comparison PeptideShaker_PSM_REPORT_to_NOVEL_peptides.ga @ 0:05ab719b9b93 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/asms_tutorial_2016 commit 6671681f22de8443c29a6c5824f14175c66daffb-dirty
author galaxyp
date Fri, 13 May 2016 09:34:49 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:05ab719b9b93
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "ASMS 2016: Session 3: Workflow for PeptideShaker PSM REPORT to NOVEL peptides",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "id": 0,
11 "input_connections": {},
12 "inputs": [
13 {
14 "description": "",
15 "name": "PSM REPORT from PeptideShaker Output"
16 }
17 ],
18 "label": null,
19 "name": "Input dataset",
20 "outputs": [],
21 "position": {
22 "left": 173.078125,
23 "top": 223.53125
24 },
25 "tool_errors": null,
26 "tool_id": null,
27 "tool_state": "{\"name\": \"PSM REPORT from PeptideShaker Output\"}",
28 "tool_version": null,
29 "type": "data_input",
30 "uuid": "57ddf9d9-243a-494e-ab80-9e4e847b1bb3",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "b766949c-89c0-4596-90c9-5a7cc2e6ba9f"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": "Remove beginning1",
42 "id": 1,
43 "input_connections": {
44 "input": {
45 "id": 0,
46 "output_name": "output"
47 }
48 },
49 "inputs": [],
50 "label": null,
51 "name": "Remove beginning",
52 "outputs": [
53 {
54 "name": "out_file1",
55 "type": "input"
56 }
57 ],
58 "position": {
59 "left": 358.078125,
60 "top": 341.03125
61 },
62 "post_job_actions": {
63 "HideDatasetActionout_file1": {
64 "action_arguments": {},
65 "action_type": "HideDatasetAction",
66 "output_name": "out_file1"
67 }
68 },
69 "tool_errors": null,
70 "tool_id": "Remove beginning1",
71 "tool_state": "{\"__page__\": 0, \"num_lines\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
72 "tool_version": "1.0.0",
73 "type": "tool",
74 "uuid": "39a390bf-a9ce-4b87-8003-67affe217cbc",
75 "workflow_outputs": []
76 },
77 "2": {
78 "annotation": "",
79 "content_id": "sort1",
80 "id": 2,
81 "input_connections": {
82 "input": {
83 "id": 1,
84 "output_name": "out_file1"
85 }
86 },
87 "inputs": [],
88 "label": null,
89 "name": "Sort",
90 "outputs": [
91 {
92 "name": "out_file1",
93 "type": "input"
94 }
95 ],
96 "position": {
97 "left": 357.0625,
98 "top": 438.96875
99 },
100 "post_job_actions": {
101 "HideDatasetActionout_file1": {
102 "action_arguments": {},
103 "action_type": "HideDatasetAction",
104 "output_name": "out_file1"
105 }
106 },
107 "tool_errors": null,
108 "tool_id": "sort1",
109 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"num\\\"\", \"column\": \"\\\"7\\\"\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"DESC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": \\\"19\\\", \\\"other_style\\\": \\\"num\\\"}]\"}",
110 "tool_version": "1.0.3",
111 "type": "tool",
112 "uuid": "621fcb57-968e-40e1-b759-fdc2b5b7db49",
113 "workflow_outputs": []
114 },
115 "3": {
116 "annotation": "",
117 "content_id": "addValue",
118 "id": 3,
119 "input_connections": {
120 "input": {
121 "id": 2,
122 "output_name": "out_file1"
123 }
124 },
125 "inputs": [],
126 "label": null,
127 "name": "Add column",
128 "outputs": [
129 {
130 "name": "out_file1",
131 "type": "input"
132 }
133 ],
134 "position": {
135 "left": 378.078125,
136 "top": 528
137 },
138 "post_job_actions": {
139 "HideDatasetActionout_file1": {
140 "action_arguments": {},
141 "action_type": "HideDatasetAction",
142 "output_name": "out_file1"
143 }
144 },
145 "tool_errors": null,
146 "tool_id": "addValue",
147 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"exp\": \"\\\"1\\\"\", \"iterate\": \"\\\"yes\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
148 "tool_version": "1.0.0",
149 "type": "tool",
150 "uuid": "5587f07a-f6da-4125-a287-4850a65905d5",
151 "workflow_outputs": []
152 },
153 "4": {
154 "annotation": "",
155 "content_id": "Grouping1",
156 "id": 4,
157 "input_connections": {
158 "input1": {
159 "id": 3,
160 "output_name": "out_file1"
161 }
162 },
163 "inputs": [],
164 "label": null,
165 "name": "Group",
166 "outputs": [
167 {
168 "name": "out_file1",
169 "type": "tabular"
170 }
171 ],
172 "position": {
173 "left": 379.078125,
174 "top": 671.015625
175 },
176 "post_job_actions": {
177 "HideDatasetActionout_file1": {
178 "action_arguments": {},
179 "action_type": "HideDatasetAction",
180 "output_name": "out_file1"
181 }
182 },
183 "tool_errors": null,
184 "tool_id": "Grouping1",
185 "tool_state": "{\"operations\": \"[{\\\"opcol\\\": \\\"21\\\", \\\"__index__\\\": 0, \\\"optype\\\": \\\"min\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"\\\"7\\\"\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}",
186 "tool_version": "2.1.0",
187 "type": "tool",
188 "uuid": "5f5ec71a-3e02-46b8-891c-53987abd52ce",
189 "workflow_outputs": []
190 },
191 "5": {
192 "annotation": "",
193 "content_id": "join1",
194 "id": 5,
195 "input_connections": {
196 "input1": {
197 "id": 3,
198 "output_name": "out_file1"
199 },
200 "input2": {
201 "id": 4,
202 "output_name": "out_file1"
203 }
204 },
205 "inputs": [],
206 "label": null,
207 "name": "Join two Datasets",
208 "outputs": [
209 {
210 "name": "out_file1",
211 "type": "input"
212 }
213 ],
214 "position": {
215 "left": 603.09375,
216 "top": 594.03125
217 },
218 "post_job_actions": {
219 "HideDatasetActionout_file1": {
220 "action_arguments": {},
221 "action_type": "HideDatasetAction",
222 "output_name": "out_file1"
223 }
224 },
225 "tool_errors": null,
226 "tool_id": "join1",
227 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"21\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input1\": \"null\", \"unmatched\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
228 "tool_version": "2.0.2",
229 "type": "tool",
230 "uuid": "2d1ab280-cc31-4331-9442-50ed2c9e5ee7",
231 "workflow_outputs": []
232 },
233 "6": {
234 "annotation": "",
235 "content_id": "Cut1",
236 "id": 6,
237 "input_connections": {
238 "input": {
239 "id": 5,
240 "output_name": "out_file1"
241 }
242 },
243 "inputs": [],
244 "label": null,
245 "name": "Cut",
246 "outputs": [
247 {
248 "name": "out_file1",
249 "type": "tabular"
250 }
251 ],
252 "position": {
253 "left": 384.078125,
254 "top": 804.015625
255 },
256 "post_job_actions": {
257 "HideDatasetActionout_file1": {
258 "action_arguments": {},
259 "action_type": "HideDatasetAction",
260 "output_name": "out_file1"
261 }
262 },
263 "tool_errors": null,
264 "tool_id": "Cut1",
265 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1-c21\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
266 "tool_version": "1.0.2",
267 "type": "tool",
268 "uuid": "52912df8-4b48-4c2e-8a0d-6f587c6efea4",
269 "workflow_outputs": []
270 },
271 "7": {
272 "annotation": "",
273 "content_id": "Grep1",
274 "id": 7,
275 "input_connections": {
276 "input": {
277 "id": 6,
278 "output_name": "out_file1"
279 }
280 },
281 "inputs": [],
282 "label": null,
283 "name": "Select",
284 "outputs": [
285 {
286 "name": "out_file1",
287 "type": "input"
288 }
289 ],
290 "position": {
291 "left": 496.09375,
292 "top": 916.015625
293 },
294 "post_job_actions": {
295 "HideDatasetActionout_file1": {
296 "action_arguments": {},
297 "action_type": "HideDatasetAction",
298 "output_name": "out_file1"
299 }
300 },
301 "tool_errors": null,
302 "tool_id": "Grep1",
303 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"^\\\\\\\\d+\\\\\\\\tpr.B[^\\\\\\\\t,]*(, pr.B[^\\\\\\\\t,]*)*\\\\\\\\t.*$\\\"\"}",
304 "tool_version": "1.0.1",
305 "type": "tool",
306 "uuid": "52423717-3315-490a-b695-2bb491dcdedf",
307 "workflow_outputs": []
308 },
309 "8": {
310 "annotation": "",
311 "content_id": "Cut1",
312 "id": 8,
313 "input_connections": {
314 "input": {
315 "id": 7,
316 "output_name": "out_file1"
317 }
318 },
319 "inputs": [],
320 "label": null,
321 "name": "Cut",
322 "outputs": [
323 {
324 "name": "out_file1",
325 "type": "tabular"
326 }
327 ],
328 "position": {
329 "left": 886.0625,
330 "top": 216.96875
331 },
332 "post_job_actions": {
333 "RenameDatasetActionout_file1": {
334 "action_arguments": {
335 "newname": "PSM REPORT of potential novel PEPTIDES"
336 },
337 "action_type": "RenameDatasetAction",
338 "output_name": "out_file1"
339 }
340 },
341 "tool_errors": null,
342 "tool_id": "Cut1",
343 "tool_state": "{\"columnList\": \"\\\"c1-c20\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
344 "tool_version": "1.0.2",
345 "type": "tool",
346 "uuid": "b76031af-3ac7-4905-9727-5807b61f5478",
347 "workflow_outputs": [
348 {
349 "label": null,
350 "output_name": "out_file1",
351 "uuid": "e6bb92fb-57b2-4165-a0b8-eaae69762cf8"
352 }
353 ]
354 },
355 "9": {
356 "annotation": "",
357 "content_id": "Cut1",
358 "id": 9,
359 "input_connections": {
360 "input": {
361 "id": 7,
362 "output_name": "out_file1"
363 }
364 },
365 "inputs": [],
366 "label": null,
367 "name": "Cut",
368 "outputs": [
369 {
370 "name": "out_file1",
371 "type": "tabular"
372 }
373 ],
374 "position": {
375 "left": 551.078125,
376 "top": 1038
377 },
378 "post_job_actions": {
379 "HideDatasetActionout_file1": {
380 "action_arguments": {},
381 "action_type": "HideDatasetAction",
382 "output_name": "out_file1"
383 }
384 },
385 "tool_errors": null,
386 "tool_id": "Cut1",
387 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c3,c21\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
388 "tool_version": "1.0.2",
389 "type": "tool",
390 "uuid": "a80ae099-7298-432d-9884-9e68248efe4e",
391 "workflow_outputs": []
392 },
393 "10": {
394 "annotation": "",
395 "content_id": "Cut1",
396 "id": 10,
397 "input_connections": {
398 "input": {
399 "id": 8,
400 "output_name": "out_file1"
401 }
402 },
403 "inputs": [],
404 "label": null,
405 "name": "Cut",
406 "outputs": [
407 {
408 "name": "out_file1",
409 "type": "tabular"
410 }
411 ],
412 "position": {
413 "left": 893.0625,
414 "top": 326.015625
415 },
416 "post_job_actions": {
417 "RenameDatasetActionout_file1": {
418 "action_arguments": {
419 "newname": "Potential Novel PEPTIDES"
420 },
421 "action_type": "RenameDatasetAction",
422 "output_name": "out_file1"
423 }
424 },
425 "tool_errors": null,
426 "tool_id": "Cut1",
427 "tool_state": "{\"columnList\": \"\\\"c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
428 "tool_version": "1.0.2",
429 "type": "tool",
430 "uuid": "08714c16-4992-429b-a719-eee903206f8e",
431 "workflow_outputs": [
432 {
433 "label": null,
434 "output_name": "out_file1",
435 "uuid": "97dcd310-1fee-43bc-ba96-e763c6146ffc"
436 }
437 ]
438 },
439 "11": {
440 "annotation": "",
441 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
442 "id": 11,
443 "input_connections": {
444 "input": {
445 "id": 10,
446 "output_name": "out_file1"
447 }
448 },
449 "inputs": [],
450 "label": null,
451 "name": "Tabular-to-FASTA",
452 "outputs": [
453 {
454 "name": "output",
455 "type": "fasta"
456 }
457 ],
458 "position": {
459 "left": 902.078125,
460 "top": 440
461 },
462 "post_job_actions": {
463 "HideDatasetActionoutput": {
464 "action_arguments": {},
465 "action_type": "HideDatasetAction",
466 "output_name": "output"
467 }
468 },
469 "tool_errors": null,
470 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
471 "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
472 "tool_version": "1.1.0",
473 "type": "tool",
474 "uuid": "2903a6de-b7c6-4b1d-84bb-df4423471748",
475 "workflow_outputs": []
476 },
477 "12": {
478 "annotation": "",
479 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0",
480 "id": 12,
481 "input_connections": {
482 "input": {
483 "id": 11,
484 "output_name": "output"
485 }
486 },
487 "inputs": [],
488 "label": null,
489 "name": "Compute sequence length",
490 "outputs": [
491 {
492 "name": "output",
493 "type": "tabular"
494 }
495 ],
496 "position": {
497 "left": 857.125,
498 "top": 564.015625
499 },
500 "post_job_actions": {
501 "HideDatasetActionoutput": {
502 "action_arguments": {},
503 "action_type": "HideDatasetAction",
504 "output_name": "output"
505 }
506 },
507 "tool_errors": null,
508 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0",
509 "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"__rerun_remap_job_id__\": null}",
510 "tool_version": "1.0.0",
511 "type": "tool",
512 "uuid": "f9da80f6-6a7e-4800-bbef-393632c3b89a",
513 "workflow_outputs": []
514 },
515 "13": {
516 "annotation": "",
517 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
518 "id": 13,
519 "input_connections": {
520 "input": {
521 "id": 12,
522 "output_name": "output"
523 }
524 },
525 "inputs": [],
526 "label": null,
527 "name": "Tabular-to-FASTA",
528 "outputs": [
529 {
530 "name": "output",
531 "type": "fasta"
532 }
533 ],
534 "position": {
535 "left": 886.078125,
536 "top": 704
537 },
538 "post_job_actions": {
539 "HideDatasetActionoutput": {
540 "action_arguments": {},
541 "action_type": "HideDatasetAction",
542 "output_name": "output"
543 }
544 },
545 "tool_errors": null,
546 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
547 "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\", \\\"2\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
548 "tool_version": "1.1.0",
549 "type": "tool",
550 "uuid": "ef2c69a2-4b1e-4694-b264-b0d69cdd3212",
551 "workflow_outputs": []
552 },
553 "14": {
554 "annotation": "",
555 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
556 "id": 14,
557 "input_connections": {
558 "input": {
559 "id": 13,
560 "output_name": "output"
561 }
562 },
563 "inputs": [],
564 "label": null,
565 "name": "Filter sequences by length",
566 "outputs": [
567 {
568 "name": "output",
569 "type": "fasta"
570 }
571 ],
572 "position": {
573 "left": 888.0625,
574 "top": 842.96875
575 },
576 "post_job_actions": {
577 "HideDatasetActionoutput": {
578 "action_arguments": {},
579 "action_type": "HideDatasetAction",
580 "output_name": "output"
581 }
582 },
583 "tool_errors": null,
584 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
585 "tool_state": "{\"__page__\": 0, \"min_length\": \"\\\"8\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"max_length\": \"\\\"30\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
586 "tool_version": "1.1",
587 "type": "tool",
588 "uuid": "f1ede0d2-305b-49a3-8d75-4e43963d95cf",
589 "workflow_outputs": []
590 },
591 "15": {
592 "annotation": "",
593 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
594 "id": 15,
595 "input_connections": {
596 "input": {
597 "id": 13,
598 "output_name": "output"
599 }
600 },
601 "inputs": [],
602 "label": null,
603 "name": "Filter sequences by length",
604 "outputs": [
605 {
606 "name": "output",
607 "type": "fasta"
608 }
609 ],
610 "position": {
611 "left": 1163.078125,
612 "top": 842.46875
613 },
614 "post_job_actions": {
615 "HideDatasetActionoutput": {
616 "action_arguments": {},
617 "action_type": "HideDatasetAction",
618 "output_name": "output"
619 },
620 "RenameDatasetActionoutput": {
621 "action_arguments": {
622 "newname": "FASTA file with peptides with length greater than 30 aas"
623 },
624 "action_type": "RenameDatasetAction",
625 "output_name": "output"
626 }
627 },
628 "tool_errors": null,
629 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
630 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"50\\\"\", \"min_length\": \"\\\"31\\\"\"}",
631 "tool_version": "1.1",
632 "type": "tool",
633 "uuid": "fa317af8-ed94-41b9-b6b8-74445dd86ef7",
634 "workflow_outputs": []
635 },
636 "16": {
637 "annotation": "",
638 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
639 "id": 16,
640 "input_connections": {
641 "input": {
642 "id": 14,
643 "output_name": "output"
644 }
645 },
646 "inputs": [],
647 "label": null,
648 "name": "Regex Find And Replace",
649 "outputs": [
650 {
651 "name": "out_file1",
652 "type": "input"
653 }
654 ],
655 "position": {
656 "left": 924.078125,
657 "top": 1055
658 },
659 "post_job_actions": {
660 "HideDatasetActionout_file1": {
661 "action_arguments": {},
662 "action_type": "HideDatasetAction",
663 "output_name": "out_file1"
664 }
665 },
666 "tool_errors": null,
667 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
668 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\"\\\\\\\\1 sequence length=\\\\\\\\2 aa\\\", \\\"pattern\\\": \\\"^(>.*)_([0-9]+)$\\\"}]\"}",
669 "tool_version": "0.1.0",
670 "type": "tool",
671 "uuid": "696021fc-c7d2-4e47-8c28-252c394b49c4",
672 "workflow_outputs": []
673 },
674 "17": {
675 "annotation": "",
676 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
677 "id": 17,
678 "input_connections": {
679 "input": {
680 "id": 15,
681 "output_name": "output"
682 }
683 },
684 "inputs": [],
685 "label": null,
686 "name": "Regex Find And Replace",
687 "outputs": [
688 {
689 "name": "out_file1",
690 "type": "input"
691 }
692 ],
693 "position": {
694 "left": 1199.71875,
695 "top": 1049
696 },
697 "post_job_actions": {
698 "HideDatasetActionout_file1": {
699 "action_arguments": {},
700 "action_type": "HideDatasetAction",
701 "output_name": "out_file1"
702 }
703 },
704 "tool_errors": null,
705 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
706 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\"\\\\\\\\1 sequence length=\\\\\\\\2 aa\\\", \\\"pattern\\\": \\\"^(>.*)_([0-9]+)$\\\"}]\", \"__page__\": 0}",
707 "tool_version": "0.1.0",
708 "type": "tool",
709 "uuid": "aff244a8-5208-478f-a647-2b13542af873",
710 "workflow_outputs": []
711 },
712 "18": {
713 "annotation": "",
714 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0",
715 "id": 18,
716 "input_connections": {
717 "query": {
718 "id": 16,
719 "output_name": "out_file1"
720 }
721 },
722 "inputs": [],
723 "label": null,
724 "name": "NCBI BLAST+ remote blastp",
725 "outputs": [
726 {
727 "name": "output_tabular",
728 "type": "tabular"
729 },
730 {
731 "name": "output_xml",
732 "type": "blastxml"
733 },
734 {
735 "name": "output_txt",
736 "type": "txt"
737 },
738 {
739 "name": "output_html",
740 "type": "html"
741 }
742 ],
743 "position": {
744 "left": 1290.078125,
745 "top": 200
746 },
747 "post_job_actions": {
748 "HideDatasetActionoutput_html": {
749 "action_arguments": {},
750 "action_type": "HideDatasetAction",
751 "output_name": "output_html"
752 },
753 "HideDatasetActionoutput_tabular": {
754 "action_arguments": {},
755 "action_type": "HideDatasetAction",
756 "output_name": "output_tabular"
757 },
758 "HideDatasetActionoutput_txt": {
759 "action_arguments": {},
760 "action_type": "HideDatasetAction",
761 "output_name": "output_txt"
762 },
763 "HideDatasetActionoutput_xml": {
764 "action_arguments": {},
765 "action_type": "HideDatasetAction",
766 "output_name": "output_xml"
767 }
768 },
769 "tool_errors": null,
770 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0",
771 "tool_state": "{\"evalue_cutoff\": \"\\\"200000.0\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"scoring\\\": {\\\"gap_costs\\\": \\\"-gapopen 9 -gapextend 1\\\", \\\"matrix\\\": \\\"PAM30\\\", \\\"__current_case__\\\": 7}, \\\"use_sw_tback\\\": \\\"False\\\", \\\"window_size\\\": \\\"15\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"comp_based_stats\\\": \\\"0\\\", \\\"parse_deflines\\\": \\\"True\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"2\\\", \\\"__current_case__\\\": 1, \\\"threshold\\\": \\\"16\\\"}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"remote\\\", \\\"taxid_repeat\\\": [{\\\"__index__\\\": 0, \\\"taxid\\\": \\\"10090\\\", \\\"exclude\\\": \\\"False\\\"}], \\\"__current_case__\\\": 2, \\\"database\\\": \\\"nr\\\"}\", \"blast_type\": \"\\\"blastp-short\\\"\", \"fmt_opt\": \"{\\\"out_format\\\": \\\"blastxml\\\", \\\"outfmt\\\": \\\"5\\\", \\\"max_target_seqs\\\": \\\"1\\\", \\\"__current_case__\\\": 1}\", \"query\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
772 "tool_version": "1.0",
773 "type": "tool",
774 "uuid": "0623c7ec-4140-4364-a4bd-f7ea9629b631",
775 "workflow_outputs": []
776 },
777 "19": {
778 "annotation": "",
779 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0.1",
780 "id": 19,
781 "input_connections": {
782 "query": {
783 "id": 17,
784 "output_name": "out_file1"
785 }
786 },
787 "inputs": [],
788 "label": null,
789 "name": "NCBI BLAST+ remote blastp",
790 "outputs": [
791 {
792 "name": "output_tabular",
793 "type": "tabular"
794 },
795 {
796 "name": "output_xml",
797 "type": "blastxml"
798 },
799 {
800 "name": "output_txt",
801 "type": "txt"
802 },
803 {
804 "name": "output_html",
805 "type": "html"
806 }
807 ],
808 "position": {
809 "left": 1423.21875,
810 "top": 1050
811 },
812 "post_job_actions": {
813 "HideDatasetActionoutput_html": {
814 "action_arguments": {},
815 "action_type": "HideDatasetAction",
816 "output_name": "output_html"
817 },
818 "HideDatasetActionoutput_tabular": {
819 "action_arguments": {},
820 "action_type": "HideDatasetAction",
821 "output_name": "output_tabular"
822 },
823 "HideDatasetActionoutput_txt": {
824 "action_arguments": {},
825 "action_type": "HideDatasetAction",
826 "output_name": "output_txt"
827 },
828 "HideDatasetActionoutput_xml": {
829 "action_arguments": {},
830 "action_type": "HideDatasetAction",
831 "output_name": "output_xml"
832 }
833 },
834 "tool_errors": null,
835 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0.1",
836 "tool_state": "{\"evalue_cutoff\": \"\\\"10.0\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"scoring\\\": {\\\"gap_costs\\\": \\\"-gapopen 11 -gapextend 1\\\", \\\"matrix\\\": \\\"BLOSUM62\\\", \\\"__current_case__\\\": 2}, \\\"use_sw_tback\\\": \\\"False\\\", \\\"window_size\\\": \\\"40\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"comp_based_stats\\\": \\\"2\\\", \\\"parse_deflines\\\": \\\"True\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"threshold\\\": \\\"11\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"remote\\\", \\\"taxid_repeat\\\": [{\\\"__index__\\\": 0, \\\"taxid\\\": \\\"10090\\\", \\\"exclude\\\": \\\"False\\\"}], \\\"__current_case__\\\": 2, \\\"database\\\": \\\"nr\\\"}\", \"blast_type\": \"\\\"blastp\\\"\", \"fmt_opt\": \"{\\\"out_format\\\": \\\"blastxml\\\", \\\"outfmt\\\": \\\"5\\\", \\\"max_target_seqs\\\": \\\"1\\\", \\\"__current_case__\\\": 1}\", \"query\": \"null\"}",
837 "tool_version": "1.0.1",
838 "type": "tool",
839 "uuid": "bbca1b78-3170-44fe-ae0f-b727377987cc",
840 "workflow_outputs": []
841 },
842 "20": {
843 "annotation": "",
844 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
845 "id": 20,
846 "input_connections": {
847 "blastxml_file": {
848 "id": 18,
849 "output_name": "output_xml"
850 }
851 },
852 "inputs": [],
853 "label": null,
854 "name": "BLAST XML to selected tabular columns",
855 "outputs": [
856 {
857 "name": "tabular_file",
858 "type": "tabular"
859 },
860 {
861 "name": "unmatched_file",
862 "type": "tabular"
863 }
864 ],
865 "position": {
866 "left": 1265.0625,
867 "top": 375
868 },
869 "post_job_actions": {
870 "HideDatasetActiontabular_file": {
871 "action_arguments": {},
872 "action_type": "HideDatasetAction",
873 "output_name": "tabular_file"
874 },
875 "HideDatasetActionunmatched_file": {
876 "action_arguments": {},
877 "action_type": "HideDatasetAction",
878 "output_name": "unmatched_file"
879 }
880 },
881 "tool_errors": null,
882 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
883 "tool_state": "{\"__page__\": 0, \"qdef\": \"\\\"False\\\"\", \"blastxml_file\": \"null\", \"__rerun_remap_job_id__\": null, \"maxhits\": \"\\\"1\\\"\", \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"allqueries\": \"\\\"False\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"columns\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\", \\\"sallseqid\\\", \\\"score\\\", \\\"nident\\\", \\\"positive\\\", \\\"gaps\\\", \\\"ppos\\\", \\\"qframe\\\", \\\"sframe\\\", \\\"qseq\\\", \\\"sseq\\\", \\\"qlen\\\", \\\"slen\\\"], \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"maxhsps\": \"\\\"1\\\"\", \"unmatched\": \"\\\"True\\\"\"}",
884 "tool_version": "1.0.0",
885 "type": "tool",
886 "uuid": "3a9c02cf-45ec-42ab-84e2-4544e252e832",
887 "workflow_outputs": []
888 },
889 "21": {
890 "annotation": "",
891 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
892 "id": 21,
893 "input_connections": {
894 "blastxml_file": {
895 "id": 19,
896 "output_name": "output_xml"
897 }
898 },
899 "inputs": [],
900 "label": null,
901 "name": "BLAST XML to selected tabular columns",
902 "outputs": [
903 {
904 "name": "tabular_file",
905 "type": "tabular"
906 },
907 {
908 "name": "unmatched_file",
909 "type": "tabular"
910 }
911 ],
912 "position": {
913 "left": 1677.578125,
914 "top": 1049.265625
915 },
916 "post_job_actions": {
917 "HideDatasetActiontabular_file": {
918 "action_arguments": {},
919 "action_type": "HideDatasetAction",
920 "output_name": "tabular_file"
921 },
922 "HideDatasetActionunmatched_file": {
923 "action_arguments": {},
924 "action_type": "HideDatasetAction",
925 "output_name": "unmatched_file"
926 }
927 },
928 "tool_errors": null,
929 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
930 "tool_state": "{\"__page__\": 0, \"qdef\": \"\\\"False\\\"\", \"blastxml_file\": \"null\", \"__rerun_remap_job_id__\": null, \"maxhits\": \"\\\"1\\\"\", \"unmatched\": \"\\\"True\\\"\", \"allqueries\": \"\\\"False\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"columns\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\", \\\"sallseqid\\\", \\\"score\\\", \\\"nident\\\", \\\"positive\\\", \\\"gaps\\\", \\\"ppos\\\", \\\"qframe\\\", \\\"sframe\\\", \\\"qseq\\\", \\\"sseq\\\", \\\"qlen\\\", \\\"slen\\\"], \\\"__current_case__\\\": 2}\", \"maxhsps\": \"\\\"1\\\"\"}",
931 "tool_version": "1.0.0",
932 "type": "tool",
933 "uuid": "c534ca6c-2876-4f62-b9e9-a164f3829bd2",
934 "workflow_outputs": []
935 },
936 "22": {
937 "annotation": "",
938 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
939 "id": 22,
940 "input_connections": {
941 "input": {
942 "id": 20,
943 "output_name": "tabular_file"
944 }
945 },
946 "inputs": [],
947 "label": null,
948 "name": "Compute",
949 "outputs": [
950 {
951 "name": "out_file1",
952 "type": "input"
953 }
954 ],
955 "position": {
956 "left": 1350.09375,
957 "top": 532.015625
958 },
959 "post_job_actions": {
960 "HideDatasetActionout_file1": {
961 "action_arguments": {},
962 "action_type": "HideDatasetAction",
963 "output_name": "out_file1"
964 }
965 },
966 "tool_errors": null,
967 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
968 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"cond\": \"\\\"(c4/c23)*100\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"round\": \"\\\"no\\\"\"}",
969 "tool_version": "1.1.0",
970 "type": "tool",
971 "uuid": "1b02fcdc-b9dc-4497-8eba-2b79f81b2168",
972 "workflow_outputs": []
973 },
974 "23": {
975 "annotation": "",
976 "content_id": "Filter1",
977 "id": 23,
978 "input_connections": {
979 "input": {
980 "id": 22,
981 "output_name": "out_file1"
982 }
983 },
984 "inputs": [],
985 "label": null,
986 "name": "Filter",
987 "outputs": [
988 {
989 "name": "out_file1",
990 "type": "input"
991 }
992 ],
993 "position": {
994 "left": 1364.09375,
995 "top": 635.015625
996 },
997 "post_job_actions": {
998 "HideDatasetActionout_file1": {
999 "action_arguments": {},
1000 "action_type": "HideDatasetAction",
1001 "output_name": "out_file1"
1002 }
1003 },
1004 "tool_errors": null,
1005 "tool_id": "Filter1",
1006 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"cond\": \"\\\"c3<100 or c17>=1 or c25<100\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
1007 "tool_version": "1.1.0",
1008 "type": "tool",
1009 "uuid": "58e54e01-c935-46e9-9b3f-8d91dc157c36",
1010 "workflow_outputs": []
1011 },
1012 "24": {
1013 "annotation": "",
1014 "content_id": "Cut1",
1015 "id": 24,
1016 "input_connections": {
1017 "input": {
1018 "id": 23,
1019 "output_name": "out_file1"
1020 }
1021 },
1022 "inputs": [],
1023 "label": null,
1024 "name": "Cut",
1025 "outputs": [
1026 {
1027 "name": "out_file1",
1028 "type": "tabular"
1029 }
1030 ],
1031 "position": {
1032 "left": 1376.09375,
1033 "top": 750.03125
1034 },
1035 "post_job_actions": {
1036 "HideDatasetActionout_file1": {
1037 "action_arguments": {},
1038 "action_type": "HideDatasetAction",
1039 "output_name": "out_file1"
1040 }
1041 },
1042 "tool_errors": null,
1043 "tool_id": "Cut1",
1044 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
1045 "tool_version": "1.0.2",
1046 "type": "tool",
1047 "uuid": "a1fdb8b9-dcb0-4c6c-97dd-d6e2373f1421",
1048 "workflow_outputs": []
1049 },
1050 "25": {
1051 "annotation": "",
1052 "content_id": "cat1",
1053 "id": 25,
1054 "input_connections": {
1055 "input1": {
1056 "id": 20,
1057 "output_name": "unmatched_file"
1058 },
1059 "queries_0|input2": {
1060 "id": 24,
1061 "output_name": "out_file1"
1062 }
1063 },
1064 "inputs": [],
1065 "label": null,
1066 "name": "Concatenate datasets",
1067 "outputs": [
1068 {
1069 "name": "out_file1",
1070 "type": "input"
1071 }
1072 ],
1073 "position": {
1074 "left": 1588.0625,
1075 "top": 602
1076 },
1077 "post_job_actions": {
1078 "HideDatasetActionout_file1": {
1079 "action_arguments": {},
1080 "action_type": "HideDatasetAction",
1081 "output_name": "out_file1"
1082 }
1083 },
1084 "tool_errors": null,
1085 "tool_id": "cat1",
1086 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
1087 "tool_version": "1.0.0",
1088 "type": "tool",
1089 "uuid": "64b3b833-6d3a-4aaa-b666-1206fea216d9",
1090 "workflow_outputs": []
1091 },
1092 "26": {
1093 "annotation": "",
1094 "content_id": "cat1",
1095 "id": 26,
1096 "input_connections": {
1097 "input1": {
1098 "id": 25,
1099 "output_name": "out_file1"
1100 },
1101 "queries_0|input2": {
1102 "id": 21,
1103 "output_name": "unmatched_file"
1104 }
1105 },
1106 "inputs": [],
1107 "label": null,
1108 "name": "Concatenate datasets",
1109 "outputs": [
1110 {
1111 "name": "out_file1",
1112 "type": "input"
1113 }
1114 ],
1115 "position": {
1116 "left": 1894.578125,
1117 "top": 805.265625
1118 },
1119 "post_job_actions": {
1120 "RenameDatasetActionout_file1": {
1121 "action_arguments": {
1122 "newname": "PEPTIDES corresponding to novel proteoforms"
1123 },
1124 "action_type": "RenameDatasetAction",
1125 "output_name": "out_file1"
1126 }
1127 },
1128 "tool_errors": null,
1129 "tool_id": "cat1",
1130 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
1131 "tool_version": "1.0.0",
1132 "type": "tool",
1133 "uuid": "52f35f03-ba84-4f80-b8fc-2696e7035efe",
1134 "workflow_outputs": [
1135 {
1136 "label": null,
1137 "output_name": "out_file1",
1138 "uuid": "65f5d2f4-6d95-4085-af01-c0b3e65f454a"
1139 }
1140 ]
1141 },
1142 "27": {
1143 "annotation": "",
1144 "content_id": "join1",
1145 "id": 27,
1146 "input_connections": {
1147 "input1": {
1148 "id": 26,
1149 "output_name": "out_file1"
1150 },
1151 "input2": {
1152 "id": 9,
1153 "output_name": "out_file1"
1154 }
1155 },
1156 "inputs": [],
1157 "label": null,
1158 "name": "Join two Datasets",
1159 "outputs": [
1160 {
1161 "name": "out_file1",
1162 "type": "input"
1163 }
1164 ],
1165 "position": {
1166 "left": 1937.96875,
1167 "top": 205.9375
1168 },
1169 "post_job_actions": {
1170 "HideDatasetActionout_file1": {
1171 "action_arguments": {},
1172 "action_type": "HideDatasetAction",
1173 "output_name": "out_file1"
1174 }
1175 },
1176 "tool_errors": null,
1177 "tool_id": "join1",
1178 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"__workflow_invocation_uuid__\": \"\\\"68b9090ea5e911e58b28fa163e14a73a\\\"\", \"input1\": \"null\", \"unmatched\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
1179 "tool_version": "2.0.2",
1180 "type": "tool",
1181 "uuid": "447ad2ac-0485-4f64-a225-ba8720f8e3fd",
1182 "workflow_outputs": []
1183 },
1184 "28": {
1185 "annotation": "",
1186 "content_id": "Grouping1",
1187 "id": 28,
1188 "input_connections": {
1189 "input1": {
1190 "id": 27,
1191 "output_name": "out_file1"
1192 }
1193 },
1194 "inputs": [],
1195 "label": null,
1196 "name": "Group",
1197 "outputs": [
1198 {
1199 "name": "out_file1",
1200 "type": "tabular"
1201 }
1202 ],
1203 "position": {
1204 "left": 2038.875,
1205 "top": 359.28125
1206 },
1207 "post_job_actions": {
1208 "HideDatasetActionout_file1": {
1209 "action_arguments": {},
1210 "action_type": "HideDatasetAction",
1211 "output_name": "out_file1"
1212 }
1213 },
1214 "tool_errors": null,
1215 "tool_id": "Grouping1",
1216 "tool_state": "{\"operations\": \"[{\\\"opcol\\\": \\\"3\\\", \\\"__index__\\\": 0, \\\"optype\\\": \\\"min\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}",
1217 "tool_version": "2.1.0",
1218 "type": "tool",
1219 "uuid": "e8b67b52-e50e-4d9d-a83c-2f89a4f4f53d",
1220 "workflow_outputs": []
1221 },
1222 "29": {
1223 "annotation": "",
1224 "content_id": "join1",
1225 "id": 29,
1226 "input_connections": {
1227 "input1": {
1228 "id": 7,
1229 "output_name": "out_file1"
1230 },
1231 "input2": {
1232 "id": 28,
1233 "output_name": "out_file1"
1234 }
1235 },
1236 "inputs": [],
1237 "label": null,
1238 "name": "Join two Datasets",
1239 "outputs": [
1240 {
1241 "name": "out_file1",
1242 "type": "input"
1243 }
1244 ],
1245 "position": {
1246 "left": 1855.0625,
1247 "top": 378.96875
1248 },
1249 "post_job_actions": {
1250 "HideDatasetActionout_file1": {
1251 "action_arguments": {},
1252 "action_type": "HideDatasetAction",
1253 "output_name": "out_file1"
1254 }
1255 },
1256 "tool_errors": null,
1257 "tool_id": "join1",
1258 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"\\\"21\\\"\", \"partial\": \"\\\"\\\"\", \"field2\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\"}",
1259 "tool_version": "2.0.2",
1260 "type": "tool",
1261 "uuid": "cef8aa6f-66a1-4ceb-adb2-ad2a11d50f33",
1262 "workflow_outputs": []
1263 },
1264 "30": {
1265 "annotation": "",
1266 "content_id": "Cut1",
1267 "id": 30,
1268 "input_connections": {
1269 "input": {
1270 "id": 29,
1271 "output_name": "out_file1"
1272 }
1273 },
1274 "inputs": [],
1275 "label": null,
1276 "name": "Cut",
1277 "outputs": [
1278 {
1279 "name": "out_file1",
1280 "type": "tabular"
1281 }
1282 ],
1283 "position": {
1284 "left": 2116.03125,
1285 "top": 520
1286 },
1287 "post_job_actions": {
1288 "RenameDatasetActionout_file1": {
1289 "action_arguments": {
1290 "newname": "PSM REPORT of PEPTIDES corresponding to novel proteoforms"
1291 },
1292 "action_type": "RenameDatasetAction",
1293 "output_name": "out_file1"
1294 }
1295 },
1296 "tool_errors": null,
1297 "tool_id": "Cut1",
1298 "tool_state": "{\"columnList\": \"\\\"c1-c20\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
1299 "tool_version": "1.0.2",
1300 "type": "tool",
1301 "uuid": "dd3616b1-17fb-403c-86c5-49364a33dfa6",
1302 "workflow_outputs": [
1303 {
1304 "label": null,
1305 "output_name": "out_file1",
1306 "uuid": "95e9b117-1291-4787-b3f3-ca968f15178d"
1307 }
1308 ]
1309 }
1310 },
1311 "uuid": "19b7ca0f-ca39-496a-b727-af2b6b63d7e7"
1312 }