|
0
|
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": {
|
|
|
591 "formatType2|inputFileName2": {
|
|
|
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",
|
|
|
806 "outputs": [
|
|
|
807 {
|
|
|
808 "name": "outputFileGff",
|
|
|
809 "type": "gff3"
|
|
|
810 },
|
|
|
811 {
|
|
|
812 "name": "outputFileLog",
|
|
|
813 "type": "txt"
|
|
|
814 }
|
|
|
815 ],
|
|
|
816 "position": {
|
|
|
817 "left": 1602,
|
|
|
818 "top": 797
|
|
|
819 },
|
|
|
820 "post_job_actions": {
|
|
|
821 "RenameDatasetActionoutputFileGff": {
|
|
|
822 "action_arguments": {
|
|
|
823 "newname": "sRNA list modified (sRNA clusters)"
|
|
|
824 },
|
|
|
825 "action_type": "RenameDatasetAction",
|
|
|
826 "output_name": "outputFileGff"
|
|
|
827 }
|
|
|
828 },
|
|
|
829 "tool_errors": null,
|
|
|
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": {
|
|
|
897 "newname": "asRNA list modified (without \"exon\" lines)"
|
|
|
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 ],
|
|
|
927 "position": {
|
|
|
928 "left": 1804,
|
|
|
929 "top": 813
|
|
|
930 },
|
|
|
931 "post_job_actions": {
|
|
|
932 "RenameDatasetActionout_file1": {
|
|
|
933 "action_arguments": {
|
|
|
934 "newname": "sRNA list modified (without \"exon\" lines)"
|
|
|
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": [
|
|
|
957 {
|
|
|
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 },
|
|
|
982 "tool_errors": null,
|
|
|
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 }
|
|
|
1168 ],
|
|
|
1169 "position": {
|
|
|
1170 "left": 2247,
|
|
|
1171 "top": 838
|
|
|
1172 },
|
|
|
1173 "post_job_actions": {
|
|
|
1174 "RenameDatasetActionoutputFile": {
|
|
|
1175 "action_arguments": {
|
|
|
1176 "newname": "sRNA list modified (annotation color)"
|
|
|
1177 },
|
|
|
1178 "action_type": "RenameDatasetAction",
|
|
|
1179 "output_name": "outputFile"
|
|
|
1180 }
|
|
|
1181 },
|
|
|
1182 "tool_errors": null,
|
|
|
1183 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0",
|
|
|
1184 "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"250 128 114\\\"\"}",
|
|
|
1185 "tool_version": "1.0.0",
|
|
|
1186 "type": "tool",
|
|
|
1187 "user_outputs": []
|
|
|
1188 },
|
|
|
1189 "30": {
|
|
|
1190 "annotation": "Uses an RGB color tag for visualization of long 5' UTRs in the Artemis environment.",
|
|
|
1191 "id": 30,
|
|
|
1192 "input_connections": {
|
|
|
1193 "referenciesFile": {
|
|
|
1194 "id": 27,
|
|
|
1195 "output_name": "outputFileGff"
|
|
|
1196 }
|
|
|
1197 },
|
|
|
1198 "inputs": [],
|
|
|
1199 "name": "colorGff",
|
|
|
1200 "outputs": [
|
|
|
1201 {
|
|
|
1202 "name": "outputFile",
|
|
|
1203 "type": "gff"
|
|
|
1204 }
|
|
|
1205 ],
|
|
|
1206 "position": {
|
|
|
1207 "left": 2525,
|
|
|
1208 "top": 610
|
|
|
1209 },
|
|
|
1210 "post_job_actions": {
|
|
|
1211 "RenameDatasetActionoutputFile": {
|
|
|
1212 "action_arguments": {
|
|
|
1213 "newname": "final long 5'UTR list (with the annotation color)"
|
|
|
1214 },
|
|
|
1215 "action_type": "RenameDatasetAction",
|
|
|
1216 "output_name": "outputFile"
|
|
|
1217 }
|
|
|
1218 },
|
|
|
1219 "tool_errors": null,
|
|
|
1220 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0",
|
|
|
1221 "tool_state": "{\"__page__\": 0, \"referenciesFile\": \"null\", \"RGBcolor\": \"\\\"255 105 180\\\"\"}",
|
|
|
1222 "tool_version": "1.0.0",
|
|
|
1223 "type": "tool",
|
|
|
1224 "user_outputs": []
|
|
|
1225 },
|
|
|
1226 "31": {
|
|
|
1227 "annotation": "Technical step: changes \"transcript\" for \"asRNA\" in the 3rd column.",
|
|
|
1228 "id": 31,
|
|
|
1229 "input_connections": {
|
|
|
1230 "inputFile": {
|
|
|
1231 "id": 28,
|
|
|
1232 "output_name": "outputFile"
|
|
|
1233 }
|
|
|
1234 },
|
|
|
1235 "inputs": [],
|
|
|
1236 "name": "change gff Features",
|
|
|
1237 "outputs": [
|
|
|
1238 {
|
|
|
1239 "name": "outputFile",
|
|
|
1240 "type": "gff"
|
|
|
1241 }
|
|
|
1242 ],
|
|
|
1243 "position": {
|
|
|
1244 "left": 2542,
|
|
|
1245 "top": 727
|
|
|
1246 },
|
|
|
1247 "post_job_actions": {
|
|
|
1248 "RenameDatasetActionoutputFile": {
|
|
|
1249 "action_arguments": {
|
|
|
1250 "newname": "final asRNA list (with the annotation color)"
|
|
|
1251 },
|
|
|
1252 "action_type": "RenameDatasetAction",
|
|
|
1253 "output_name": "outputFile"
|
|
|
1254 }
|
|
|
1255 },
|
|
|
1256 "tool_errors": null,
|
|
|
1257 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0",
|
|
|
1258 "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"transcript\\\"\", \"outputFeature\": \"\\\"asRNA\\\"\", \"inputFile\": \"null\"}",
|
|
|
1259 "tool_version": "1.0.0",
|
|
|
1260 "type": "tool",
|
|
|
1261 "user_outputs": []
|
|
|
1262 },
|
|
|
1263 "32": {
|
|
|
1264 "annotation": "Technical step: changes \"transcript\" for \"sRNA\" in the 3rd column.",
|
|
|
1265 "id": 32,
|
|
|
1266 "input_connections": {
|
|
|
1267 "inputFile": {
|
|
|
1268 "id": 29,
|
|
|
1269 "output_name": "outputFile"
|
|
|
1270 }
|
|
|
1271 },
|
|
|
1272 "inputs": [],
|
|
|
1273 "name": "change gff Features",
|
|
|
1274 "outputs": [
|
|
|
1275 {
|
|
|
1276 "name": "outputFile",
|
|
|
1277 "type": "gff"
|
|
|
1278 }
|
|
|
1279 ],
|
|
|
1280 "position": {
|
|
|
1281 "left": 2464,
|
|
|
1282 "top": 827
|
|
|
1283 },
|
|
|
1284 "post_job_actions": {
|
|
|
1285 "RenameDatasetActionoutputFile": {
|
|
|
1286 "action_arguments": {
|
|
|
1287 "newname": "final sRNA list (with the annotation color)"
|
|
|
1288 },
|
|
|
1289 "action_type": "RenameDatasetAction",
|
|
|
1290 "output_name": "outputFile"
|
|
|
1291 }
|
|
|
1292 },
|
|
|
1293 "tool_errors": null,
|
|
|
1294 "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0",
|
|
|
1295 "tool_state": "{\"__page__\": 0, \"inputFeature\": \"\\\"transcript\\\"\", \"outputFeature\": \"\\\"sRNA\\\"\", \"inputFile\": \"null\"}",
|
|
|
1296 "tool_version": "1.0.0",
|
|
|
1297 "type": "tool",
|
|
|
1298 "user_outputs": []
|
|
|
1299 }
|
|
|
1300 }
|
|
|
1301 } |
