Mercurial > repos > galaxyp > proteogenomics_splice_junc_search_db

comparison Proteomics_Splice_DB_from_Paired_End_RNAseq_cached_ref.ga @ 0:3e7ebf62c90f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
author galaxyp
date Tue, 10 May 2016 18:12:00 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:3e7ebf62c90f
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Paired End \nRNAseq data",
4 "format-version": "0.1",
5 "name": "Proteomics Splice DB from Paired End RNAseq cached ref",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": null,
10 "id": 0,
11 "input_connections": {},
12 "inputs": [
13 {
14 "description": "",
15 "name": "RNA-Seq left mate pair fastq"
16 }
17 ],
18 "label": null,
19 "name": "Input dataset",
20 "outputs": [],
21 "position": {
22 "left": 186,
23 "top": 459
24 },
25 "tool_errors": null,
26 "tool_id": null,
27 "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}",
28 "tool_version": null,
29 "type": "data_input",
30 "uuid": "None",
31 "workflow_outputs": [
32 {
33 "label": null,
34 "output_name": "output",
35 "uuid": "c3fdc9d3-63ee-4cfb-81a4-75ac27d150c7"
36 }
37 ]
38 },
39 "1": {
40 "annotation": "",
41 "content_id": null,
42 "id": 1,
43 "input_connections": {},
44 "inputs": [
45 {
46 "description": "",
47 "name": "RNA-Seq right mate pair fastq"
48 }
49 ],
50 "label": null,
51 "name": "Input dataset",
52 "outputs": [],
53 "position": {
54 "left": 190,
55 "top": 527
56 },
57 "tool_errors": null,
58 "tool_id": null,
59 "tool_state": "{\"name\": \"RNA-Seq right mate pair fastq\"}",
60 "tool_version": null,
61 "type": "data_input",
62 "uuid": "None",
63 "workflow_outputs": [
64 {
65 "label": null,
66 "output_name": "output",
67 "uuid": "14a32851-9e26-4eaf-b36c-0ab67e513d1d"
68 }
69 ]
70 },
71 "2": {
72 "annotation": "",
73 "content_id": null,
74 "id": 2,
75 "input_connections": {},
76 "inputs": [
77 {
78 "description": "",
79 "name": "Reference genome GTF"
80 }
81 ],
82 "label": null,
83 "name": "Input dataset",
84 "outputs": [],
85 "position": {
86 "left": 192.5,
87 "top": 600
88 },
89 "tool_errors": null,
90 "tool_id": null,
91 "tool_state": "{\"name\": \"Reference genome GTF\"}",
92 "tool_version": null,
93 "type": "data_input",
94 "uuid": "80c391df-89f8-4846-97f1-ecad1ce5abaa",
95 "workflow_outputs": [
96 {
97 "label": null,
98 "output_name": "output",
99 "uuid": "ed6e53c9-4937-4ada-a2af-e6d86267fe43"
100 }
101 ]
102 },
103 "3": {
104 "annotation": "Allow novel junctions, not from the GTF\n\nBe sure to select the correct Genome Reference",
105 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
106 "id": 3,
107 "input_connections": {
108 "input1": {
109 "id": 0,
110 "output_name": "output"
111 },
112 "singlePaired|input2": {
113 "id": 1,
114 "output_name": "output"
115 },
116 "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": {
117 "id": 2,
118 "output_name": "output"
119 }
120 },
121 "inputs": [
122 {
123 "description": "runtime parameter for tool TopHat for Illumina",
124 "name": "refGenomeSource"
125 }
126 ],
127 "label": null,
128 "name": "TopHat for Illumina",
129 "outputs": [
130 {
131 "name": "insertions",
132 "type": "bed"
133 },
134 {
135 "name": "deletions",
136 "type": "bed"
137 },
138 {
139 "name": "junctions",
140 "type": "bed"
141 },
142 {
143 "name": "accepted_hits",
144 "type": "bam"
145 }
146 ],
147 "position": {
148 "left": 726,
149 "top": 259
150 },
151 "post_job_actions": {},
152 "tool_errors": null,
153 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
154 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}",
155 "tool_version": "1.5.0",
156 "type": "tool",
157 "uuid": "None",
158 "workflow_outputs": [
159 {
160 "label": null,
161 "output_name": "deletions",
162 "uuid": "1eb9eafa-90f7-4717-a196-4704592381e0"
163 },
164 {
165 "label": null,
166 "output_name": "insertions",
167 "uuid": "92733c89-05ea-4815-96ba-7ab1d3f753d2"
168 },
169 {
170 "label": null,
171 "output_name": "accepted_hits",
172 "uuid": "22eeb200-0a5b-4580-8572-777913cda04a"
173 },
174 {
175 "label": null,
176 "output_name": "junctions",
177 "uuid": "89706986-f95d-423a-b0ad-c616aa8e924e"
178 }
179 ]
180 },
181 "4": {
182 "annotation": "Only look for supplied junctions\n\nBe sure to select the correct Genome Reference",
183 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
184 "id": 4,
185 "input_connections": {
186 "input1": {
187 "id": 0,
188 "output_name": "output"
189 },
190 "singlePaired|input2": {
191 "id": 1,
192 "output_name": "output"
193 },
194 "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": {
195 "id": 2,
196 "output_name": "output"
197 }
198 },
199 "inputs": [
200 {
201 "description": "runtime parameter for tool TopHat for Illumina",
202 "name": "refGenomeSource"
203 }
204 ],
205 "label": null,
206 "name": "TopHat for Illumina",
207 "outputs": [
208 {
209 "name": "insertions",
210 "type": "bed"
211 },
212 {
213 "name": "deletions",
214 "type": "bed"
215 },
216 {
217 "name": "junctions",
218 "type": "bed"
219 },
220 {
221 "name": "accepted_hits",
222 "type": "bam"
223 }
224 ],
225 "position": {
226 "left": 721,
227 "top": 658
228 },
229 "post_job_actions": {},
230 "tool_errors": null,
231 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
232 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"Yes\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}",
233 "tool_version": "1.5.0",
234 "type": "tool",
235 "uuid": "None",
236 "workflow_outputs": [
237 {
238 "label": null,
239 "output_name": "deletions",
240 "uuid": "6937a7bd-c33d-4052-8594-50761dd454ea"
241 },
242 {
243 "label": null,
244 "output_name": "insertions",
245 "uuid": "30e64406-f47d-476c-858b-4ba873c5486b"
246 },
247 {
248 "label": null,
249 "output_name": "accepted_hits",
250 "uuid": "2fd2c931-de38-4950-b6db-dfe1c8407a00"
251 },
252 {
253 "label": null,
254 "output_name": "junctions",
255 "uuid": "e2d804b6-7bab-4746-92eb-58db4bcfed3f"
256 }
257 ]
258 },
259 "5": {
260 "annotation": "",
261 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1",
262 "id": 5,
263 "input_connections": {
264 "guided_junctions": {
265 "id": 4,
266 "output_name": "junctions"
267 },
268 "input_bed": {
269 "id": 3,
270 "output_name": "junctions"
271 }
272 },
273 "inputs": [],
274 "label": null,
275 "name": "Filter BED on splice junctions",
276 "outputs": [
277 {
278 "name": "novel_junctions",
279 "type": "bed"
280 }
281 ],
282 "position": {
283 "left": 1014,
284 "top": 415
285 },
286 "post_job_actions": {
287 "HideDatasetActionnovel_junctions": {
288 "action_arguments": {},
289 "action_type": "HideDatasetAction",
290 "output_name": "novel_junctions"
291 }
292 },
293 "tool_errors": null,
294 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1",
295 "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}",
296 "tool_version": "0.0.1",
297 "type": "tool",
298 "uuid": "None",
299 "workflow_outputs": []
300 },
301 "6": {
302 "annotation": "",
303 "content_id": "Extract genomic DNA 1",
304 "id": 6,
305 "input_connections": {
306 "input": {
307 "id": 5,
308 "output_name": "novel_junctions"
309 }
310 },
311 "inputs": [],
312 "label": null,
313 "name": "Extract Genomic DNA",
314 "outputs": [
315 {
316 "name": "out_file1",
317 "type": "input"
318 }
319 ],
320 "position": {
321 "left": 1213,
322 "top": 621
323 },
324 "post_job_actions": {
325 "HideDatasetActionout_file1": {
326 "action_arguments": {},
327 "action_type": "HideDatasetAction",
328 "output_name": "out_file1"
329 }
330 },
331 "tool_errors": null,
332 "tool_id": "Extract genomic DNA 1",
333 "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}",
334 "tool_version": "2.2.3",
335 "type": "tool",
336 "uuid": "None",
337 "workflow_outputs": []
338 },
339 "7": {
340 "annotation": "Set the ID prefix for generated IDs \nwhen you intend to merge multiple samples from multiple fastq inputs",
341 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0",
342 "id": 7,
343 "input_connections": {
344 "input": {
345 "id": 6,
346 "output_name": "out_file1"
347 }
348 },
349 "inputs": [
350 {
351 "description": "runtime parameter for tool Translate BED Sequences",
352 "name": "min_length"
353 },
354 {
355 "description": "runtime parameter for tool Translate BED Sequences",
356 "name": "filter"
357 },
358 {
359 "description": "runtime parameter for tool Translate BED Sequences",
360 "name": "filter"
361 }
362 ],
363 "label": null,
364 "name": "Translate BED Sequences",
365 "outputs": [
366 {
367 "name": "translated_bed",
368 "type": "bed"
369 },
370 {
371 "name": "output",
372 "type": "fasta"
373 }
374 ],
375 "position": {
376 "left": 1431.5,
377 "top": 451.5
378 },
379 "post_job_actions": {},
380 "tool_errors": null,
381 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0",
382 "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}",
383 "tool_version": "0.1.0",
384 "type": "tool",
385 "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde",
386 "workflow_outputs": [
387 {
388 "label": null,
389 "output_name": "translated_bed",
390 "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f"
391 },
392 {
393 "label": "protein fasta",
394 "output_name": "output",
395 "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb"
396 }
397 ]
398 }
399 },
400 "uuid": "7799d59b-149b-457c-a248-0ae65c1b8f63"
401 }