Mercurial > repos > clairetn > detrprok_wf

comparison Galaxy-Workflow-Detrprok_wf.ga @ 0:c265b11e7277 draft

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author clairetn
date Mon, 25 Mar 2013 05:51:08 -0400
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children 20e004d0292b
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-1:000000000000 0:c265b11e7277
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "Detrprok_current",
6 "steps": {
7 "0": {
8 "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.",
14 "name": "positions list of all genome known annotations"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 166,
21 "top": 364
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"positions list of all genome known annotations\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).",
37 "name": "read alignments on genome"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 215,
44 "top": 484
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"read alignments on genome\"}",
49 "tool_version": null,
50 "type": "data_input",
51 "user_outputs": []
52 },
53 "2": {
54 "annotation": "",
55 "id": 2,
56 "input_connections": {
57 "inputFile": {
58 "id": 0,
59 "output_name": "output"
60 }
61 },
62 "inputs": [],
63 "name": "clean Gff",
64 "outputs": [
65 {
66 "name": "outputFile",
67 "type": "gff3"
68 }
69 ],
70 "position": {
71 "left": 361,
72 "top": 327
73 },
74 "post_job_actions": {},
75 "tool_errors": null,
76 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/cleanGff/1.0.0",
77 "tool_state": "{\"__page__\": 0, \"type\": \"\\\"tRNA,rRNA,ncRNA,CDS\\\"\", \"inputFile\": \"null\"}",
78 "tool_version": "1.0.0",
79 "type": "tool",
80 "user_outputs": []
81 },
82 "3": {
83 "annotation": "Technical step (format change).",
84 "id": 3,
85 "input_connections": {
86 "input1": {
87 "id": 1,
88 "output_name": "output"
89 }
90 },
91 "inputs": [],
92 "name": "BAM-to-SAM",
93 "outputs": [
94 {
95 "name": "output1",
96 "type": "sam"
97 }
98 ],
99 "position": {
100 "left": 418,
101 "top": 479
102 },
103 "post_job_actions": {
104 "RenameDatasetActionoutput1": {
105 "action_arguments": {
106 "newname": "Read alignments in SAM format"
107 },
108 "action_type": "RenameDatasetAction",
109 "output_name": "output1"
110 }
111 },
112 "tool_errors": null,
113 "tool_id": "bam_to_sam",
114 "tool_state": "{\"header\": \"\\\"False\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
115 "tool_version": "1.0.3",
116 "type": "tool",
117 "user_outputs": []
118 },
119 "4": {
120 "annotation": "Clusters annotated proximal genes into operons. \nParameter to be set: op_gap. \nGenes separated by a gap smaller than op_gap are clustered \n(suggested value: 10 to 150).",
121 "id": 4,
122 "input_connections": {
123 "formatType|inputFileName": {
124 "id": 2,
125 "output_name": "outputFile"
126 }
127 },
128 "inputs": [
129 {
130 "description": "runtime parameter for tool Clusterize",
131 "name": "distance"
132 }
133 ],
134 "name": "Clusterize",
135 "outputs": [
136 {
137 "name": "outputFileGff",
138 "type": "gff3"
139 },
140 {
141 "name": "outputFileLog",
142 "type": "txt"
143 }
144 ],
145 "position": {
146 "left": 547,
147 "top": 297
148 },
149 "post_job_actions": {
150 "RenameDatasetActionoutputFileGff": {
151 "action_arguments": {
152 "newname": "Annotation with \"operon\""
153 },
154 "action_type": "RenameDatasetAction",
155 "output_name": "outputFileGff"
156 }
157 },
158 "tool_errors": null,
159 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
160 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}",
161 "tool_version": "1.0.0",
162 "type": "tool",
163 "user_outputs": []
164 },
165 "5": {
166 "annotation": "Clusters overlapping or proximal reads to produce read clusters. \nParameter to be set: clust_gap. \nReads separated by a gap smaller than \nclust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart).",
167 "id": 5,
168 "input_connections": {
169 "formatType|inputFileName": {
170 "id": 3,
171 "output_name": "output1"
172 }
173 },
174 "inputs": [
175 {
176 "description": "runtime parameter for tool Clusterize",
177 "name": "distance"
178 }
179 ],
180 "name": "Clusterize",
181 "outputs": [
182 {
183 "name": "outputFileGff",
184 "type": "gff3"
185 },
186 {
187 "name": "outputFileLog",
188 "type": "txt"
189 }
190 ],
191 "position": {
192 "left": 496,
193 "top": 596
194 },
195 "post_job_actions": {
196 "RenameDatasetActionoutputFileGff": {
197 "action_arguments": {
198 "newname": "Read clusters"
199 },
200 "action_type": "RenameDatasetAction",
201 "output_name": "outputFileGff"
202 }
203 },
204 "tool_errors": null,
205 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
206 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 5, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
207 "tool_version": "1.0.0",
208 "type": "tool",
209 "user_outputs": []
210 },
211 "6": {
212 "annotation": "Selects read clusters that overlap annotations in the same direction. \nParameter to be set: RNA_gap.\nA read cluster separated from an annotation by a gap smaller than RNA_gap is selected (suggested value: 25).",
213 "id": 6,
214 "input_connections": {
215 "formatType2|inputFileName2": {
216 "id": 4,
217 "output_name": "outputFileGff"
218 },
219 "formatType|inputFileName1": {
220 "id": 5,
221 "output_name": "outputFileGff"
222 }
223 },
224 "inputs": [
225 {
226 "description": "runtime parameter for tool Compare Overlapping Small Query",
227 "name": "OptionDistance"
228 }
229 ],
230 "name": "Compare Overlapping Small Query",
231 "outputs": [
232 {
233 "name": "outputFileGff",
234 "type": "gff3"
235 }
236 ],
237 "position": {
238 "left": 659,
239 "top": 417
240 },
241 "post_job_actions": {
242 "RenameDatasetActionoutputFileGff": {
243 "action_arguments": {
244 "newname": "Read clusters overlapping annotation"
245 },
246 "action_type": "RenameDatasetAction",
247 "output_name": "outputFileGff"
248 }
249 },
250 "tool_errors": null,
251 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
252 "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
253 "tool_version": "1.0.0",
254 "type": "tool",
255 "user_outputs": []
256 },
257 "7": {
258 "annotation": "Selects read clusters that form new independent annotations. \nParameter to be set: RNA_gap.\nRead clusters at a distance from existing annotations larger than RNA_gap are selected. Caution: use same RNA_gap value as in previous step!",
259 "id": 7,
260 "input_connections": {
261 "formatType2|inputFileName2": {
262 "id": 4,
263 "output_name": "outputFileGff"
264 },
265 "formatType|inputFileName1": {
266 "id": 5,
267 "output_name": "outputFileGff"
268 }
269 },
270 "inputs": [
271 {
272 "description": "runtime parameter for tool Compare Overlapping Small Query",
273 "name": "OptionDistance"
274 }
275 ],
276 "name": "Compare Overlapping Small Query",
277 "outputs": [
278 {
279 "name": "outputFileGff",
280 "type": "gff3"
281 }
282 ],
283 "position": {
284 "left": 742,
285 "top": 588
286 },
287 "post_job_actions": {
288 "RenameDatasetActionoutputFileGff": {
289 "action_arguments": {
290 "newname": "Read clusters not overlapping annotation"
291 },
292 "action_type": "RenameDatasetAction",
293 "output_name": "outputFileGff"
294 }
295 },
296 "tool_errors": null,
297 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
298 "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
299 "tool_version": "1.0.0",
300 "type": "tool",
301 "user_outputs": []
302 },
303 "8": {
304 "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.",
305 "id": 8,
306 "input_connections": {
307 "input1": {
308 "id": 4,
309 "output_name": "outputFileGff"
310 },
311 "queries_0|input2": {
312 "id": 6,
313 "output_name": "outputFileGff"
314 }
315 },
316 "inputs": [],
317 "name": "Concatenate datasets",
318 "outputs": [
319 {
320 "name": "out_file1",
321 "type": "input"
322 }
323 ],
324 "position": {
325 "left": 819,
326 "top": 294
327 },
328 "post_job_actions": {
329 "RenameDatasetActionout_file1": {
330 "action_arguments": {
331 "newname": "Annotations and read clusters overlapping them"
332 },
333 "action_type": "RenameDatasetAction",
334 "output_name": "out_file1"
335 }
336 },
337 "tool_errors": null,
338 "tool_id": "cat1",
339 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
340 "tool_version": "1.0.0",
341 "type": "tool",
342 "user_outputs": []
343 },
344 "9": {
345 "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. \nParameter to be set: RNA_gap.\nRead cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!",
346 "id": 9,
347 "input_connections": {
348 "formatType|inputFileName": {
349 "id": 8,
350 "output_name": "out_file1"
351 }
352 },
353 "inputs": [
354 {
355 "description": "runtime parameter for tool Clusterize",
356 "name": "distance"
357 }
358 ],
359 "name": "Clusterize",
360 "outputs": [
361 {
362 "name": "outputFileGff",
363 "type": "gff3"
364 },
365 {
366 "name": "outputFileLog",
367 "type": "txt"
368 }
369 ],
370 "position": {
371 "left": 1036,
372 "top": 307
373 },
374 "post_job_actions": {
375 "RenameDatasetActionoutputFileGff": {
376 "action_arguments": {
377 "newname": "Extended annotation"
378 },
379 "action_type": "RenameDatasetAction",
380 "output_name": "outputFileGff"
381 }
382 },
383 "tool_errors": null,
384 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
385 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
386 "tool_version": "1.0.0",
387 "type": "tool",
388 "user_outputs": []
389 },
390 "10": {
391 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.",
392 "id": 10,
393 "input_connections": {
394 "input": {
395 "id": 9,
396 "output_name": "outputFileGff"
397 }
398 },
399 "inputs": [],
400 "name": "Select",
401 "outputs": [
402 {
403 "name": "out_file1",
404 "type": "input"
405 }
406 ],
407 "position": {
408 "left": 1232,
409 "top": 319
410 },
411 "post_job_actions": {
412 "RenameDatasetActionout_file1": {
413 "action_arguments": {
414 "newname": "Extended annotation without \"exon\" lines"
415 },
416 "action_type": "RenameDatasetAction",
417 "output_name": "out_file1"
418 }
419 },
420 "tool_errors": null,
421 "tool_id": "Grep1",
422 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}",
423 "tool_version": "1.0.1",
424 "type": "tool",
425 "user_outputs": []
426 },
427 "11": {
428 "annotation": "Technical step: orders extended annotations by positions.",
429 "id": 11,
430 "input_connections": {
431 "formatType|inputFileName": {
432 "id": 10,
433 "output_name": "out_file1"
434 }
435 },
436 "inputs": [],
437 "name": "collapse reads",
438 "outputs": [
439 {
440 "name": "outputFileGff",
441 "type": "gff3"
442 }
443 ],
444 "position": {
445 "left": 973,
446 "top": 460
447 },
448 "post_job_actions": {
449 "RenameDatasetActionoutputFileGff": {
450 "action_arguments": {
451 "newname": "Ordrered and extended annotation"
452 },
453 "action_type": "RenameDatasetAction",
454 "output_name": "outputFileGff"
455 }
456 },
457 "tool_errors": null,
458 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0",
459 "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}",
460 "tool_version": "1.0.0",
461 "type": "tool",
462 "user_outputs": []
463 },
464 "12": {
465 "annotation": "Splits extended annotations into UTRs, CDS and/or operon spacers.",
466 "id": 12,
467 "input_connections": {
468 "referenciesFile": {
469 "id": 4,
470 "output_name": "outputFileGff"
471 },
472 "transcriptsFile": {
473 "id": 11,
474 "output_name": "outputFileGff"
475 }
476 },
477 "inputs": [],
478 "name": "splitTranscriptGff",
479 "outputs": [
480 {
481 "name": "outputFile",
482 "type": "gff3"
483 }
484 ],
485 "position": {
486 "left": 1221,
487 "top": 456
488 },
489 "post_job_actions": {
490 "RenameDatasetActionoutputFile": {
491 "action_arguments": {
492 "newname": "UTRs, CDSs and/or operons"
493 },
494 "action_type": "RenameDatasetAction",
495 "output_name": "outputFile"
496 }
497 },
498 "tool_errors": null,
499 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/splitTranscriptGff/1.0.0",
500 "tool_state": "{\"transcriptsFile\": \"null\", \"__page__\": 0, \"referenciesFile\": \"null\"}",
501 "tool_version": "1.0.0",
502 "type": "tool",
503 "user_outputs": []
504 },
505 "13": {
506 "annotation": "Selection of read clusters that are antisense of an extended annotation. \nThis step produces a first list of antisense candidates.",
507 "id": 13,
508 "input_connections": {
509 "formatType2|inputFileName2": {
510 "id": 11,
511 "output_name": "outputFileGff"
512 },
513 "formatType|inputFileName1": {
514 "id": 7,
515 "output_name": "outputFileGff"
516 }
517 },
518 "inputs": [],
519 "name": "Compare Overlapping Small Query",
520 "outputs": [
521 {
522 "name": "outputFileGff",
523 "type": "gff3"
524 }
525 ],
526 "position": {
527 "left": 1155,
528 "top": 617
529 },
530 "post_job_actions": {
531 "RenameDatasetActionoutputFileGff": {
532 "action_arguments": {
533 "newname": "first list of asRNA"
534 },
535 "action_type": "RenameDatasetAction",
536 "output_name": "outputFileGff"
537 }
538 },
539 "tool_errors": null,
540 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
541 "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
542 "tool_version": "1.0.0",
543 "type": "tool",
544 "user_outputs": []
545 },
546 "14": {
547 "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation.\nThis step produces a first list of small RNAs.",
548 "id": 14,
549 "input_connections": {
550 "formatType2|inputFileName2": {
551 "id": 11,
552 "output_name": "outputFileGff"
553 },
554 "formatType|inputFileName1": {
555 "id": 7,
556 "output_name": "outputFileGff"
557 }
558 },
559 "inputs": [],
560 "name": "Compare Overlapping Small Query",
561 "outputs": [
562 {
563 "name": "outputFileGff",
564 "type": "gff3"
565 }
566 ],
567 "position": {
568 "left": 1068,
569 "top": 766
570 },
571 "post_job_actions": {
572 "RenameDatasetActionoutputFileGff": {
573 "action_arguments": {
574 "newname": "first list of sRNA"
575 },
576 "action_type": "RenameDatasetAction",
577 "output_name": "outputFileGff"
578 }
579 },
580 "tool_errors": null,
581 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0",
582 "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
583 "tool_version": "1.0.0",
584 "type": "tool",
585 "user_outputs": []
586 },
587 "15": {
588 "annotation": "Counts reads overlapping UTRs, CDSs and/or operon spacers in order to compute read coverage (with a minimal overlapping region of 10 nt between read and genetic element). Output file of this step can be used to obtain read coverage of 5'UTRs, 3'UTRs, CDSs, or operon spacers.",
589 "id": 15,
590 "input_connections": {
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592 "id": 3,
593 "output_name": "output1"
594 },
595 "formatType|inputFileName1": {
596 "id": 12,
597 "output_name": "outputFile"
598 }
599 },
600 "inputs": [],
601 "name": "Compare Overlapping Small Reference",
602 "outputs": [
603 {
604 "name": "outputFileGff",
605 "type": "gff3"
606 }
607 ],
608 "position": {
609 "left": 1417,
610 "top": 506
611 },
612 "post_job_actions": {
613 "RenameDatasetActionoutputFileGff": {
614 "action_arguments": {
615 "newname": "UTRs, CDSs and operons (with the number of overlapping reads)"
616 },
617 "action_type": "RenameDatasetAction",
618 "output_name": "outputFileGff"
619 }
620 },
621 "tool_errors": null,
622 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallRef/1.0.0",
623 "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"sam\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 4}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"10\\\"}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
624 "tool_version": "1.0.0",
625 "type": "tool",
626 "user_outputs": []
627 },
628 "16": {
629 "annotation": "Filters antisense RNA candidates based on their number of overlapping reads.\nParameter to be set: as_min_reads.\nAntisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).",
630 "id": 16,
631 "input_connections": {
632 "formatType|inputFileName": {
633 "id": 13,
634 "output_name": "outputFileGff"
635 }
636 },
637 "inputs": [
638 {
639 "description": "runtime parameter for tool select by tag",
640 "name": "OptionMin"
641 }
642 ],
643 "name": "select by tag",
644 "outputs": [
645 {
646 "name": "outputFileGff",
647 "type": "gff3"
648 }
649 ],
650 "position": {
651 "left": 1461,
652 "top": 663
653 },
654 "post_job_actions": {
655 "RenameDatasetActionoutputFileGff": {
656 "action_arguments": {
657 "newname": "asRNA list modified (filtered on their number of overlapping reads)"
658 },
659 "action_type": "RenameDatasetAction",
660 "output_name": "outputFileGff"
661 }
662 },
663 "tool_errors": null,
664 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0",
665 "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}",
666 "tool_version": "1.0.0",
667 "type": "tool",
668 "user_outputs": []
669 },
670 "17": {
671 "annotation": "Filters sRNA candidates based on their number of overlapping reads.\nParameter to be set: sRNA_min_reads.\nSmall RNAs with a number of reads higher than sRNA_min_reads are selected (suggested value: 12).",
672 "id": 17,
673 "input_connections": {
674 "formatType|inputFileName": {
675 "id": 14,
676 "output_name": "outputFileGff"
677 }
678 },
679 "inputs": [
680 {
681 "description": "runtime parameter for tool select by tag",
682 "name": "OptionMin"
683 }
684 ],
685 "name": "select by tag",
686 "outputs": [
687 {
688 "name": "outputFileGff",
689 "type": "gff3"
690 }
691 ],
692 "position": {
693 "left": 1389,
694 "top": 794
695 },
696 "post_job_actions": {
697 "RenameDatasetActionoutputFileGff": {
698 "action_arguments": {
699 "newname": "sRNA list modified (filtered on their number of overlapping reads)"
700 },
701 "action_type": "RenameDatasetAction",
702 "output_name": "outputFileGff"
703 }
704 },
705 "tool_errors": null,
706 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0",
707 "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}",
708 "tool_version": "1.0.0",
709 "type": "tool",
710 "user_outputs": []
711 },
712 "18": {
713 "annotation": "Technical step: coverage computation needs \"nbElements\" tag in place of \"nbOverlaps\".",
714 "id": 18,
715 "input_connections": {
716 "formatType|inputFileName": {
717 "id": 15,
718 "output_name": "outputFileGff"
719 }
720 },
721 "inputs": [],
722 "name": "change tag name",
723 "outputs": [
724 {
725 "name": "outputFileGff",
726 "type": "gff3"
727 }
728 ],
729 "position": {
730 "left": 1696,
731 "top": 541
732 },
733 "post_job_actions": {
734 "RenameDatasetActionoutputFileGff": {
735 "action_arguments": {
736 "newname": "long 5'UTR list modified (tag \"nbElements\")"
737 },
738 "action_type": "RenameDatasetAction",
739 "output_name": "outputFileGff"
740 }
741 },
742 "tool_errors": null,
743 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0",
744 "tool_state": "{\"__page__\": 0, \"Tag\": \"\\\"nbOverlaps\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"name\": \"\\\"nbElements\\\"\"}",
745 "tool_version": "1.0.0",
746 "type": "tool",
747 "user_outputs": []
748 },
749 "19": {
750 "annotation": "Clusters proximal antisense RNAs in the same direction.\nParameter to be set: RNA_merge.\nAntisense RNAs located less than RNA_merge apart are merged (suggestion: 50).",
751 "id": 19,
752 "input_connections": {
753 "formatType|inputFileName": {
754 "id": 16,
755 "output_name": "outputFileGff"
756 }
757 },
758 "inputs": [
759 {
760 "description": "runtime parameter for tool Clusterize",
761 "name": "distance"
762 }
763 ],
764 "name": "Clusterize",
765 "outputs": [
766 {
767 "name": "outputFileGff",
768 "type": "gff3"
769 },
770 {
771 "name": "outputFileLog",
772 "type": "txt"
773 }
774 ],
775 "position": {
776 "left": 1658,
777 "top": 660
778 },
779 "post_job_actions": {
780 "RenameDatasetActionoutputFileGff": {
781 "action_arguments": {
782 "newname": "asRNA list modified (asRNA clusters)"
783 },
784 "action_type": "RenameDatasetAction",
785 "output_name": "outputFileGff"
786 }
787 },
788 "tool_errors": null,
789 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
790 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}",
791 "tool_version": "1.0.0",
792 "type": "tool",
793 "user_outputs": []
794 },
795 "20": {
796 "annotation": "Clusters proximal small RNAs in the same direction.\nParameter to be set: RNA_merge.\nSmall RNAs located less than RNA_merge apart are merged (suggestion: 50).",
797 "id": 20,
798 "input_connections": {
799 "formatType|inputFileName": {
800 "id": 17,
801 "output_name": "outputFileGff"
802 }
803 },
804 "inputs": [],
805 "name": "Clusterize",
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807 {
808 "name": "outputFileGff",
809 "type": "gff3"
810 },
811 {
812 "name": "outputFileLog",
813 "type": "txt"
814 }
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816 "position": {
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818 "top": 797
819 },
820 "post_job_actions": {
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825 "action_type": "RenameDatasetAction",
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827 }
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830 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0",
831 "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"\\\"50\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
832 "tool_version": "1.0.0",
833 "type": "tool",
834 "user_outputs": []
835 },
836 "21": {
837 "annotation": "Technical step: extracts 5'UTR features for following steps.",
838 "id": 21,
839 "input_connections": {
840 "input1": {
841 "id": 18,
842 "output_name": "outputFileGff"
843 }
844 },
845 "inputs": [],
846 "name": "Extract features",
847 "outputs": [
848 {
849 "name": "out_file1",
850 "type": "input"
851 }
852 ],
853 "position": {
854 "left": 1917,
855 "top": 547
856 },
857 "post_job_actions": {
858 "RenameDatasetActionout_file1": {
859 "action_arguments": {
860 "newname": "first list of long 5'UTR"
861 },
862 "action_type": "RenameDatasetAction",
863 "output_name": "out_file1"
864 }
865 },
866 "tool_errors": null,
867 "tool_id": "Extract_features1",
868 "tool_state": "{\"column_choice\": \"{\\\"col\\\": \\\"2\\\", \\\"__current_case__\\\": 2, \\\"feature\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"utr5\\\"]}}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
869 "tool_version": "1.0.0",
870 "type": "tool",
871 "user_outputs": []
872 },
873 "22": {
874 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.",
875 "id": 22,
876 "input_connections": {
877 "input": {
878 "id": 19,
879 "output_name": "outputFileGff"
880 }
881 },
882 "inputs": [],
883 "name": "Select",
884 "outputs": [
885 {
886 "name": "out_file1",
887 "type": "input"
888 }
889 ],
890 "position": {
891 "left": 1859,
892 "top": 682
893 },
894 "post_job_actions": {
895 "RenameDatasetActionout_file1": {
896 "action_arguments": {
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898 },
899 "action_type": "RenameDatasetAction",
900 "output_name": "out_file1"
901 }
902 },
903 "tool_errors": null,
904 "tool_id": "Grep1",
905 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"pattern\": \"\\\"exon\\\"\"}",
906 "tool_version": "1.0.1",
907 "type": "tool",
908 "user_outputs": []
909 },
910 "23": {
911 "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.",
912 "id": 23,
913 "input_connections": {
914 "input": {
915 "id": 20,
916 "output_name": "outputFileGff"
917 }
918 },
919 "inputs": [],
920 "name": "Select",
921 "outputs": [
922 {
923 "name": "out_file1",
924 "type": "input"
925 }
926 ],
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928 "left": 1804,
929 "top": 813
930 },
931 "post_job_actions": {
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935 },
936 "action_type": "RenameDatasetAction",
937 "output_name": "out_file1"
938 }
939 },
940 "tool_errors": null,
941 "tool_id": "Grep1",
942 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}",
943 "tool_version": "1.0.1",
944 "type": "tool",
945 "user_outputs": []
946 },
947 "24": {
948 "annotation": "Filters 5'UTR based on their size.\nParameter to be set: 5UTR_min_size.\n5'UTRs larger than 5UTR_min_size are selected (suggestion value: 50).",
949 "id": 24,
950 "input_connections": {
951 "formatType|inputFileName": {
952 "id": 21,
953 "output_name": "out_file1"
954 }
955 },
956 "inputs": [
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958 "description": "runtime parameter for tool restrict from size",
959 "name": "OptionMin"
960 }
961 ],
962 "name": "restrict from size",
963 "outputs": [
964 {
965 "name": "outputFileGff",
966 "type": "gff3"
967 }
968 ],
969 "position": {
970 "left": 2132,
971 "top": 570
972 },
973 "post_job_actions": {
974 "RenameDatasetActionoutputFileGff": {
975 "action_arguments": {
976 "newname": "long 5'UTR list modified (filtered on their size)"
977 },
978 "action_type": "RenameDatasetAction",
979 "output_name": "outputFileGff"
980 }
981 },
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983 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0",
984 "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
985 "tool_version": "1.0.0",
986 "type": "tool",
987 "user_outputs": []
988 },
989 "25": {
990 "annotation": "Filters antisense RNAs based on their size.\nParameter to be set: as_min_size.\nas_min_size is the minimal size for calling an antisense RNA (suggestion: 50).",
991 "id": 25,
992 "input_connections": {
993 "formatType|inputFileName": {
994 "id": 22,
995 "output_name": "out_file1"
996 }
997 },
998 "inputs": [
999 {
1000 "description": "runtime parameter for tool restrict from size",
1001 "name": "OptionMin"
1002 }
1003 ],
1004 "name": "restrict from size",
1005 "outputs": [
1006 {
1007 "name": "outputFileGff",
1008 "type": "gff3"
1009 }
1010 ],
1011 "position": {
1012 "left": 2085,
1013 "top": 691
1014 },
1015 "post_job_actions": {
1016 "RenameDatasetActionoutputFileGff": {
1017 "action_arguments": {
1018 "newname": "asRNA list modified (filtered on their size)"
1019 },
1020 "action_type": "RenameDatasetAction",
1021 "output_name": "outputFileGff"
1022 }
1023 },
1024 "tool_errors": null,
1025 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0",
1026 "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
1027 "tool_version": "1.0.0",
1028 "type": "tool",
1029 "user_outputs": []
1030 },
1031 "26": {
1032 "annotation": "Filters small RNAs based on their size.\nParameter to be set: sRNA_min_size.\nsRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).",
1033 "id": 26,
1034 "input_connections": {
1035 "formatType|inputFileName": {
1036 "id": 23,
1037 "output_name": "out_file1"
1038 }
1039 },
1040 "inputs": [
1041 {
1042 "description": "runtime parameter for tool restrict from size",
1043 "name": "OptionMin"
1044 }
1045 ],
1046 "name": "restrict from size",
1047 "outputs": [
1048 {
1049 "name": "outputFileGff",
1050 "type": "gff3"
1051 }
1052 ],
1053 "position": {
1054 "left": 2017,
1055 "top": 824
1056 },
1057 "post_job_actions": {
1058 "RenameDatasetActionoutputFileGff": {
1059 "action_arguments": {
1060 "newname": "sRNA list modified (filtered on their size)"
1061 },
1062 "action_type": "RenameDatasetAction",
1063 "output_name": "outputFileGff"
1064 }
1065 },
1066 "tool_errors": null,
1067 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0",
1068 "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
1069 "tool_version": "1.0.0",
1070 "type": "tool",
1071 "user_outputs": []
1072 },
1073 "27": {
1074 "annotation": "Filters long 5' UTR candidates based on their number of overlapping reads.\nParameter to be set: 5UTR_min_reads.\nLong 5'UTR with a number of reads higher than 5UTR_min_reads is selected (suggested value: 10).",
1075 "id": 27,
1076 "input_connections": {
1077 "formatType|inputFileName": {
1078 "id": 24,
1079 "output_name": "outputFileGff"
1080 }
1081 },
1082 "inputs": [
1083 {
1084 "description": "runtime parameter for tool select by tag",
1085 "name": "OptionMin"
1086 }
1087 ],
1088 "name": "select by tag",
1089 "outputs": [
1090 {
1091 "name": "outputFileGff",
1092 "type": "gff3"
1093 }
1094 ],
1095 "position": {
1096 "left": 2344,
1097 "top": 577
1098 },
1099 "post_job_actions": {
1100 "RenameDatasetActionoutputFileGff": {
1101 "action_arguments": {
1102 "newname": "long 5'UTR list modified (filtered on their number of overlapping reads)"
1103 },
1104 "action_type": "RenameDatasetAction",
1105 "output_name": "outputFileGff"
1106 }
1107 },
1108 "tool_errors": null,
1109 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0",
1110 "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}",
1111 "tool_version": "1.0.0",
1112 "type": "tool",
1113 "user_outputs": []
1114 },
1115 "28": {
1116 "annotation": "Uses an RGB color tag for visualization of antisense RNAs in the Artemis environment.",
1117 "id": 28,
1118 "input_connections": {
1119 "referenciesFile": {
1120 "id": 25,
1121 "output_name": "outputFileGff"
1122 }
1123 },
1124 "inputs": [],
1125 "name": "colorGff",
1126 "outputs": [
1127 {
1128 "name": "outputFile",
1129 "type": "gff"
1130 }
1131 ],
1132 "position": {
1133 "left": 2321,
1134 "top": 715
1135 },
1136 "post_job_actions": {
1137 "RenameDatasetActionoutputFile": {
1138 "action_arguments": {
1139 "newname": "asRNA list modified (annotation color)"
1140 },
1141 "action_type": "RenameDatasetAction",
1142 "output_name": "outputFile"
1143 }
1144 },
1145 "tool_errors": null,
1146 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0",
1147 "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"147 112 219\\\"\"}",
1148 "tool_version": "1.0.0",
1149 "type": "tool",
1150 "user_outputs": []
1151 },
1152 "29": {
1153 "annotation": "Uses an RGB color tag for visualization of small RNAs in the Artemis environment.",
1154 "id": 29,
1155 "input_connections": {
1156 "referenciesFile": {
1157 "id": 26,
1158 "output_name": "outputFileGff"
1159 }
1160 },
1161 "inputs": [],
1162 "name": "colorGff",
1163 "outputs": [
1164 {
1165 "name": "outputFile",
1166 "type": "gff"
1167 }
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