comparison Workflow_2_for_GCC_2016.ga @ 0:ec32f7039106 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/gcc2016_tutorial commit 078c2920db4203a2b7525fd819716507e9346546-dirty
author galaxyp
date Fri, 17 Jun 2016 15:29:03 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:ec32f7039106
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "Workflow 2 for GCC 2016",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "id": 0,
11 "input_connections": {},
12 "inputs": [
13 {
14 "description": "",
15 "name": "Peptide Shaker on data 8: PSM Report"
16 }
17 ],
18 "label": null,
19 "name": "Input dataset",
20 "outputs": [],
21 "position": {
22 "left": 200,
23 "top": 444.5
24 },
25 "tool_errors": null,
26 "tool_id": null,
27 "tool_state": "{\"name\": \"Peptide Shaker on data 8: PSM Report\"}",
28 "tool_version": null,
29 "type": "data_input",
30 "uuid": "8f47437d-c94c-449c-93ec-cc7ac4bfd3ba",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "26bf893a-e00d-4be3-a2cf-d4450f69e330"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": null,
42 "id": 1,
43 "input_connections": {},
44 "inputs": [
45 {
46 "description": "",
47 "name": "Translate BED Sequences on proB data"
48 }
49 ],
50 "label": null,
51 "name": "Input dataset",
52 "outputs": [],
53 "position": {
54 "left": 5833.5,
55 "top": 227.5
56 },
57 "tool_errors": null,
58 "tool_id": null,
59 "tool_state": "{\"name\": \"Translate BED Sequences on proB data\"}",
60 "tool_version": null,
61 "type": "data_input",
62 "uuid": "892f3617-6c86-4b54-b9c2-9e130209b0db",
63 "workflow_outputs": [
64 {
65 "label": null,
66 "output_name": "output",
67 "uuid": "de67cdb9-525d-4ebf-9184-33881be54867"
68 }
69 ]
70 },
71 "2": {
72 "annotation": "",
73 "content_id": null,
74 "id": 2,
75 "input_connections": {},
76 "inputs": [
77 {
78 "description": "",
79 "name": "Translate BED Sequences on preB data"
80 }
81 ],
82 "label": null,
83 "name": "Input dataset",
84 "outputs": [],
85 "position": {
86 "left": 5813.5,
87 "top": 537.5
88 },
89 "tool_errors": null,
90 "tool_id": null,
91 "tool_state": "{\"name\": \"Translate BED Sequences on preB data\"}",
92 "tool_version": null,
93 "type": "data_input",
94 "uuid": "1c48d009-43d3-4819-a16d-f03cc72597dd",
95 "workflow_outputs": [
96 {
97 "label": null,
98 "output_name": "output",
99 "uuid": "3fac5a48-b350-4f4d-a540-12fd4e610bdb"
100 }
101 ]
102 },
103 "3": {
104 "annotation": "",
105 "content_id": "Remove beginning1",
106 "id": 3,
107 "input_connections": {
108 "input": {
109 "id": 0,
110 "output_name": "output"
111 }
112 },
113 "inputs": [],
114 "label": null,
115 "name": "Remove beginning",
116 "outputs": [
117 {
118 "name": "out_file1",
119 "type": "input"
120 }
121 ],
122 "position": {
123 "left": 459.5,
124 "top": 450
125 },
126 "post_job_actions": {},
127 "tool_errors": null,
128 "tool_id": "Remove beginning1",
129 "tool_state": "{\"__page__\": 0, \"num_lines\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
130 "tool_version": null,
131 "type": "tool",
132 "uuid": "1b1f7f03-0c3f-4b91-8874-900ba5660f4f",
133 "workflow_outputs": []
134 },
135 "4": {
136 "annotation": "",
137 "content_id": "sort1",
138 "id": 4,
139 "input_connections": {
140 "input": {
141 "id": 3,
142 "output_name": "out_file1"
143 }
144 },
145 "inputs": [],
146 "label": null,
147 "name": "Sort",
148 "outputs": [
149 {
150 "name": "out_file1",
151 "type": "input"
152 }
153 ],
154 "position": {
155 "left": 755.5,
156 "top": 334
157 },
158 "post_job_actions": {},
159 "tool_errors": null,
160 "tool_id": "sort1",
161 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"num\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"column_set\": \"[{\\\"other_order\\\": \\\"DESC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"19\\\"}, \\\"other_style\\\": \\\"num\\\"}]\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"order\": \"\\\"ASC\\\"\"}",
162 "tool_version": null,
163 "type": "tool",
164 "uuid": "3bcca325-a1b5-4707-a20c-5ddcee5be770",
165 "workflow_outputs": []
166 },
167 "5": {
168 "annotation": "",
169 "content_id": "addValue",
170 "id": 5,
171 "input_connections": {
172 "input": {
173 "id": 4,
174 "output_name": "out_file1"
175 }
176 },
177 "inputs": [],
178 "label": null,
179 "name": "Add column",
180 "outputs": [
181 {
182 "name": "out_file1",
183 "type": "input"
184 }
185 ],
186 "position": {
187 "left": 975.5,
188 "top": 334
189 },
190 "post_job_actions": {},
191 "tool_errors": null,
192 "tool_id": "addValue",
193 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"exp\": \"\\\"1\\\"\", \"iterate\": \"\\\"yes\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
194 "tool_version": null,
195 "type": "tool",
196 "uuid": "7bc2112c-04ad-436a-8807-0c8ef5ba603e",
197 "workflow_outputs": []
198 },
199 "6": {
200 "annotation": "",
201 "content_id": "Grouping1",
202 "id": 6,
203 "input_connections": {
204 "input1": {
205 "id": 5,
206 "output_name": "out_file1"
207 }
208 },
209 "inputs": [],
210 "label": null,
211 "name": "Group",
212 "outputs": [
213 {
214 "name": "out_file1",
215 "type": "tabular"
216 }
217 ],
218 "position": {
219 "left": 1195.5,
220 "top": 334
221 },
222 "post_job_actions": {},
223 "tool_errors": null,
224 "tool_id": "Grouping1",
225 "tool_state": "{\"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"21\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"min\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"ignorecase\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
226 "tool_version": null,
227 "type": "tool",
228 "uuid": "d53962e1-4293-4d25-a0f3-bb5fedeb2932",
229 "workflow_outputs": []
230 },
231 "7": {
232 "annotation": "",
233 "content_id": "join1",
234 "id": 7,
235 "input_connections": {
236 "input1": {
237 "id": 5,
238 "output_name": "out_file1"
239 },
240 "input2": {
241 "id": 6,
242 "output_name": "out_file1"
243 }
244 },
245 "inputs": [],
246 "label": null,
247 "name": "Join two Datasets",
248 "outputs": [
249 {
250 "name": "out_file1",
251 "type": "input"
252 }
253 ],
254 "position": {
255 "left": 1415.5,
256 "top": 334
257 },
258 "post_job_actions": {},
259 "tool_errors": null,
260 "tool_id": "join1",
261 "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__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input1\": \"null\", \"unmatched\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
262 "tool_version": null,
263 "type": "tool",
264 "uuid": "d59afbf1-e500-4a7c-b00c-8c6d6b6c7f2c",
265 "workflow_outputs": []
266 },
267 "8": {
268 "annotation": "",
269 "content_id": "Cut1",
270 "id": 8,
271 "input_connections": {
272 "input": {
273 "id": 7,
274 "output_name": "out_file1"
275 }
276 },
277 "inputs": [],
278 "label": null,
279 "name": "Cut",
280 "outputs": [
281 {
282 "name": "out_file1",
283 "type": "tabular"
284 }
285 ],
286 "position": {
287 "left": 1635.5,
288 "top": 334
289 },
290 "post_job_actions": {},
291 "tool_errors": null,
292 "tool_id": "Cut1",
293 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1-c21\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
294 "tool_version": null,
295 "type": "tool",
296 "uuid": "de03852c-45fa-4254-a411-272a77982559",
297 "workflow_outputs": []
298 },
299 "9": {
300 "annotation": "",
301 "content_id": "Grep1",
302 "id": 9,
303 "input_connections": {
304 "input": {
305 "id": 8,
306 "output_name": "out_file1"
307 }
308 },
309 "inputs": [],
310 "label": null,
311 "name": "Select",
312 "outputs": [
313 {
314 "name": "out_file1",
315 "type": "input"
316 }
317 ],
318 "position": {
319 "left": 1855.5,
320 "top": 334
321 },
322 "post_job_actions": {},
323 "tool_errors": null,
324 "tool_id": "Grep1",
325 "tool_state": "{\"__page__\": 0, \"pattern\": \"\\\"^\\\\\\\\d+\\\\\\\\tpr.B[^\\\\\\\\t,]*(, pr.B[^\\\\\\\\t,]*)*\\\\\\\\t.*$\\\"\", \"invert\": \"\\\"false\\\"\", \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"__rerun_remap_job_id__\": null}",
326 "tool_version": null,
327 "type": "tool",
328 "uuid": "08f2a559-8328-4b04-a6b5-9a55e565de14",
329 "workflow_outputs": []
330 },
331 "10": {
332 "annotation": "",
333 "content_id": "Cut1",
334 "id": 10,
335 "input_connections": {
336 "input": {
337 "id": 9,
338 "output_name": "out_file1"
339 }
340 },
341 "inputs": [],
342 "label": null,
343 "name": "Cut",
344 "outputs": [
345 {
346 "name": "out_file1",
347 "type": "tabular"
348 }
349 ],
350 "position": {
351 "left": 2075.5,
352 "top": 334
353 },
354 "post_job_actions": {},
355 "tool_errors": null,
356 "tool_id": "Cut1",
357 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1-c20\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
358 "tool_version": null,
359 "type": "tool",
360 "uuid": "3416e999-6eb5-4bfc-861a-e4cde431056f",
361 "workflow_outputs": []
362 },
363 "11": {
364 "annotation": "",
365 "content_id": "Cut1",
366 "id": 11,
367 "input_connections": {
368 "input": {
369 "id": 9,
370 "output_name": "out_file1"
371 }
372 },
373 "inputs": [],
374 "label": null,
375 "name": "Cut",
376 "outputs": [
377 {
378 "name": "out_file1",
379 "type": "tabular"
380 }
381 ],
382 "position": {
383 "left": 2075.5,
384 "top": 454
385 },
386 "post_job_actions": {},
387 "tool_errors": null,
388 "tool_id": "Cut1",
389 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c3,c21\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
390 "tool_version": null,
391 "type": "tool",
392 "uuid": "70adbd3e-fce5-4de0-94ff-0d17c82d693c",
393 "workflow_outputs": []
394 },
395 "12": {
396 "annotation": "",
397 "content_id": "Cut1",
398 "id": 12,
399 "input_connections": {
400 "input": {
401 "id": 10,
402 "output_name": "out_file1"
403 }
404 },
405 "inputs": [],
406 "label": null,
407 "name": "Cut",
408 "outputs": [
409 {
410 "name": "out_file1",
411 "type": "tabular"
412 }
413 ],
414 "position": {
415 "left": 2295.5,
416 "top": 334
417 },
418 "post_job_actions": {},
419 "tool_errors": null,
420 "tool_id": "Cut1",
421 "tool_state": "{\"columnList\": \"\\\"c3\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
422 "tool_version": null,
423 "type": "tool",
424 "uuid": "06d05726-0cb5-4351-ab2c-bb6fe7f0f39f",
425 "workflow_outputs": [
426 {
427 "label": null,
428 "output_name": "out_file1",
429 "uuid": "e828f231-3a6b-4226-99d1-82d6e857902d"
430 }
431 ]
432 },
433 "13": {
434 "annotation": "",
435 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
436 "id": 13,
437 "input_connections": {
438 "input": {
439 "id": 12,
440 "output_name": "out_file1"
441 }
442 },
443 "inputs": [],
444 "label": null,
445 "name": "Tabular-to-FASTA",
446 "outputs": [
447 {
448 "name": "output",
449 "type": "fasta"
450 }
451 ],
452 "position": {
453 "left": 2515.5,
454 "top": 334
455 },
456 "post_job_actions": {},
457 "tool_errors": null,
458 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
459 "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
460 "tool_version": null,
461 "type": "tool",
462 "uuid": "f729fa41-e0e8-4fe5-986c-cccb339b934c",
463 "workflow_outputs": []
464 },
465 "14": {
466 "annotation": "",
467 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0",
468 "id": 14,
469 "input_connections": {
470 "input": {
471 "id": 13,
472 "output_name": "output"
473 }
474 },
475 "inputs": [],
476 "label": null,
477 "name": "Compute sequence length",
478 "outputs": [
479 {
480 "name": "output",
481 "type": "tabular"
482 }
483 ],
484 "position": {
485 "left": 2735.5,
486 "top": 334
487 },
488 "post_job_actions": {},
489 "tool_errors": null,
490 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.0",
491 "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"__rerun_remap_job_id__\": null}",
492 "tool_version": null,
493 "type": "tool",
494 "uuid": "0a98bfad-b975-414b-8802-f13ae2e13d01",
495 "workflow_outputs": []
496 },
497 "15": {
498 "annotation": "",
499 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
500 "id": 15,
501 "input_connections": {
502 "input": {
503 "id": 14,
504 "output_name": "output"
505 }
506 },
507 "inputs": [],
508 "label": null,
509 "name": "Tabular-to-FASTA",
510 "outputs": [
511 {
512 "name": "output",
513 "type": "fasta"
514 }
515 ],
516 "position": {
517 "left": 2955.5,
518 "top": 334
519 },
520 "post_job_actions": {},
521 "tool_errors": null,
522 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0",
523 "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__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
524 "tool_version": null,
525 "type": "tool",
526 "uuid": "8e9fc011-4eed-4f3d-88b2-bb019cfdc6a5",
527 "workflow_outputs": []
528 },
529 "16": {
530 "annotation": "",
531 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
532 "id": 16,
533 "input_connections": {
534 "input": {
535 "id": 15,
536 "output_name": "output"
537 }
538 },
539 "inputs": [],
540 "label": null,
541 "name": "Filter sequences by length",
542 "outputs": [
543 {
544 "name": "output",
545 "type": "fasta"
546 }
547 ],
548 "position": {
549 "left": 3175.5,
550 "top": 334
551 },
552 "post_job_actions": {},
553 "tool_errors": null,
554 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
555 "tool_state": "{\"__page__\": 0, \"min_length\": \"\\\"8\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"max_length\": \"\\\"30\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
556 "tool_version": null,
557 "type": "tool",
558 "uuid": "53c56738-08c6-4777-8412-14cb817be57e",
559 "workflow_outputs": []
560 },
561 "17": {
562 "annotation": "",
563 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
564 "id": 17,
565 "input_connections": {
566 "input": {
567 "id": 15,
568 "output_name": "output"
569 }
570 },
571 "inputs": [],
572 "label": null,
573 "name": "Filter sequences by length",
574 "outputs": [
575 {
576 "name": "output",
577 "type": "fasta"
578 }
579 ],
580 "position": {
581 "left": 3175.5,
582 "top": 454
583 },
584 "post_job_actions": {},
585 "tool_errors": null,
586 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
587 "tool_state": "{\"__page__\": 0, \"min_length\": \"\\\"31\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"max_length\": \"\\\"50\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
588 "tool_version": null,
589 "type": "tool",
590 "uuid": "2bddeaa9-a8bc-4986-b689-f3686338b4e2",
591 "workflow_outputs": []
592 },
593 "18": {
594 "annotation": "",
595 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
596 "id": 18,
597 "input_connections": {
598 "input": {
599 "id": 16,
600 "output_name": "output"
601 }
602 },
603 "inputs": [],
604 "label": null,
605 "name": "Regex Find And Replace",
606 "outputs": [
607 {
608 "name": "out_file1",
609 "type": "input"
610 }
611 ],
612 "position": {
613 "left": 3395.5,
614 "top": 334
615 },
616 "post_job_actions": {},
617 "tool_errors": null,
618 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
619 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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]+)$\\\"}]\"}",
620 "tool_version": null,
621 "type": "tool",
622 "uuid": "dc0027b8-fbd3-434f-ab81-1dff2be6bfbc",
623 "workflow_outputs": []
624 },
625 "19": {
626 "annotation": "",
627 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
628 "id": 19,
629 "input_connections": {
630 "input": {
631 "id": 17,
632 "output_name": "output"
633 }
634 },
635 "inputs": [],
636 "label": null,
637 "name": "Regex Find And Replace",
638 "outputs": [
639 {
640 "name": "out_file1",
641 "type": "input"
642 }
643 ],
644 "position": {
645 "left": 3395.5,
646 "top": 454
647 },
648 "post_job_actions": {},
649 "tool_errors": null,
650 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0",
651 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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]+)$\\\"}]\"}",
652 "tool_version": null,
653 "type": "tool",
654 "uuid": "e5dc68a7-5890-4d0c-b92e-4b77fc239157",
655 "workflow_outputs": []
656 },
657 "20": {
658 "annotation": "",
659 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0",
660 "id": 20,
661 "input_connections": {
662 "query": {
663 "id": 18,
664 "output_name": "out_file1"
665 }
666 },
667 "inputs": [],
668 "label": null,
669 "name": "NCBI BLAST+ remote blastp",
670 "outputs": [
671 {
672 "name": "output_tabular",
673 "type": "tabular"
674 },
675 {
676 "name": "output_xml",
677 "type": "blastxml"
678 },
679 {
680 "name": "output_txt",
681 "type": "txt"
682 },
683 {
684 "name": "output_html",
685 "type": "html"
686 }
687 ],
688 "position": {
689 "left": 3615.5,
690 "top": 334
691 },
692 "post_job_actions": {},
693 "tool_errors": null,
694 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0",
695 "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__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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\\\"\"}",
696 "tool_version": null,
697 "type": "tool",
698 "uuid": "dbccb49c-828a-4e90-a6fc-98053a93ab3b",
699 "workflow_outputs": []
700 },
701 "21": {
702 "annotation": "",
703 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0.1",
704 "id": 21,
705 "input_connections": {
706 "query": {
707 "id": 19,
708 "output_name": "out_file1"
709 }
710 },
711 "inputs": [],
712 "label": null,
713 "name": "NCBI BLAST+ remote blastp",
714 "outputs": [
715 {
716 "name": "output_tabular",
717 "type": "tabular"
718 },
719 {
720 "name": "output_xml",
721 "type": "blastxml"
722 },
723 {
724 "name": "output_txt",
725 "type": "txt"
726 },
727 {
728 "name": "output_html",
729 "type": "html"
730 }
731 ],
732 "position": {
733 "left": 3614.5,
734 "top": 454
735 },
736 "post_job_actions": {},
737 "tool_errors": null,
738 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blast_plus_remote_blastp/blast_plus_remote_blastp/1.0.1",
739 "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, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
740 "tool_version": null,
741 "type": "tool",
742 "uuid": "7952be1e-5ca1-40a5-991a-5234a256815e",
743 "workflow_outputs": []
744 },
745 "22": {
746 "annotation": "",
747 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
748 "id": 22,
749 "input_connections": {
750 "blastxml_file": {
751 "id": 20,
752 "output_name": "output_xml"
753 }
754 },
755 "inputs": [],
756 "label": null,
757 "name": "BLAST XML to selected tabular columns",
758 "outputs": [
759 {
760 "name": "tabular_file",
761 "type": "tabular"
762 },
763 {
764 "name": "unmatched_file",
765 "type": "tabular"
766 }
767 ],
768 "position": {
769 "left": 3835.5,
770 "top": 333
771 },
772 "post_job_actions": {},
773 "tool_errors": null,
774 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
775 "tool_state": "{\"__page__\": 0, \"qdef\": \"\\\"False\\\"\", \"blastxml_file\": \"null\", \"__rerun_remap_job_id__\": null, \"maxhits\": \"\\\"1\\\"\", \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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\\\"\"}",
776 "tool_version": null,
777 "type": "tool",
778 "uuid": "32bed7c8-52a3-4e55-a0e0-ab0eef49ff20",
779 "workflow_outputs": []
780 },
781 "23": {
782 "annotation": "",
783 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
784 "id": 23,
785 "input_connections": {
786 "blastxml_file": {
787 "id": 21,
788 "output_name": "output_xml"
789 }
790 },
791 "inputs": [],
792 "label": null,
793 "name": "BLAST XML to selected tabular columns",
794 "outputs": [
795 {
796 "name": "tabular_file",
797 "type": "tabular"
798 },
799 {
800 "name": "unmatched_file",
801 "type": "tabular"
802 }
803 ],
804 "position": {
805 "left": 3901.5,
806 "top": 566
807 },
808 "post_job_actions": {},
809 "tool_errors": null,
810 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/blastxml_to_tabular_selectable/blastxml_to_tabular_selectable/1.0.0",
811 "tool_state": "{\"__page__\": 0, \"qdef\": \"\\\"False\\\"\", \"blastxml_file\": \"null\", \"__rerun_remap_job_id__\": null, \"maxhits\": \"\\\"1\\\"\", \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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\\\"\"}",
812 "tool_version": null,
813 "type": "tool",
814 "uuid": "bffa4aee-79df-4558-96ab-a707a6b3fc30",
815 "workflow_outputs": []
816 },
817 "24": {
818 "annotation": "",
819 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
820 "id": 24,
821 "input_connections": {
822 "input": {
823 "id": 22,
824 "output_name": "tabular_file"
825 }
826 },
827 "inputs": [],
828 "label": null,
829 "name": "Compute",
830 "outputs": [
831 {
832 "name": "out_file1",
833 "type": "input"
834 }
835 ],
836 "position": {
837 "left": 4134.5,
838 "top": 372
839 },
840 "post_job_actions": {},
841 "tool_errors": null,
842 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0",
843 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"cond\": \"\\\"(c4/c23)*100\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"round\": \"\\\"no\\\"\"}",
844 "tool_version": null,
845 "type": "tool",
846 "uuid": "a50ea365-68b8-4095-ae5e-881d01070326",
847 "workflow_outputs": []
848 },
849 "25": {
850 "annotation": "",
851 "content_id": "Filter1",
852 "id": 25,
853 "input_connections": {
854 "input": {
855 "id": 24,
856 "output_name": "out_file1"
857 }
858 },
859 "inputs": [],
860 "label": null,
861 "name": "Filter",
862 "outputs": [
863 {
864 "name": "out_file1",
865 "type": "input"
866 }
867 ],
868 "position": {
869 "left": 4275.5,
870 "top": 334
871 },
872 "post_job_actions": {},
873 "tool_errors": null,
874 "tool_id": "Filter1",
875 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"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\\\"\"}",
876 "tool_version": null,
877 "type": "tool",
878 "uuid": "7ae581fb-b37f-41c4-9b2b-1b42fc12f389",
879 "workflow_outputs": []
880 },
881 "26": {
882 "annotation": "",
883 "content_id": "Cut1",
884 "id": 26,
885 "input_connections": {
886 "input": {
887 "id": 25,
888 "output_name": "out_file1"
889 }
890 },
891 "inputs": [],
892 "label": null,
893 "name": "Cut",
894 "outputs": [
895 {
896 "name": "out_file1",
897 "type": "tabular"
898 }
899 ],
900 "position": {
901 "left": 4495.5,
902 "top": 334
903 },
904 "post_job_actions": {},
905 "tool_errors": null,
906 "tool_id": "Cut1",
907 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
908 "tool_version": null,
909 "type": "tool",
910 "uuid": "267ec4dd-3440-4663-9820-88270c75bf23",
911 "workflow_outputs": []
912 },
913 "27": {
914 "annotation": "",
915 "content_id": "cat1",
916 "id": 27,
917 "input_connections": {
918 "input1": {
919 "id": 22,
920 "output_name": "unmatched_file"
921 },
922 "queries_0|input2": {
923 "id": 26,
924 "output_name": "out_file1"
925 }
926 },
927 "inputs": [],
928 "label": null,
929 "name": "Concatenate datasets",
930 "outputs": [
931 {
932 "name": "out_file1",
933 "type": "input"
934 }
935 ],
936 "position": {
937 "left": 4715.5,
938 "top": 334
939 },
940 "post_job_actions": {},
941 "tool_errors": null,
942 "tool_id": "cat1",
943 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
944 "tool_version": null,
945 "type": "tool",
946 "uuid": "4bad8aba-4815-445b-8437-17caca81569c",
947 "workflow_outputs": []
948 },
949 "28": {
950 "annotation": "",
951 "content_id": "cat1",
952 "id": 28,
953 "input_connections": {
954 "input1": {
955 "id": 27,
956 "output_name": "out_file1"
957 },
958 "queries_0|input2": {
959 "id": 23,
960 "output_name": "unmatched_file"
961 }
962 },
963 "inputs": [],
964 "label": null,
965 "name": "Concatenate datasets",
966 "outputs": [
967 {
968 "name": "out_file1",
969 "type": "input"
970 }
971 ],
972 "position": {
973 "left": 4935.5,
974 "top": 334
975 },
976 "post_job_actions": {},
977 "tool_errors": null,
978 "tool_id": "cat1",
979 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
980 "tool_version": null,
981 "type": "tool",
982 "uuid": "6c18dc27-e600-42fe-a5f6-1bb51fd7fad2",
983 "workflow_outputs": [
984 {
985 "label": null,
986 "output_name": "out_file1",
987 "uuid": "6291706f-09be-471d-a97f-a3e94cff7a5c"
988 }
989 ]
990 },
991 "29": {
992 "annotation": "",
993 "content_id": "join1",
994 "id": 29,
995 "input_connections": {
996 "input1": {
997 "id": 28,
998 "output_name": "out_file1"
999 },
1000 "input2": {
1001 "id": 11,
1002 "output_name": "out_file1"
1003 }
1004 },
1005 "inputs": [],
1006 "label": null,
1007 "name": "Join two Datasets",
1008 "outputs": [
1009 {
1010 "name": "out_file1",
1011 "type": "input"
1012 }
1013 ],
1014 "position": {
1015 "left": 5155.5,
1016 "top": 334
1017 },
1018 "post_job_actions": {},
1019 "tool_errors": null,
1020 "tool_id": "join1",
1021 "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__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input1\": \"null\", \"unmatched\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
1022 "tool_version": null,
1023 "type": "tool",
1024 "uuid": "08ea3482-672e-4d88-b403-3047dcad4ac8",
1025 "workflow_outputs": []
1026 },
1027 "30": {
1028 "annotation": "",
1029 "content_id": "Grouping1",
1030 "id": 30,
1031 "input_connections": {
1032 "input1": {
1033 "id": 29,
1034 "output_name": "out_file1"
1035 }
1036 },
1037 "inputs": [],
1038 "label": null,
1039 "name": "Group",
1040 "outputs": [
1041 {
1042 "name": "out_file1",
1043 "type": "tabular"
1044 }
1045 ],
1046 "position": {
1047 "left": 5375.5,
1048 "top": 334
1049 },
1050 "post_job_actions": {},
1051 "tool_errors": null,
1052 "tool_id": "Grouping1",
1053 "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\\\"\"}",
1054 "tool_version": null,
1055 "type": "tool",
1056 "uuid": "f5045725-e3c7-48d9-8b81-59641d4a01f5",
1057 "workflow_outputs": []
1058 },
1059 "31": {
1060 "annotation": "",
1061 "content_id": "join1",
1062 "id": 31,
1063 "input_connections": {
1064 "input1": {
1065 "id": 9,
1066 "output_name": "out_file1"
1067 },
1068 "input2": {
1069 "id": 30,
1070 "output_name": "out_file1"
1071 }
1072 },
1073 "inputs": [],
1074 "label": null,
1075 "name": "Join two Datasets",
1076 "outputs": [
1077 {
1078 "name": "out_file1",
1079 "type": "input"
1080 }
1081 ],
1082 "position": {
1083 "left": 5597.5,
1084 "top": 334
1085 },
1086 "post_job_actions": {},
1087 "tool_errors": null,
1088 "tool_id": "join1",
1089 "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__\": \"\\\"cc3aede233bc11e686bffa163e14a73a\\\"\", \"input1\": \"null\", \"unmatched\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/website/galaxyp2014.msi.umn.edu/galaxy-central/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}",
1090 "tool_version": null,
1091 "type": "tool",
1092 "uuid": "a386ba9a-dfea-4501-a0f6-10dd4993b225",
1093 "workflow_outputs": []
1094 },
1095 "32": {
1096 "annotation": "",
1097 "content_id": "Cut1",
1098 "id": 32,
1099 "input_connections": {
1100 "input": {
1101 "id": 31,
1102 "output_name": "out_file1"
1103 }
1104 },
1105 "inputs": [],
1106 "label": null,
1107 "name": "Cut",
1108 "outputs": [
1109 {
1110 "name": "out_file1",
1111 "type": "tabular"
1112 }
1113 ],
1114 "position": {
1115 "left": 5815.5,
1116 "top": 334
1117 },
1118 "post_job_actions": {},
1119 "tool_errors": null,
1120 "tool_id": "Cut1",
1121 "tool_state": "{\"columnList\": \"\\\"c1-c20\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
1122 "tool_version": null,
1123 "type": "tool",
1124 "uuid": "98867a3a-7f35-429f-b9a0-bd915f973c0c",
1125 "workflow_outputs": [
1126 {
1127 "label": null,
1128 "output_name": "out_file1",
1129 "uuid": "32aaabbe-f0c0-4cbf-89bb-5503abd62a1d"
1130 }
1131 ]
1132 },
1133 "33": {
1134 "annotation": "",
1135 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/map_peptides_to_bed/map_peptides_to_bed/0.1.0",
1136 "id": 33,
1137 "input_connections": {
1138 "input": {
1139 "id": 32,
1140 "output_name": "out_file1"
1141 },
1142 "translated_bed": {
1143 "id": 1,
1144 "output_name": "output"
1145 }
1146 },
1147 "inputs": [],
1148 "label": null,
1149 "name": "Map peptides to a bed file",
1150 "outputs": [
1151 {
1152 "name": "mapped_peptides",
1153 "type": "bed"
1154 }
1155 ],
1156 "position": {
1157 "left": 6057.5,
1158 "top": 269
1159 },
1160 "post_job_actions": {},
1161 "tool_errors": null,
1162 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/map_peptides_to_bed/map_peptides_to_bed/0.1.0",
1163 "tool_state": "{\"translated_bed\": \"null\", \"__page__\": 0, \"name_column\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"gffTags\": \"\\\"True\\\"\", \"input\": \"null\", \"start_column\": \"null\", \"peptide_column\": \"\\\"3\\\"\"}",
1164 "tool_version": null,
1165 "type": "tool",
1166 "uuid": "adde3db1-8638-4665-8fb4-cda1bb072afd",
1167 "workflow_outputs": [
1168 {
1169 "label": null,
1170 "output_name": "mapped_peptides",
1171 "uuid": "2fb4bf92-ebb6-434d-8419-27d2a4fda0f1"
1172 }
1173 ]
1174 },
1175 "34": {
1176 "annotation": "",
1177 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/map_peptides_to_bed/map_peptides_to_bed/0.1.0",
1178 "id": 34,
1179 "input_connections": {
1180 "input": {
1181 "id": 32,
1182 "output_name": "out_file1"
1183 },
1184 "translated_bed": {
1185 "id": 2,
1186 "output_name": "output"
1187 }
1188 },
1189 "inputs": [],
1190 "label": null,
1191 "name": "Map peptides to a bed file",
1192 "outputs": [
1193 {
1194 "name": "mapped_peptides",
1195 "type": "bed"
1196 }
1197 ],
1198 "position": {
1199 "left": 6103.5,
1200 "top": 500
1201 },
1202 "post_job_actions": {},
1203 "tool_errors": null,
1204 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/map_peptides_to_bed/map_peptides_to_bed/0.1.0",
1205 "tool_state": "{\"translated_bed\": \"null\", \"__page__\": 0, \"name_column\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"gffTags\": \"\\\"True\\\"\", \"input\": \"null\", \"start_column\": \"null\", \"peptide_column\": \"\\\"3\\\"\"}",
1206 "tool_version": null,
1207 "type": "tool",
1208 "uuid": "3d662ced-aea0-44e5-b2c2-3549a947d6f4",
1209 "workflow_outputs": [
1210 {
1211 "label": null,
1212 "output_name": "mapped_peptides",
1213 "uuid": "bc075177-e214-444d-9141-d60c1a77e8eb"
1214 }
1215 ]
1216 }
1217 },
1218 "uuid": "43c7ff8f-007b-4c15-b8df-ed362012f8b5"
1219 }