Mercurial > repos > bgruening > find_genes_located_nearby_workflow

comparison find_genes_located_nearby.ga @ 0:db68266f7364 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 24 Feb 2015 04:48:44 -0500
parents
children 38b08a771e7e
comparison
equal deleted inserted replaced
-1:000000000000 0:db68266f7364
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "Input are two protein genes in FASTA format. They will be blasted with tblastn against the NCBI NR database. Both results are compared and hits are returned that are close to each other.",
4 "format-version": "0.1",
5 "name": "Finding 2 genes close to each other",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Protein in FASTA format"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 247,
21 "top": 307
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Protein in FASTA format\"}",
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": "Protein in FASTA format"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 244,
44 "top": 386
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"Protein in FASTA format\"}",
49 "tool_version": null,
50 "type": "data_input",
51 "user_outputs": []
52 },
53 "2": {
54 "annotation": "",
55 "id": 2,
56 "input_connections": {
57 "query": {
58 "id": 0,
59 "output_name": "output"
60 }
61 },
62 "inputs": [],
63 "name": "NCBI BLAST+ tblastn",
64 "outputs": [
65 {
66 "name": "output1",
67 "type": "tabular"
68 }
69 ],
70 "position": {
71 "left": 380.6166687011719,
72 "top": 224.61666870117188
73 },
74 "post_job_actions": {
75 "HideDatasetActionoutput1": {
76 "action_arguments": {},
77 "action_type": "HideDatasetAction",
78 "output_name": "output1"
79 }
80 },
81 "tool_errors": null,
82 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.01",
83 "tool_state": "{\"__page__\": 0, \"evalue_cutoff\": \"\\\"0.001\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": \\\"nt_28-09-14\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"sseqid\\\", \\\"sstart\\\", \\\"send\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": null}\", \"query\": \"null\"}",
84 "tool_version": "0.1.01",
85 "type": "tool",
86 "user_outputs": []
87 },
88 "3": {
89 "annotation": "",
90 "id": 3,
91 "input_connections": {
92 "query": {
93 "id": 1,
94 "output_name": "output"
95 }
96 },
97 "inputs": [],
98 "name": "NCBI BLAST+ tblastn",
99 "outputs": [
100 {
101 "name": "output1",
102 "type": "tabular"
103 }
104 ],
105 "position": {
106 "left": 393.6166687011719,
107 "top": 444.6166687011719
108 },
109 "post_job_actions": {
110 "HideDatasetActionoutput1": {
111 "action_arguments": {},
112 "action_type": "HideDatasetAction",
113 "output_name": "output1"
114 }
115 },
116 "tool_errors": null,
117 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.01",
118 "tool_state": "{\"__page__\": 0, \"evalue_cutoff\": \"\\\"0.001\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": \\\"nt_28-09-14\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"sseqid\\\", \\\"sstart\\\", \\\"send\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": null}\", \"query\": \"null\"}",
119 "tool_version": "0.1.01",
120 "type": "tool",
121 "user_outputs": []
122 },
123 "4": {
124 "annotation": "",
125 "id": 4,
126 "input_connections": {
127 "input": {
128 "id": 2,
129 "output_name": "output1"
130 }
131 },
132 "inputs": [],
133 "name": "Filter",
134 "outputs": [
135 {
136 "name": "out_file1",
137 "type": "input"
138 }
139 ],
140 "position": {
141 "left": 656.5,
142 "top": 190.5
143 },
144 "post_job_actions": {},
145 "tool_errors": null,
146 "tool_id": "Filter1",
147 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4>150\\\"\", \"__page__\": 0}",
148 "tool_version": "1.1.0",
149 "type": "tool",
150 "user_outputs": []
151 },
152 "5": {
153 "annotation": "",
154 "id": 5,
155 "input_connections": {
156 "input": {
157 "id": 3,
158 "output_name": "output1"
159 }
160 },
161 "inputs": [],
162 "name": "Filter",
163 "outputs": [
164 {
165 "name": "out_file1",
166 "type": "input"
167 }
168 ],
169 "position": {
170 "left": 609.5,
171 "top": 349.5
172 },
173 "post_job_actions": {
174 "HideDatasetActionout_file1": {
175 "action_arguments": {},
176 "action_type": "HideDatasetAction",
177 "output_name": "out_file1"
178 }
179 },
180 "tool_errors": null,
181 "tool_id": "Filter1",
182 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c4>150\\\"\", \"__page__\": 0}",
183 "tool_version": "1.1.0",
184 "type": "tool",
185 "user_outputs": []
186 },
187 "6": {
188 "annotation": "",
189 "id": 6,
190 "input_connections": {
191 "input": {
192 "id": 4,
193 "output_name": "out_file1"
194 }
195 },
196 "inputs": [],
197 "name": "Compute",
198 "outputs": [
199 {
200 "name": "out_file1",
201 "type": "input"
202 }
203 ],
204 "position": {
205 "left": 715,
206 "top": 224
207 },
208 "post_job_actions": {
209 "HideDatasetActionout_file1": {
210 "action_arguments": {},
211 "action_type": "HideDatasetAction",
212 "output_name": "out_file1"
213 }
214 },
215 "tool_errors": null,
216 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
217 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"max(c3,c2)\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"round\": \"\\\"yes\\\"\"}",
218 "tool_version": "1.1.0",
219 "type": "tool",
220 "user_outputs": []
221 },
222 "7": {
223 "annotation": "",
224 "id": 7,
225 "input_connections": {
226 "input": {
227 "id": 5,
228 "output_name": "out_file1"
229 }
230 },
231 "inputs": [],
232 "name": "Compute",
233 "outputs": [
234 {
235 "name": "out_file1",
236 "type": "input"
237 }
238 ],
239 "position": {
240 "left": 661.5,
241 "top": 381.5
242 },
243 "post_job_actions": {
244 "HideDatasetActionout_file1": {
245 "action_arguments": {},
246 "action_type": "HideDatasetAction",
247 "output_name": "out_file1"
248 }
249 },
250 "tool_errors": null,
251 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
252 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"min(c3,c2)\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
253 "tool_version": "1.1.0",
254 "type": "tool",
255 "user_outputs": []
256 },
257 "8": {
258 "annotation": "",
259 "id": 8,
260 "input_connections": {
261 "input": {
262 "id": 6,
263 "output_name": "out_file1"
264 }
265 },
266 "inputs": [],
267 "name": "Compute",
268 "outputs": [
269 {
270 "name": "out_file1",
271 "type": "input"
272 }
273 ],
274 "position": {
275 "left": 767,
276 "top": 260
277 },
278 "post_job_actions": {
279 "HideDatasetActionout_file1": {
280 "action_arguments": {},
281 "action_type": "HideDatasetAction",
282 "output_name": "out_file1"
283 }
284 },
285 "tool_errors": null,
286 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
287 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"min(c3,c2)\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"round\": \"\\\"yes\\\"\"}",
288 "tool_version": "1.1.0",
289 "type": "tool",
290 "user_outputs": []
291 },
292 "9": {
293 "annotation": "",
294 "id": 9,
295 "input_connections": {
296 "input": {
297 "id": 7,
298 "output_name": "out_file1"
299 }
300 },
301 "inputs": [],
302 "name": "Compute",
303 "outputs": [
304 {
305 "name": "out_file1",
306 "type": "input"
307 }
308 ],
309 "position": {
310 "left": 714.5,
311 "top": 416.5
312 },
313 "post_job_actions": {
314 "HideDatasetActionout_file1": {
315 "action_arguments": {},
316 "action_type": "HideDatasetAction",
317 "output_name": "out_file1"
318 }
319 },
320 "tool_errors": null,
321 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
322 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"max(c3,c2)\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
323 "tool_version": "1.1.0",
324 "type": "tool",
325 "user_outputs": []
326 },
327 "10": {
328 "annotation": "",
329 "id": 10,
330 "input_connections": {
331 "input": {
332 "id": 8,
333 "output_name": "out_file1"
334 }
335 },
336 "inputs": [],
337 "name": "Cut",
338 "outputs": [
339 {
340 "name": "out_file1",
341 "type": "tabular"
342 }
343 ],
344 "position": {
345 "left": 957,
346 "top": 271
347 },
348 "post_job_actions": {
349 "ChangeDatatypeActionout_file1": {
350 "action_arguments": {
351 "newtype": "interval"
352 },
353 "action_type": "ChangeDatatypeAction",
354 "output_name": "out_file1"
355 }
356 },
357 "tool_errors": null,
358 "tool_id": "Cut1",
359 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1,c6,c5\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
360 "tool_version": "1.0.2",
361 "type": "tool",
362 "user_outputs": []
363 },
364 "11": {
365 "annotation": "",
366 "id": 11,
367 "input_connections": {
368 "input": {
369 "id": 9,
370 "output_name": "out_file1"
371 }
372 },
373 "inputs": [],
374 "name": "Compute",
375 "outputs": [
376 {
377 "name": "out_file1",
378 "type": "input"
379 }
380 ],
381 "position": {
382 "left": 768.5,
383 "top": 452.5
384 },
385 "post_job_actions": {
386 "HideDatasetActionout_file1": {
387 "action_arguments": {},
388 "action_type": "HideDatasetAction",
389 "output_name": "out_file1"
390 }
391 },
392 "tool_errors": null,
393 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
394 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"max(c5-10000,1)\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
395 "tool_version": "1.1.0",
396 "type": "tool",
397 "user_outputs": []
398 },
399 "12": {
400 "annotation": "",
401 "id": 12,
402 "input_connections": {
403 "input": {
404 "id": 11,
405 "output_name": "out_file1"
406 }
407 },
408 "inputs": [],
409 "name": "Compute",
410 "outputs": [
411 {
412 "name": "out_file1",
413 "type": "input"
414 }
415 ],
416 "position": {
417 "left": 819.5,
418 "top": 489.5
419 },
420 "post_job_actions": {},
421 "tool_errors": null,
422 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
423 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c6+10000\\\"\", \"round\": \"\\\"yes\\\"\", \"__page__\": 0}",
424 "tool_version": "1.1.0",
425 "type": "tool",
426 "user_outputs": []
427 },
428 "13": {
429 "annotation": "",
430 "id": 13,
431 "input_connections": {
432 "input": {
433 "id": 12,
434 "output_name": "out_file1"
435 }
436 },
437 "inputs": [],
438 "name": "Cut",
439 "outputs": [
440 {
441 "name": "out_file1",
442 "type": "tabular"
443 }
444 ],
445 "position": {
446 "left": 953.5,
447 "top": 392.5
448 },
449 "post_job_actions": {
450 "ChangeDatatypeActionout_file1": {
451 "action_arguments": {
452 "newtype": "interval"
453 },
454 "action_type": "ChangeDatatypeAction",
455 "output_name": "out_file1"
456 }
457 },
458 "tool_errors": null,
459 "tool_id": "Cut1",
460 "tool_state": "{\"columnList\": \"\\\"c1,c7,c8\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
461 "tool_version": "1.0.2",
462 "type": "tool",
463 "user_outputs": []
464 },
465 "14": {
466 "annotation": "",
467 "id": 14,
468 "input_connections": {
469 "input1": {
470 "id": 10,
471 "output_name": "out_file1"
472 },
473 "input2": {
474 "id": 13,
475 "output_name": "out_file1"
476 }
477 },
478 "inputs": [],
479 "name": "Intersect",
480 "outputs": [
481 {
482 "name": "output",
483 "type": "input"
484 }
485 ],
486 "position": {
487 "left": 1136,
488 "top": 325
489 },
490 "post_job_actions": {
491 "RenameDatasetActionoutput": {
492 "action_arguments": {
493 "newname": "Protein 1 positions nearby Protein 2"
494 },
495 "action_type": "RenameDatasetAction",
496 "output_name": "output"
497 }
498 },
499 "tool_errors": null,
500 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/0.0.1",
501 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"returntype\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
502 "tool_version": "0.0.1",
503 "type": "tool",
504 "user_outputs": []
505 },
506 "15": {
507 "annotation": "",
508 "id": 15,
509 "input_connections": {
510 "input1": {
511 "id": 14,
512 "output_name": "output"
513 }
514 },
515 "inputs": [],
516 "name": "Group",
517 "outputs": [
518 {
519 "name": "out_file1",
520 "type": "tabular"
521 }
522 ],
523 "position": {
524 "left": 1139.5,
525 "top": 488
526 },
527 "post_job_actions": {
528 "RenameDatasetActionout_file1": {
529 "action_arguments": {
530 "newname": "Counting hits per genome"
531 },
532 "action_type": "RenameDatasetAction",
533 "output_name": "out_file1"
534 }
535 },
536 "tool_errors": null,
537 "tool_id": "Grouping1",
538 "tool_state": "{\"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"length\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}",
539 "tool_version": "2.1.0",
540 "type": "tool",
541 "user_outputs": []
542 }
543 },
544 "uuid": "10f50489-adf1-4257-a971-8a814ef98f6c"
545 }