0
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "NGSAP workflow 2",
|
|
4 "format-version": "0.1",
|
|
5 "name": "Reference_based_workflow",
|
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
|
9 "id": 0,
|
|
10 "input_connections": {},
|
|
11 "inputs": [
|
|
12 {
|
|
13 "description": "",
|
|
14 "name": "R1_right"
|
|
15 }
|
|
16 ],
|
|
17 "label": null,
|
|
18 "name": "Input dataset",
|
|
19 "outputs": [],
|
|
20 "position": {
|
|
21 "left": 199.99993896484375,
|
|
22 "top": 200
|
|
23 },
|
|
24 "tool_errors": null,
|
|
25 "tool_id": null,
|
|
26 "tool_state": "{\"name\": \"R1_right\"}",
|
|
27 "tool_version": null,
|
|
28 "type": "data_input",
|
|
29 "user_outputs": [],
|
|
30 "uuid": "a3398fb4-2386-41de-90f1-e2fb107f01d6"
|
|
31 },
|
|
32 "1": {
|
|
33 "annotation": "",
|
|
34 "id": 1,
|
|
35 "input_connections": {},
|
|
36 "inputs": [
|
|
37 {
|
|
38 "description": "",
|
|
39 "name": "R1_left"
|
|
40 }
|
|
41 ],
|
|
42 "label": null,
|
|
43 "name": "Input dataset",
|
|
44 "outputs": [],
|
|
45 "position": {
|
|
46 "left": 199.99993896484375,
|
|
47 "top": 285.00001525878906
|
|
48 },
|
|
49 "tool_errors": null,
|
|
50 "tool_id": null,
|
|
51 "tool_state": "{\"name\": \"R1_left\"}",
|
|
52 "tool_version": null,
|
|
53 "type": "data_input",
|
|
54 "user_outputs": [],
|
|
55 "uuid": "4cc43efc-a2ce-450f-916d-9c26950fed3a"
|
|
56 },
|
|
57 "2": {
|
|
58 "annotation": "",
|
|
59 "id": 2,
|
|
60 "input_connections": {},
|
|
61 "inputs": [
|
|
62 {
|
|
63 "description": "",
|
|
64 "name": "R2_left"
|
|
65 }
|
|
66 ],
|
|
67 "label": null,
|
|
68 "name": "Input dataset",
|
|
69 "outputs": [],
|
|
70 "position": {
|
|
71 "left": 199.99993896484375,
|
|
72 "top": 370.00001525878906
|
|
73 },
|
|
74 "tool_errors": null,
|
|
75 "tool_id": null,
|
|
76 "tool_state": "{\"name\": \"R2_left\"}",
|
|
77 "tool_version": null,
|
|
78 "type": "data_input",
|
|
79 "user_outputs": [],
|
|
80 "uuid": "64701644-7399-47be-b160-13fb7a8cf75d"
|
|
81 },
|
|
82 "3": {
|
|
83 "annotation": "",
|
|
84 "id": 3,
|
|
85 "input_connections": {},
|
|
86 "inputs": [
|
|
87 {
|
|
88 "description": "",
|
|
89 "name": "Reference Genome"
|
|
90 }
|
|
91 ],
|
|
92 "label": null,
|
|
93 "name": "Input dataset",
|
|
94 "outputs": [],
|
|
95 "position": {
|
|
96 "left": 199.99993896484375,
|
|
97 "top": 965.0000152587891
|
|
98 },
|
|
99 "tool_errors": null,
|
|
100 "tool_id": null,
|
|
101 "tool_state": "{\"name\": \"Reference Genome\"}",
|
|
102 "tool_version": null,
|
|
103 "type": "data_input",
|
|
104 "user_outputs": [],
|
|
105 "uuid": "c549640a-dd8c-4d07-9e5c-e142278e5c3b"
|
|
106 },
|
|
107 "4": {
|
|
108 "annotation": "",
|
|
109 "id": 4,
|
|
110 "input_connections": {},
|
|
111 "inputs": [
|
|
112 {
|
|
113 "description": "",
|
|
114 "name": "Gtf file"
|
|
115 }
|
|
116 ],
|
|
117 "label": null,
|
|
118 "name": "Input dataset",
|
|
119 "outputs": [],
|
|
120 "position": {
|
|
121 "left": 199.99993896484375,
|
|
122 "top": 880.0000152587891
|
|
123 },
|
|
124 "tool_errors": null,
|
|
125 "tool_id": null,
|
|
126 "tool_state": "{\"name\": \"Gtf file\"}",
|
|
127 "tool_version": null,
|
|
128 "type": "data_input",
|
|
129 "user_outputs": [],
|
|
130 "uuid": "9c1fed55-cbdd-492b-aa51-600241311211"
|
|
131 },
|
|
132 "5": {
|
|
133 "annotation": "",
|
|
134 "id": 5,
|
|
135 "input_connections": {},
|
|
136 "inputs": [
|
|
137 {
|
|
138 "description": "",
|
|
139 "name": "R2_right"
|
|
140 }
|
|
141 ],
|
|
142 "label": null,
|
|
143 "name": "Input dataset",
|
|
144 "outputs": [],
|
|
145 "position": {
|
|
146 "left": 199.99993896484375,
|
|
147 "top": 455.00001525878906
|
|
148 },
|
|
149 "tool_errors": null,
|
|
150 "tool_id": null,
|
|
151 "tool_state": "{\"name\": \"R2_right\"}",
|
|
152 "tool_version": null,
|
|
153 "type": "data_input",
|
|
154 "user_outputs": [],
|
|
155 "uuid": "bb40a254-b753-4634-990c-2c08fa3fda0b"
|
|
156 },
|
|
157 "6": {
|
|
158 "annotation": "",
|
|
159 "id": 6,
|
|
160 "input_connections": {},
|
|
161 "inputs": [
|
|
162 {
|
|
163 "description": "",
|
|
164 "name": "R3left"
|
|
165 }
|
|
166 ],
|
|
167 "label": null,
|
|
168 "name": "Input dataset",
|
|
169 "outputs": [],
|
|
170 "position": {
|
|
171 "left": 199.99993896484375,
|
|
172 "top": 540.0000152587891
|
|
173 },
|
|
174 "tool_errors": null,
|
|
175 "tool_id": null,
|
|
176 "tool_state": "{\"name\": \"R3left\"}",
|
|
177 "tool_version": null,
|
|
178 "type": "data_input",
|
|
179 "user_outputs": [],
|
|
180 "uuid": "e3158596-2e31-4be4-a276-3e37310fee7e"
|
|
181 },
|
|
182 "7": {
|
|
183 "annotation": "",
|
|
184 "id": 7,
|
|
185 "input_connections": {},
|
|
186 "inputs": [
|
|
187 {
|
|
188 "description": "",
|
|
189 "name": "R3_right"
|
|
190 }
|
|
191 ],
|
|
192 "label": null,
|
|
193 "name": "Input dataset",
|
|
194 "outputs": [],
|
|
195 "position": {
|
|
196 "left": 199.99993896484375,
|
|
197 "top": 625.0000152587891
|
|
198 },
|
|
199 "tool_errors": null,
|
|
200 "tool_id": null,
|
|
201 "tool_state": "{\"name\": \"R3_right\"}",
|
|
202 "tool_version": null,
|
|
203 "type": "data_input",
|
|
204 "user_outputs": [],
|
|
205 "uuid": "fc589358-7f3b-4315-93ac-7ff75290febe"
|
|
206 },
|
|
207 "8": {
|
|
208 "annotation": "",
|
|
209 "id": 8,
|
|
210 "input_connections": {},
|
|
211 "inputs": [
|
|
212 {
|
|
213 "description": "",
|
|
214 "name": "R4_right"
|
|
215 }
|
|
216 ],
|
|
217 "label": null,
|
|
218 "name": "Input dataset",
|
|
219 "outputs": [],
|
|
220 "position": {
|
|
221 "left": 199.99993896484375,
|
|
222 "top": 710.0000152587891
|
|
223 },
|
|
224 "tool_errors": null,
|
|
225 "tool_id": null,
|
|
226 "tool_state": "{\"name\": \"R4_right\"}",
|
|
227 "tool_version": null,
|
|
228 "type": "data_input",
|
|
229 "user_outputs": [],
|
|
230 "uuid": "43912143-367a-4214-b94d-2c8774d5f744"
|
|
231 },
|
|
232 "9": {
|
|
233 "annotation": "",
|
|
234 "id": 9,
|
|
235 "input_connections": {},
|
|
236 "inputs": [
|
|
237 {
|
|
238 "description": "",
|
|
239 "name": "R4_left"
|
|
240 }
|
|
241 ],
|
|
242 "label": null,
|
|
243 "name": "Input dataset",
|
|
244 "outputs": [],
|
|
245 "position": {
|
|
246 "left": 199.99993896484375,
|
|
247 "top": 795.0000152587891
|
|
248 },
|
|
249 "tool_errors": null,
|
|
250 "tool_id": null,
|
|
251 "tool_state": "{\"name\": \"R4_left\"}",
|
|
252 "tool_version": null,
|
|
253 "type": "data_input",
|
|
254 "user_outputs": [],
|
|
255 "uuid": "7aa39479-3ca7-47fd-a869-60f09eb7feda"
|
|
256 },
|
|
257 "10": {
|
|
258 "annotation": "",
|
|
259 "id": 10,
|
|
260 "input_connections": {
|
|
261 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
262 "id": 4,
|
|
263 "output_name": "output"
|
|
264 },
|
|
265 "refGenomeSource|ownFile": {
|
|
266 "id": 3,
|
|
267 "output_name": "output"
|
|
268 },
|
|
269 "singlePaired|input1": {
|
|
270 "id": 1,
|
|
271 "output_name": "output"
|
|
272 },
|
|
273 "singlePaired|input2": {
|
|
274 "id": 0,
|
|
275 "output_name": "output"
|
|
276 }
|
|
277 },
|
|
278 "inputs": [],
|
|
279 "label": null,
|
|
280 "name": "Tophat2",
|
|
281 "outputs": [
|
|
282 {
|
|
283 "name": "align_summary",
|
|
284 "type": "txt"
|
|
285 },
|
|
286 {
|
|
287 "name": "fusions",
|
|
288 "type": "tabular"
|
|
289 },
|
|
290 {
|
|
291 "name": "insertions",
|
|
292 "type": "bed"
|
|
293 },
|
|
294 {
|
|
295 "name": "deletions",
|
|
296 "type": "bed"
|
|
297 },
|
|
298 {
|
|
299 "name": "junctions",
|
|
300 "type": "bed"
|
|
301 },
|
|
302 {
|
|
303 "name": "accepted_hits",
|
|
304 "type": "bam"
|
|
305 }
|
|
306 ],
|
|
307 "position": {
|
|
308 "left": 427.99993896484375,
|
|
309 "top": 200
|
|
310 },
|
|
311 "post_job_actions": {},
|
|
312 "tool_errors": null,
|
|
313 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6",
|
|
314 "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}",
|
|
315 "tool_version": "0.6",
|
|
316 "type": "tool",
|
|
317 "user_outputs": [],
|
|
318 "uuid": "af13a44d-a38b-4907-b45e-9c32046379e8"
|
|
319 },
|
|
320 "11": {
|
|
321 "annotation": "",
|
|
322 "id": 11,
|
|
323 "input_connections": {
|
|
324 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
325 "id": 4,
|
|
326 "output_name": "output"
|
|
327 },
|
|
328 "refGenomeSource|ownFile": {
|
|
329 "id": 3,
|
|
330 "output_name": "output"
|
|
331 },
|
|
332 "singlePaired|input1": {
|
|
333 "id": 2,
|
|
334 "output_name": "output"
|
|
335 },
|
|
336 "singlePaired|input2": {
|
|
337 "id": 5,
|
|
338 "output_name": "output"
|
|
339 }
|
|
340 },
|
|
341 "inputs": [],
|
|
342 "label": null,
|
|
343 "name": "Tophat2",
|
|
344 "outputs": [
|
|
345 {
|
|
346 "name": "align_summary",
|
|
347 "type": "txt"
|
|
348 },
|
|
349 {
|
|
350 "name": "fusions",
|
|
351 "type": "tabular"
|
|
352 },
|
|
353 {
|
|
354 "name": "insertions",
|
|
355 "type": "bed"
|
|
356 },
|
|
357 {
|
|
358 "name": "deletions",
|
|
359 "type": "bed"
|
|
360 },
|
|
361 {
|
|
362 "name": "junctions",
|
|
363 "type": "bed"
|
|
364 },
|
|
365 {
|
|
366 "name": "accepted_hits",
|
|
367 "type": "bam"
|
|
368 }
|
|
369 ],
|
|
370 "position": {
|
|
371 "left": 427.99993896484375,
|
|
372 "top": 930.0000152587891
|
|
373 },
|
|
374 "post_job_actions": {},
|
|
375 "tool_errors": null,
|
|
376 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6",
|
|
377 "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}",
|
|
378 "tool_version": "0.6",
|
|
379 "type": "tool",
|
|
380 "user_outputs": [],
|
|
381 "uuid": "1225d96b-d5f4-4dd3-b533-91e85cb1c31b"
|
|
382 },
|
|
383 "12": {
|
|
384 "annotation": "",
|
|
385 "id": 12,
|
|
386 "input_connections": {
|
|
387 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
388 "id": 4,
|
|
389 "output_name": "output"
|
|
390 },
|
|
391 "refGenomeSource|ownFile": {
|
|
392 "id": 3,
|
|
393 "output_name": "output"
|
|
394 },
|
|
395 "singlePaired|input1": {
|
|
396 "id": 6,
|
|
397 "output_name": "output"
|
|
398 },
|
|
399 "singlePaired|input2": {
|
|
400 "id": 7,
|
|
401 "output_name": "output"
|
|
402 }
|
|
403 },
|
|
404 "inputs": [],
|
|
405 "label": null,
|
|
406 "name": "Tophat2",
|
|
407 "outputs": [
|
|
408 {
|
|
409 "name": "align_summary",
|
|
410 "type": "txt"
|
|
411 },
|
|
412 {
|
|
413 "name": "fusions",
|
|
414 "type": "tabular"
|
|
415 },
|
|
416 {
|
|
417 "name": "insertions",
|
|
418 "type": "bed"
|
|
419 },
|
|
420 {
|
|
421 "name": "deletions",
|
|
422 "type": "bed"
|
|
423 },
|
|
424 {
|
|
425 "name": "junctions",
|
|
426 "type": "bed"
|
|
427 },
|
|
428 {
|
|
429 "name": "accepted_hits",
|
|
430 "type": "bam"
|
|
431 }
|
|
432 ],
|
|
433 "position": {
|
|
434 "left": 427.99993896484375,
|
|
435 "top": 565.0000152587891
|
|
436 },
|
|
437 "post_job_actions": {},
|
|
438 "tool_errors": null,
|
|
439 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6",
|
|
440 "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}",
|
|
441 "tool_version": "0.6",
|
|
442 "type": "tool",
|
|
443 "user_outputs": [],
|
|
444 "uuid": "39c98529-55f4-498e-8ef0-9046a9d8b39d"
|
|
445 },
|
|
446 "13": {
|
|
447 "annotation": "",
|
|
448 "id": 13,
|
|
449 "input_connections": {
|
|
450 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
451 "id": 4,
|
|
452 "output_name": "output"
|
|
453 },
|
|
454 "refGenomeSource|ownFile": {
|
|
455 "id": 3,
|
|
456 "output_name": "output"
|
|
457 },
|
|
458 "singlePaired|input1": {
|
|
459 "id": 9,
|
|
460 "output_name": "output"
|
|
461 },
|
|
462 "singlePaired|input2": {
|
|
463 "id": 8,
|
|
464 "output_name": "output"
|
|
465 }
|
|
466 },
|
|
467 "inputs": [],
|
|
468 "label": null,
|
|
469 "name": "Tophat2",
|
|
470 "outputs": [
|
|
471 {
|
|
472 "name": "align_summary",
|
|
473 "type": "txt"
|
|
474 },
|
|
475 {
|
|
476 "name": "fusions",
|
|
477 "type": "tabular"
|
|
478 },
|
|
479 {
|
|
480 "name": "insertions",
|
|
481 "type": "bed"
|
|
482 },
|
|
483 {
|
|
484 "name": "deletions",
|
|
485 "type": "bed"
|
|
486 },
|
|
487 {
|
|
488 "name": "junctions",
|
|
489 "type": "bed"
|
|
490 },
|
|
491 {
|
|
492 "name": "accepted_hits",
|
|
493 "type": "bam"
|
|
494 }
|
|
495 ],
|
|
496 "position": {
|
|
497 "left": 427.99993896484375,
|
|
498 "top": 1295.000015258789
|
|
499 },
|
|
500 "post_job_actions": {},
|
|
501 "tool_errors": null,
|
|
502 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6",
|
|
503 "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"min_intron_length\\\": \\\"70\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"fusion_search\\\": {\\\"__current_case__\\\": 0, \\\"do_search\\\": \\\"No\\\"}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"library_type\\\": \\\"fr-unstranded\\\", \\\"settingsType\\\": \\\"full\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"max_multihits\\\": \\\"20\\\", \\\"bowtie_n\\\": \\\"No\\\", \\\"read_realign_edit_dist\\\": \\\"1000\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"read_edit_dist\\\": \\\"2\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": \\\"No\\\", \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_length\\\": \\\"25\\\", \\\"max_segment_intron\\\": \\\"500000\\\", \\\"bowtie2_settings\\\": {\\\"__current_case__\\\": 0, \\\"b2_settings\\\": \\\"No\\\"}, \\\"__current_case__\\\": 1, \\\"read_mismatches\\\": \\\"2\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}",
|
|
504 "tool_version": "0.6",
|
|
505 "type": "tool",
|
|
506 "user_outputs": [],
|
|
507 "uuid": "d9d1d821-17df-4bef-8097-ee241318c675"
|
|
508 },
|
|
509 "14": {
|
|
510 "annotation": "",
|
|
511 "id": 14,
|
|
512 "input_connections": {
|
|
513 "input": {
|
|
514 "id": 10,
|
|
515 "output_name": "accepted_hits"
|
|
516 }
|
|
517 },
|
|
518 "inputs": [],
|
|
519 "label": null,
|
|
520 "name": "Cufflinks",
|
|
521 "outputs": [
|
|
522 {
|
|
523 "name": "genes_expression",
|
|
524 "type": "tabular"
|
|
525 },
|
|
526 {
|
|
527 "name": "transcripts_expression",
|
|
528 "type": "tabular"
|
|
529 },
|
|
530 {
|
|
531 "name": "assembled_isoforms",
|
|
532 "type": "gtf"
|
|
533 },
|
|
534 {
|
|
535 "name": "total_map_mass",
|
|
536 "type": "txt"
|
|
537 }
|
|
538 ],
|
|
539 "position": {
|
|
540 "left": 717.9999389648438,
|
|
541 "top": 200
|
|
542 },
|
|
543 "post_job_actions": {},
|
|
544 "tool_errors": null,
|
|
545 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7",
|
|
546 "tool_state": "{\"min_isoform_fraction\": \"\\\"0.1\\\"\", \"multiread_correct\": \"\\\"No\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"effective_length_correction\": \"\\\"\\\"\", \"max_intron_len\": \"\\\"300000\\\"\", \"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"global_model\": \"null\", \"do_normalization\": \"\\\"No\\\"\", \"input\": \"null\"}",
|
|
547 "tool_version": "0.0.7",
|
|
548 "type": "tool",
|
|
549 "user_outputs": [],
|
|
550 "uuid": "1eb5e77d-ee27-4fad-aad1-0cd9164422f4"
|
|
551 },
|
|
552 "15": {
|
|
553 "annotation": "",
|
|
554 "id": 15,
|
|
555 "input_connections": {
|
|
556 "input": {
|
|
557 "id": 11,
|
|
558 "output_name": "accepted_hits"
|
|
559 }
|
|
560 },
|
|
561 "inputs": [],
|
|
562 "label": null,
|
|
563 "name": "Cufflinks",
|
|
564 "outputs": [
|
|
565 {
|
|
566 "name": "genes_expression",
|
|
567 "type": "tabular"
|
|
568 },
|
|
569 {
|
|
570 "name": "transcripts_expression",
|
|
571 "type": "tabular"
|
|
572 },
|
|
573 {
|
|
574 "name": "assembled_isoforms",
|
|
575 "type": "gtf"
|
|
576 },
|
|
577 {
|
|
578 "name": "total_map_mass",
|
|
579 "type": "txt"
|
|
580 }
|
|
581 ],
|
|
582 "position": {
|
|
583 "left": 717.9999389648438,
|
|
584 "top": 678.0000152587891
|
|
585 },
|
|
586 "post_job_actions": {},
|
|
587 "tool_errors": null,
|
|
588 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7",
|
|
589 "tool_state": "{\"min_isoform_fraction\": \"\\\"0.1\\\"\", \"multiread_correct\": \"\\\"No\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"effective_length_correction\": \"\\\"\\\"\", \"max_intron_len\": \"\\\"300000\\\"\", \"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"global_model\": \"null\", \"do_normalization\": \"\\\"No\\\"\", \"input\": \"null\"}",
|
|
590 "tool_version": "0.0.7",
|
|
591 "type": "tool",
|
|
592 "user_outputs": [],
|
|
593 "uuid": "91e98af2-3c45-4c8f-9bfd-48092ebfe153"
|
|
594 },
|
|
595 "16": {
|
|
596 "annotation": "",
|
|
597 "id": 16,
|
|
598 "input_connections": {
|
|
599 "input": {
|
|
600 "id": 12,
|
|
601 "output_name": "accepted_hits"
|
|
602 }
|
|
603 },
|
|
604 "inputs": [],
|
|
605 "label": null,
|
|
606 "name": "Cufflinks",
|
|
607 "outputs": [
|
|
608 {
|
|
609 "name": "genes_expression",
|
|
610 "type": "tabular"
|
|
611 },
|
|
612 {
|
|
613 "name": "transcripts_expression",
|
|
614 "type": "tabular"
|
|
615 },
|
|
616 {
|
|
617 "name": "assembled_isoforms",
|
|
618 "type": "gtf"
|
|
619 },
|
|
620 {
|
|
621 "name": "total_map_mass",
|
|
622 "type": "txt"
|
|
623 }
|
|
624 ],
|
|
625 "position": {
|
|
626 "left": 717.9999389648438,
|
|
627 "top": 439.00001525878906
|
|
628 },
|
|
629 "post_job_actions": {},
|
|
630 "tool_errors": null,
|
|
631 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7",
|
|
632 "tool_state": "{\"min_isoform_fraction\": \"\\\"0.1\\\"\", \"multiread_correct\": \"\\\"No\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"effective_length_correction\": \"\\\"\\\"\", \"max_intron_len\": \"\\\"300000\\\"\", \"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"global_model\": \"null\", \"do_normalization\": \"\\\"No\\\"\", \"input\": \"null\"}",
|
|
633 "tool_version": "0.0.7",
|
|
634 "type": "tool",
|
|
635 "user_outputs": [],
|
|
636 "uuid": "13aa9c83-3990-4701-ad93-def8dd722a1d"
|
|
637 },
|
|
638 "17": {
|
|
639 "annotation": "",
|
|
640 "id": 17,
|
|
641 "input_connections": {
|
|
642 "input": {
|
|
643 "id": 13,
|
|
644 "output_name": "accepted_hits"
|
|
645 }
|
|
646 },
|
|
647 "inputs": [],
|
|
648 "label": null,
|
|
649 "name": "Cufflinks",
|
|
650 "outputs": [
|
|
651 {
|
|
652 "name": "genes_expression",
|
|
653 "type": "tabular"
|
|
654 },
|
|
655 {
|
|
656 "name": "transcripts_expression",
|
|
657 "type": "tabular"
|
|
658 },
|
|
659 {
|
|
660 "name": "assembled_isoforms",
|
|
661 "type": "gtf"
|
|
662 },
|
|
663 {
|
|
664 "name": "total_map_mass",
|
|
665 "type": "txt"
|
|
666 }
|
|
667 ],
|
|
668 "position": {
|
|
669 "left": 717.9999389648438,
|
|
670 "top": 917.0000152587891
|
|
671 },
|
|
672 "post_job_actions": {},
|
|
673 "tool_errors": null,
|
|
674 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7",
|
|
675 "tool_state": "{\"min_isoform_fraction\": \"\\\"0.1\\\"\", \"multiread_correct\": \"\\\"No\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"effective_length_correction\": \"\\\"\\\"\", \"max_intron_len\": \"\\\"300000\\\"\", \"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"global_model\": \"null\", \"do_normalization\": \"\\\"No\\\"\", \"input\": \"null\"}",
|
|
676 "tool_version": "0.0.7",
|
|
677 "type": "tool",
|
|
678 "user_outputs": [],
|
|
679 "uuid": "6857759c-6767-46b2-afdd-8ca494d75867"
|
|
680 },
|
|
681 "18": {
|
|
682 "annotation": "",
|
|
683 "id": 18,
|
|
684 "input_connections": {
|
|
685 "annotation|reference_annotation": {
|
|
686 "id": 4,
|
|
687 "output_name": "output"
|
|
688 },
|
|
689 "inputs": [
|
|
690 {
|
|
691 "id": 14,
|
|
692 "output_name": "assembled_isoforms"
|
|
693 },
|
|
694 {
|
|
695 "id": 15,
|
|
696 "output_name": "assembled_isoforms"
|
|
697 },
|
|
698 {
|
|
699 "id": 16,
|
|
700 "output_name": "assembled_isoforms"
|
|
701 },
|
|
702 {
|
|
703 "id": 17,
|
|
704 "output_name": "assembled_isoforms"
|
|
705 }
|
|
706 ],
|
|
707 "seq_data|seq_source|ref_file": {
|
|
708 "id": 3,
|
|
709 "output_name": "output"
|
|
710 }
|
|
711 },
|
|
712 "inputs": [],
|
|
713 "label": null,
|
|
714 "name": "Cuffmerge",
|
|
715 "outputs": [
|
|
716 {
|
|
717 "name": "merged_transcripts",
|
|
718 "type": "gtf"
|
|
719 }
|
|
720 ],
|
|
721 "position": {
|
|
722 "left": 1045.9999389648438,
|
|
723 "top": 200
|
|
724 },
|
|
725 "post_job_actions": {},
|
|
726 "tool_errors": null,
|
|
727 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0",
|
|
728 "tool_state": "{\"seq_data\": \"{\\\"use_seq_data\\\": \\\"Yes\\\", \\\"seq_source\\\": {\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1}\", \"inputs\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"min_isoform_fraction\": \"\\\"0.05\\\"\", \"additional_inputs\": \"[]\", \"annotation\": \"{\\\"reference_annotation\\\": null, \\\"use_ref_annotation\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\"}",
|
|
729 "tool_version": "2.2.1.0",
|
|
730 "type": "tool",
|
|
731 "user_outputs": [],
|
|
732 "uuid": "b1ac54b3-9be6-41f6-ac03-0f6a1ca86d49"
|
|
733 },
|
|
734 "19": {
|
|
735 "annotation": "",
|
|
736 "id": 19,
|
|
737 "input_connections": {
|
|
738 "genome": {
|
|
739 "id": 3,
|
|
740 "output_name": "output"
|
|
741 },
|
|
742 "gtf": {
|
|
743 "id": 18,
|
|
744 "output_name": "merged_transcripts"
|
|
745 }
|
|
746 },
|
|
747 "inputs": [],
|
|
748 "label": null,
|
|
749 "name": "gtf2fasta",
|
|
750 "outputs": [
|
|
751 {
|
|
752 "name": "fasta",
|
|
753 "type": "fasta"
|
|
754 }
|
|
755 ],
|
|
756 "position": {
|
|
757 "left": 1321.9999389648438,
|
|
758 "top": 200
|
|
759 },
|
|
760 "post_job_actions": {},
|
|
761 "tool_errors": null,
|
|
762 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/id_gtf2fasta/1.0",
|
|
763 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"genome\": \"null\", \"gtf\": \"null\"}",
|
|
764 "tool_version": "1.0",
|
|
765 "type": "tool",
|
|
766 "user_outputs": [],
|
|
767 "uuid": "d4140533-7a85-469e-9da5-7f502680d6c7"
|
|
768 },
|
|
769 "20": {
|
|
770 "annotation": "",
|
|
771 "id": 20,
|
|
772 "input_connections": {
|
|
773 "transcript": {
|
|
774 "id": 19,
|
|
775 "output_name": "fasta"
|
|
776 }
|
|
777 },
|
|
778 "inputs": [],
|
|
779 "label": null,
|
|
780 "name": "transDecoder",
|
|
781 "outputs": [
|
|
782 {
|
|
783 "name": "transdecoder_pep",
|
|
784 "type": "fasta"
|
|
785 },
|
|
786 {
|
|
787 "name": "transdecoder_cds",
|
|
788 "type": "fasta"
|
|
789 },
|
|
790 {
|
|
791 "name": "transdecoder_bed",
|
|
792 "type": "bed"
|
|
793 },
|
|
794 {
|
|
795 "name": "transdecoder_gff3",
|
|
796 "type": "tabular"
|
|
797 },
|
|
798 {
|
|
799 "name": "transdecoder_mRNA",
|
|
800 "type": "fasta"
|
|
801 },
|
|
802 {
|
|
803 "name": "transdecoder_log",
|
|
804 "type": "txt"
|
|
805 }
|
|
806 ],
|
|
807 "position": {
|
|
808 "left": 1549.9999389648438,
|
|
809 "top": 200
|
|
810 },
|
|
811 "post_job_actions": {},
|
|
812 "tool_errors": null,
|
|
813 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/id_transDecoder/1.0",
|
|
814 "tool_state": "{\"pfam\": \"{\\\"options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"optional\": \"{\\\"parameters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"transcript\": \"null\", \"__page__\": 0}",
|
|
815 "tool_version": "1.0",
|
|
816 "type": "tool",
|
|
817 "user_outputs": [],
|
|
818 "uuid": "f209c0fa-91a3-4119-9bb0-df801577aef2"
|
|
819 },
|
|
820 "21": {
|
|
821 "annotation": "",
|
|
822 "id": 21,
|
|
823 "input_connections": {
|
|
824 "reads|left_input": {
|
|
825 "id": 1,
|
|
826 "output_name": "output"
|
|
827 },
|
|
828 "reads|right_input": {
|
|
829 "id": 0,
|
|
830 "output_name": "output"
|
|
831 },
|
|
832 "transcripts": {
|
|
833 "id": 19,
|
|
834 "output_name": "fasta"
|
|
835 }
|
|
836 },
|
|
837 "inputs": [],
|
|
838 "label": null,
|
|
839 "name": "align_and_estimate_abundance",
|
|
840 "outputs": [
|
|
841 {
|
|
842 "name": "align_and_estimate_abundance_log",
|
|
843 "type": "txt"
|
|
844 },
|
|
845 {
|
|
846 "name": "bowtie_bam",
|
|
847 "type": "bam"
|
|
848 },
|
|
849 {
|
|
850 "name": "rsem_isoforms",
|
|
851 "type": "tabular"
|
|
852 },
|
|
853 {
|
|
854 "name": "rsem_genes",
|
|
855 "type": "tabular"
|
|
856 }
|
|
857 ],
|
|
858 "position": {
|
|
859 "left": 1549.9999389648438,
|
|
860 "top": 449.00001525878906
|
|
861 },
|
|
862 "post_job_actions": {},
|
|
863 "tool_errors": null,
|
|
864 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/id_align_and_estimate_abundance/1.0",
|
|
865 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}",
|
|
866 "tool_version": "1.0",
|
|
867 "type": "tool",
|
|
868 "user_outputs": [],
|
|
869 "uuid": "abadfe21-91bf-4bb8-8b7f-bcc0d8620c30"
|
|
870 },
|
|
871 "22": {
|
|
872 "annotation": "",
|
|
873 "id": 22,
|
|
874 "input_connections": {
|
|
875 "reads|left_input": {
|
|
876 "id": 2,
|
|
877 "output_name": "output"
|
|
878 },
|
|
879 "reads|right_input": {
|
|
880 "id": 5,
|
|
881 "output_name": "output"
|
|
882 },
|
|
883 "transcripts": {
|
|
884 "id": 19,
|
|
885 "output_name": "fasta"
|
|
886 }
|
|
887 },
|
|
888 "inputs": [],
|
|
889 "label": null,
|
|
890 "name": "align_and_estimate_abundance",
|
|
891 "outputs": [
|
|
892 {
|
|
893 "name": "align_and_estimate_abundance_log",
|
|
894 "type": "txt"
|
|
895 },
|
|
896 {
|
|
897 "name": "bowtie_bam",
|
|
898 "type": "bam"
|
|
899 },
|
|
900 {
|
|
901 "name": "rsem_isoforms",
|
|
902 "type": "tabular"
|
|
903 },
|
|
904 {
|
|
905 "name": "rsem_genes",
|
|
906 "type": "tabular"
|
|
907 }
|
|
908 ],
|
|
909 "position": {
|
|
910 "left": 1549.9999389648438,
|
|
911 "top": 698.0000152587891
|
|
912 },
|
|
913 "post_job_actions": {},
|
|
914 "tool_errors": null,
|
|
915 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/id_align_and_estimate_abundance/1.0",
|
|
916 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}",
|
|
917 "tool_version": "1.0",
|
|
918 "type": "tool",
|
|
919 "user_outputs": [],
|
|
920 "uuid": "4e019fee-6308-4d2c-a1b7-2c596650803d"
|
|
921 },
|
|
922 "23": {
|
|
923 "annotation": "",
|
|
924 "id": 23,
|
|
925 "input_connections": {
|
|
926 "reads|left_input": {
|
|
927 "id": 6,
|
|
928 "output_name": "output"
|
|
929 },
|
|
930 "reads|right_input": {
|
|
931 "id": 7,
|
|
932 "output_name": "output"
|
|
933 },
|
|
934 "transcripts": {
|
|
935 "id": 19,
|
|
936 "output_name": "fasta"
|
|
937 }
|
|
938 },
|
|
939 "inputs": [],
|
|
940 "label": null,
|
|
941 "name": "align_and_estimate_abundance",
|
|
942 "outputs": [
|
|
943 {
|
|
944 "name": "align_and_estimate_abundance_log",
|
|
945 "type": "txt"
|
|
946 },
|
|
947 {
|
|
948 "name": "bowtie_bam",
|
|
949 "type": "bam"
|
|
950 },
|
|
951 {
|
|
952 "name": "rsem_isoforms",
|
|
953 "type": "tabular"
|
|
954 },
|
|
955 {
|
|
956 "name": "rsem_genes",
|
|
957 "type": "tabular"
|
|
958 }
|
|
959 ],
|
|
960 "position": {
|
|
961 "left": 1549.9999389648438,
|
|
962 "top": 947.0000152587891
|
|
963 },
|
|
964 "post_job_actions": {},
|
|
965 "tool_errors": null,
|
|
966 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/id_align_and_estimate_abundance/1.0",
|
|
967 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}",
|
|
968 "tool_version": "1.0",
|
|
969 "type": "tool",
|
|
970 "user_outputs": [],
|
|
971 "uuid": "d6146eb9-3986-4652-aa47-4c7f14d71f74"
|
|
972 },
|
|
973 "24": {
|
|
974 "annotation": "",
|
|
975 "id": 24,
|
|
976 "input_connections": {
|
|
977 "reads|left_input": {
|
|
978 "id": 9,
|
|
979 "output_name": "output"
|
|
980 },
|
|
981 "reads|right_input": {
|
|
982 "id": 8,
|
|
983 "output_name": "output"
|
|
984 },
|
|
985 "transcripts": {
|
|
986 "id": 19,
|
|
987 "output_name": "fasta"
|
|
988 }
|
|
989 },
|
|
990 "inputs": [],
|
|
991 "label": null,
|
|
992 "name": "align_and_estimate_abundance",
|
|
993 "outputs": [
|
|
994 {
|
|
995 "name": "align_and_estimate_abundance_log",
|
|
996 "type": "txt"
|
|
997 },
|
|
998 {
|
|
999 "name": "bowtie_bam",
|
|
1000 "type": "bam"
|
|
1001 },
|
|
1002 {
|
|
1003 "name": "rsem_isoforms",
|
|
1004 "type": "tabular"
|
|
1005 },
|
|
1006 {
|
|
1007 "name": "rsem_genes",
|
|
1008 "type": "tabular"
|
|
1009 }
|
|
1010 ],
|
|
1011 "position": {
|
|
1012 "left": 1549.9999389648438,
|
|
1013 "top": 1213.000015258789
|
|
1014 },
|
|
1015 "post_job_actions": {},
|
|
1016 "tool_errors": null,
|
|
1017 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/id_align_and_estimate_abundance/1.0",
|
|
1018 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reads\": \"{\\\"paired_or_single\\\": \\\"paired\\\", \\\"optional\\\": {\\\"use_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"left_input\\\": null, \\\"__current_case__\\\": 0, \\\"seqtype\\\": \\\"fq\\\", \\\"right_input\\\": null}\", \"aln_method\": \"\\\"bowtie\\\"\", \"est_method\": \"\\\"RSEM\\\"\", \"transcripts\": \"null\"}",
|
|
1019 "tool_version": "1.0",
|
|
1020 "type": "tool",
|
|
1021 "user_outputs": [],
|
|
1022 "uuid": "baa07de1-a733-4753-b052-a1cf409671c2"
|
|
1023 },
|
|
1024 "25": {
|
|
1025 "annotation": "",
|
|
1026 "id": 25,
|
|
1027 "input_connections": {
|
|
1028 "query": {
|
|
1029 "id": 20,
|
|
1030 "output_name": "transdecoder_pep"
|
|
1031 }
|
|
1032 },
|
|
1033 "inputs": [],
|
|
1034 "label": null,
|
|
1035 "name": "NCBI BLAST+ blastp",
|
|
1036 "outputs": [
|
|
1037 {
|
|
1038 "name": "output1",
|
|
1039 "type": "tabular"
|
|
1040 }
|
|
1041 ],
|
|
1042 "position": {
|
|
1043 "left": 1877.9999389648438,
|
|
1044 "top": 200
|
|
1045 },
|
|
1046 "post_job_actions": {},
|
|
1047 "tool_errors": null,
|
|
1048 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.01",
|
|
1049 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastp\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": null}}\", \"output\": \"{\\\"out_format\\\": \\\"ext\\\", \\\"__current_case__\\\": 1}\", \"query\": \"null\"}",
|
|
1050 "tool_version": "0.1.01",
|
|
1051 "type": "tool",
|
|
1052 "user_outputs": [],
|
|
1053 "uuid": "1913d15b-1314-4865-bd88-f3b857249162"
|
|
1054 },
|
|
1055 "26": {
|
|
1056 "annotation": "",
|
|
1057 "id": 26,
|
|
1058 "input_connections": {
|
|
1059 "isoform_sample_0|isoform_sample_matrix": {
|
|
1060 "id": 21,
|
|
1061 "output_name": "rsem_isoforms"
|
|
1062 },
|
|
1063 "isoform_sample_1|isoform_sample_matrix": {
|
|
1064 "id": 22,
|
|
1065 "output_name": "rsem_isoforms"
|
|
1066 },
|
|
1067 "isoform_sample_2|isoform_sample_matrix": {
|
|
1068 "id": 24,
|
|
1069 "output_name": "rsem_isoforms"
|
|
1070 },
|
|
1071 "isoform_sample_3|isoform_sample_matrix": {
|
|
1072 "id": 23,
|
|
1073 "output_name": "rsem_isoforms"
|
|
1074 }
|
|
1075 },
|
|
1076 "inputs": [],
|
|
1077 "label": null,
|
|
1078 "name": "Differential Expression",
|
|
1079 "outputs": [
|
|
1080 {
|
|
1081 "name": "de_output",
|
|
1082 "type": "zip"
|
|
1083 },
|
|
1084 {
|
|
1085 "name": "output_log",
|
|
1086 "type": "txt"
|
|
1087 }
|
|
1088 ],
|
|
1089 "position": {
|
|
1090 "left": 1877.9999389648438,
|
|
1091 "top": 313.00001525878906
|
|
1092 },
|
|
1093 "post_job_actions": {},
|
|
1094 "tool_errors": null,
|
|
1095 "tool_id": "toolshed.g2.bx.psu.edu/repos/mytest/testing8/differential_expression/1.0",
|
|
1096 "tool_state": "{\"isoform_sample\": \"[{\\\"__index__\\\": 0, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample1\\\"}, {\\\"__index__\\\": 1, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample2\\\"}, {\\\"__index__\\\": 2, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample3\\\"}, {\\\"__index__\\\": 3, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"Sample4\\\"}]\", \"__page__\": 0, \"est_method\": \"\\\"RSEM\\\"\", \"__rerun_remap_job_id__\": null, \"method\": \"\\\"edgeR\\\"\"}",
|
|
1097 "tool_version": "1.0",
|
|
1098 "type": "tool",
|
|
1099 "user_outputs": [],
|
|
1100 "uuid": "c2312c50-41de-47d4-8079-0ca346815ce6"
|
|
1101 }
|
|
1102 },
|
|
1103 "uuid": "89f77838-1d8a-4c51-ad97-fd7b558f199d"
|
|
1104 } |