"
|
|
835 }
|
|
836 ],
|
|
837 "position": {
|
|
838 "left": 2098.5,
|
|
839 "top": 453
|
|
840 },
|
|
841 "post_job_actions": {
|
|
842 "RenameDatasetActionoutput_file": {
|
|
843 "action_arguments": {
|
|
844 "newname": "test_03"
|
|
845 },
|
|
846 "action_type": "RenameDatasetAction",
|
|
847 "output_name": "output_file"
|
|
848 }
|
|
849 },
|
|
850 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
851 "tool_shed_repository": {
|
|
852 "changeset_revision": "b87749d7a24c",
|
|
853 "name": "refinery_test",
|
|
854 "owner": "refinery-platform",
|
|
855 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
856 },
|
|
857 "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
858 "tool_version": "0.1",
|
|
859 "type": "tool",
|
|
860 "uuid": "f6ba1608-8c0d-41de-8774-6b69c7808370",
|
|
861 "workflow_outputs": [
|
|
862 {
|
|
863 "label": null,
|
|
864 "output_name": "output_file",
|
|
865 "uuid": "2bdd91bd-d2b9-4516-b638-c0545fc46f9d"
|
|
866 }
|
|
867 ]
|
|
868 },
|
|
869 "16": {
|
|
870 "annotation": "",
|
|
871 "content_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
872 "errors": null,
|
|
873 "id": 16,
|
|
874 "input_connections": {
|
|
875 "input_file": {
|
|
876 "id": 14,
|
|
877 "output_name": "output_file"
|
|
878 }
|
|
879 },
|
|
880 "inputs": [
|
|
881 {
|
|
882 "description": "runtime parameter for tool Refinery test tool 1-1",
|
|
883 "name": "input_file"
|
|
884 }
|
|
885 ],
|
|
886 "label": null,
|
|
887 "name": "Refinery test tool 1-1",
|
|
888 "outputs": [
|
|
889 {
|
|
890 "name": "output_file",
|
|
891 "type": "txt"
|
|
892 }
|
|
893 ],
|
|
894 "position": {
|
|
895 "left": 2096.5,
|
|
896 "top": 574
|
|
897 },
|
|
898 "post_job_actions": {
|
|
899 "RenameDatasetActionoutput_file": {
|
|
900 "action_arguments": {
|
|
901 "newname": "test_04"
|
|
902 },
|
|
903 "action_type": "RenameDatasetAction",
|
|
904 "output_name": "output_file"
|
|
905 }
|
|
906 },
|
|
907 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/refinery-platform/refinery_test/refinery_test_1-1/0.1",
|
|
908 "tool_shed_repository": {
|
|
909 "changeset_revision": "b87749d7a24c",
|
|
910 "name": "refinery_test",
|
|
911 "owner": "refinery-platform",
|
|
912 "tool_shed": "testtoolshed.g2.bx.psu.edu"
|
|
913 },
|
|
914 "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"stdout\": \"\\\"false\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"false\\\"\", \"stderr\": \"\\\"false\\\"\", \"sleep_time\": \"\\\"0\\\"\"}",
|
|
915 "tool_version": "0.1",
|
|
916 "type": "tool",
|
|
917 "uuid": "cf9af5ab-4aab-4db2-953c-e507c9c3b04a",
|
|
918 "workflow_outputs": [
|
|
919 {
|
|
920 "label": null,
|
|
921 "output_name": "output_file",
|
|
922 "uuid": "a36ae36f-67bb-41da-b288-574ab16acc58"
|
|
923 }
|
|
924 ]
|
|
925 }
|
|
926 },
|
|
927 "uuid": "098ea63d-c314-4e77-b154-7711077f3d5d"
|
|
928 } |