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": "C1_R1"
|
|
15 }
|
|
16 ],
|
|
17 "label": null,
|
|
18 "name": "Input dataset",
|
|
19 "outputs": [],
|
|
20 "position": {
|
|
21 "left": 361.683349609375,
|
|
22 "top": 263
|
|
23 },
|
|
24 "tool_errors": null,
|
|
25 "tool_id": null,
|
|
26 "tool_state": "{\"name\": \"C1_R1\"}",
|
|
27 "tool_version": null,
|
|
28 "type": "data_input",
|
|
29 "user_outputs": [],
|
|
30 "uuid": "d466bcf1-44fd-48e5-b25b-24db8173941f"
|
|
31 },
|
|
32 "1": {
|
|
33 "annotation": "",
|
|
34 "id": 1,
|
|
35 "input_connections": {},
|
|
36 "inputs": [
|
|
37 {
|
|
38 "description": "",
|
|
39 "name": "C1_R2"
|
|
40 }
|
|
41 ],
|
|
42 "label": null,
|
|
43 "name": "Input dataset",
|
|
44 "outputs": [],
|
|
45 "position": {
|
|
46 "left": 383.683349609375,
|
|
47 "top": 383
|
|
48 },
|
|
49 "tool_errors": null,
|
|
50 "tool_id": null,
|
|
51 "tool_state": "{\"name\": \"C1_R2\"}",
|
|
52 "tool_version": null,
|
|
53 "type": "data_input",
|
|
54 "user_outputs": [],
|
|
55 "uuid": "2a107ff8-0c09-40ec-bc7d-0b6f5b87fc8e"
|
|
56 },
|
|
57 "2": {
|
|
58 "annotation": "",
|
|
59 "id": 2,
|
|
60 "input_connections": {},
|
|
61 "inputs": [
|
|
62 {
|
|
63 "description": "",
|
|
64 "name": "C2_R2"
|
|
65 }
|
|
66 ],
|
|
67 "label": null,
|
|
68 "name": "Input dataset",
|
|
69 "outputs": [],
|
|
70 "position": {
|
|
71 "left": 358.683349609375,
|
|
72 "top": 496
|
|
73 },
|
|
74 "tool_errors": null,
|
|
75 "tool_id": null,
|
|
76 "tool_state": "{\"name\": \"C2_R2\"}",
|
|
77 "tool_version": null,
|
|
78 "type": "data_input",
|
|
79 "user_outputs": [],
|
|
80 "uuid": "a030d9b3-55ed-4668-acb0-5cfffc4eabc4"
|
|
81 },
|
|
82 "3": {
|
|
83 "annotation": "",
|
|
84 "id": 3,
|
|
85 "input_connections": {},
|
|
86 "inputs": [
|
|
87 {
|
|
88 "description": "",
|
|
89 "name": "C2_R2"
|
|
90 }
|
|
91 ],
|
|
92 "label": null,
|
|
93 "name": "Input dataset",
|
|
94 "outputs": [],
|
|
95 "position": {
|
|
96 "left": 348.683349609375,
|
|
97 "top": 601.99996948242188
|
|
98 },
|
|
99 "tool_errors": null,
|
|
100 "tool_id": null,
|
|
101 "tool_state": "{\"name\": \"C2_R2\"}",
|
|
102 "tool_version": null,
|
|
103 "type": "data_input",
|
|
104 "user_outputs": [],
|
|
105 "uuid": "ea00291e-3b19-4887-9e35-a7be6c141572"
|
|
106 },
|
|
107 "4": {
|
|
108 "annotation": "",
|
|
109 "id": 4,
|
|
110 "input_connections": {},
|
|
111 "inputs": [
|
|
112 {
|
|
113 "description": "",
|
|
114 "name": "reference genome"
|
|
115 }
|
|
116 ],
|
|
117 "label": null,
|
|
118 "name": "Input dataset",
|
|
119 "outputs": [],
|
|
120 "position": {
|
|
121 "left": 200.00006103515625,
|
|
122 "top": 1418.8166198730469
|
|
123 },
|
|
124 "tool_errors": null,
|
|
125 "tool_id": null,
|
|
126 "tool_state": "{\"name\": \"reference genome\"}",
|
|
127 "tool_version": null,
|
|
128 "type": "data_input",
|
|
129 "user_outputs": [],
|
|
130 "uuid": "93b290b0-e871-4308-b078-60729e7e6716"
|
|
131 },
|
|
132 "5": {
|
|
133 "annotation": "",
|
|
134 "id": 5,
|
|
135 "input_connections": {},
|
|
136 "inputs": [
|
|
137 {
|
|
138 "description": "",
|
|
139 "name": "gtf "
|
|
140 }
|
|
141 ],
|
|
142 "label": null,
|
|
143 "name": "Input dataset",
|
|
144 "outputs": [],
|
|
145 "position": {
|
|
146 "left": 120.00006103515625,
|
|
147 "top": 1306.8166198730469
|
|
148 },
|
|
149 "tool_errors": null,
|
|
150 "tool_id": null,
|
|
151 "tool_state": "{\"name\": \"gtf \"}",
|
|
152 "tool_version": null,
|
|
153 "type": "data_input",
|
|
154 "user_outputs": [],
|
|
155 "uuid": "368a70e9-b151-459b-a086-5cccb591189f"
|
|
156 },
|
|
157 "6": {
|
|
158 "annotation": "",
|
|
159 "id": 6,
|
|
160 "input_connections": {},
|
|
161 "inputs": [
|
|
162 {
|
|
163 "description": "",
|
|
164 "name": "C3_R1"
|
|
165 }
|
|
166 ],
|
|
167 "label": null,
|
|
168 "name": "Input dataset",
|
|
169 "outputs": [],
|
|
170 "position": {
|
|
171 "left": 401.683349609375,
|
|
172 "top": 859.99996948242188
|
|
173 },
|
|
174 "tool_errors": null,
|
|
175 "tool_id": null,
|
|
176 "tool_state": "{\"name\": \"C3_R1\"}",
|
|
177 "tool_version": null,
|
|
178 "type": "data_input",
|
|
179 "user_outputs": [],
|
|
180 "uuid": "43324cce-d02f-42cb-8a33-e1c119ce3958"
|
|
181 },
|
|
182 "7": {
|
|
183 "annotation": "",
|
|
184 "id": 7,
|
|
185 "input_connections": {},
|
|
186 "inputs": [
|
|
187 {
|
|
188 "description": "",
|
|
189 "name": "C3_R2"
|
|
190 }
|
|
191 ],
|
|
192 "label": null,
|
|
193 "name": "Input dataset",
|
|
194 "outputs": [],
|
|
195 "position": {
|
|
196 "left": 389.683349609375,
|
|
197 "top": 1095.9999694824219
|
|
198 },
|
|
199 "tool_errors": null,
|
|
200 "tool_id": null,
|
|
201 "tool_state": "{\"name\": \"C3_R2\"}",
|
|
202 "tool_version": null,
|
|
203 "type": "data_input",
|
|
204 "user_outputs": [],
|
|
205 "uuid": "d99af4eb-fcca-4a66-a23c-5b9e94fedab2"
|
|
206 },
|
|
207 "8": {
|
|
208 "annotation": "",
|
|
209 "id": 8,
|
|
210 "input_connections": {},
|
|
211 "inputs": [
|
|
212 {
|
|
213 "description": "",
|
|
214 "name": "C4_R1"
|
|
215 }
|
|
216 ],
|
|
217 "label": null,
|
|
218 "name": "Input dataset",
|
|
219 "outputs": [],
|
|
220 "position": {
|
|
221 "left": 354.683349609375,
|
|
222 "top": 1262.9999694824219
|
|
223 },
|
|
224 "tool_errors": null,
|
|
225 "tool_id": null,
|
|
226 "tool_state": "{\"name\": \"C4_R1\"}",
|
|
227 "tool_version": null,
|
|
228 "type": "data_input",
|
|
229 "user_outputs": [],
|
|
230 "uuid": "a0cf2919-0a57-4277-b1a2-137b450a0024"
|
|
231 },
|
|
232 "9": {
|
|
233 "annotation": "",
|
|
234 "id": 9,
|
|
235 "input_connections": {},
|
|
236 "inputs": [
|
|
237 {
|
|
238 "description": "",
|
|
239 "name": "C4_R2"
|
|
240 }
|
|
241 ],
|
|
242 "label": null,
|
|
243 "name": "Input dataset",
|
|
244 "outputs": [],
|
|
245 "position": {
|
|
246 "left": 312.683349609375,
|
|
247 "top": 1348.9999694824219
|
|
248 },
|
|
249 "tool_errors": null,
|
|
250 "tool_id": null,
|
|
251 "tool_state": "{\"name\": \"C4_R2\"}",
|
|
252 "tool_version": null,
|
|
253 "type": "data_input",
|
|
254 "user_outputs": [],
|
|
255 "uuid": "79f03ce4-a711-4013-8a29-6c5e010591c4"
|
|
256 },
|
|
257 "10": {
|
|
258 "annotation": "",
|
|
259 "id": 10,
|
|
260 "input_connections": {
|
|
261 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
262 "id": 5,
|
|
263 "output_name": "output"
|
|
264 },
|
|
265 "refGenomeSource|ownFile": {
|
|
266 "id": 4,
|
|
267 "output_name": "output"
|
|
268 },
|
|
269 "singlePaired|input1": {
|
|
270 "id": 0,
|
|
271 "output_name": "output"
|
|
272 },
|
|
273 "singlePaired|input2": {
|
|
274 "id": 1,
|
|
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": 712.68338012695312,
|
|
309 "top": 242
|
|
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": "4d3bb525-d233-498f-9aed-9453379091d1"
|
|
319 },
|
|
320 "11": {
|
|
321 "annotation": "",
|
|
322 "id": 11,
|
|
323 "input_connections": {
|
|
324 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
325 "id": 5,
|
|
326 "output_name": "output"
|
|
327 },
|
|
328 "refGenomeSource|ownFile": {
|
|
329 "id": 4,
|
|
330 "output_name": "output"
|
|
331 },
|
|
332 "singlePaired|input1": {
|
|
333 "id": 2,
|
|
334 "output_name": "output"
|
|
335 },
|
|
336 "singlePaired|input2": {
|
|
337 "id": 3,
|
|
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": 778.68338012695312,
|
|
372 "top": 683.99996948242188
|
|
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": "81e8a87f-b6b0-4618-8720-529418754ef9"
|
|
382 },
|
|
383 "12": {
|
|
384 "annotation": "",
|
|
385 "id": 12,
|
|
386 "input_connections": {
|
|
387 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
388 "id": 5,
|
|
389 "output_name": "output"
|
|
390 },
|
|
391 "refGenomeSource|ownFile": {
|
|
392 "id": 4,
|
|
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": 951.68338012695312,
|
|
435 "top": 1008.9999694824219
|
|
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": "534ea8a1-67d0-4d9f-8af3-25c5ab4d83a2"
|
|
445 },
|
|
446 "13": {
|
|
447 "annotation": "",
|
|
448 "id": 13,
|
|
449 "input_connections": {
|
|
450 "params|own_junctions|gene_model_ann|gene_annotation_model": {
|
|
451 "id": 5,
|
|
452 "output_name": "output"
|
|
453 },
|
|
454 "refGenomeSource|ownFile": {
|
|
455 "id": 4,
|
|
456 "output_name": "output"
|
|
457 },
|
|
458 "singlePaired|input1": {
|
|
459 "id": 8,
|
|
460 "output_name": "output"
|
|
461 },
|
|
462 "singlePaired|input2": {
|
|
463 "id": 9,
|
|
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": 711.68338012695312,
|
|
498 "top": 1238.9999694824219
|
|
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": "a301a721-c300-4322-92f2-56236be26ee9"
|
|
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 "name": "skipped",
|
|
540 "type": "gtf"
|
|
541 }
|
|
542 ],
|
|
543 "position": {
|
|
544 "left": 1921.5667114257812,
|
|
545 "top": 344.38333129882812
|
|
546 },
|
|
547 "post_job_actions": {},
|
|
548 "tool_errors": null,
|
|
549 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0",
|
|
550 "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"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}\", \"max_intron_len\": \"\\\"300000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"length_correction\": \"\\\"\\\"\", \"advanced_settings\": \"{\\\"__current_case__\\\": 0, \\\"use_advanced_settings\\\": \\\"No\\\"}\"}",
|
|
551 "tool_version": "2.2.1.0",
|
|
552 "type": "tool",
|
|
553 "user_outputs": [],
|
|
554 "uuid": "45793133-e88c-4107-9860-3018483d14de"
|
|
555 },
|
|
556 "15": {
|
|
557 "annotation": "",
|
|
558 "id": 15,
|
|
559 "input_connections": {
|
|
560 "input": {
|
|
561 "id": 11,
|
|
562 "output_name": "accepted_hits"
|
|
563 }
|
|
564 },
|
|
565 "inputs": [],
|
|
566 "label": null,
|
|
567 "name": "Cufflinks",
|
|
568 "outputs": [
|
|
569 {
|
|
570 "name": "genes_expression",
|
|
571 "type": "tabular"
|
|
572 },
|
|
573 {
|
|
574 "name": "transcripts_expression",
|
|
575 "type": "tabular"
|
|
576 },
|
|
577 {
|
|
578 "name": "assembled_isoforms",
|
|
579 "type": "gtf"
|
|
580 },
|
|
581 {
|
|
582 "name": "total_map_mass",
|
|
583 "type": "txt"
|
|
584 },
|
|
585 {
|
|
586 "name": "skipped",
|
|
587 "type": "gtf"
|
|
588 }
|
|
589 ],
|
|
590 "position": {
|
|
591 "left": 1928.5667114257812,
|
|
592 "top": 612.38333129882812
|
|
593 },
|
|
594 "post_job_actions": {},
|
|
595 "tool_errors": null,
|
|
596 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0",
|
|
597 "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"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}\", \"max_intron_len\": \"\\\"300000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"length_correction\": \"\\\"\\\"\", \"advanced_settings\": \"{\\\"__current_case__\\\": 0, \\\"use_advanced_settings\\\": \\\"No\\\"}\"}",
|
|
598 "tool_version": "2.2.1.0",
|
|
599 "type": "tool",
|
|
600 "user_outputs": [],
|
|
601 "uuid": "00a851a2-7802-4258-ab9c-74227a7c0f3f"
|
|
602 },
|
|
603 "16": {
|
|
604 "annotation": "",
|
|
605 "id": 16,
|
|
606 "input_connections": {
|
|
607 "input": {
|
|
608 "id": 12,
|
|
609 "output_name": "accepted_hits"
|
|
610 }
|
|
611 },
|
|
612 "inputs": [],
|
|
613 "label": null,
|
|
614 "name": "Cufflinks",
|
|
615 "outputs": [
|
|
616 {
|
|
617 "name": "genes_expression",
|
|
618 "type": "tabular"
|
|
619 },
|
|
620 {
|
|
621 "name": "transcripts_expression",
|
|
622 "type": "tabular"
|
|
623 },
|
|
624 {
|
|
625 "name": "assembled_isoforms",
|
|
626 "type": "gtf"
|
|
627 },
|
|
628 {
|
|
629 "name": "total_map_mass",
|
|
630 "type": "txt"
|
|
631 },
|
|
632 {
|
|
633 "name": "skipped",
|
|
634 "type": "gtf"
|
|
635 }
|
|
636 ],
|
|
637 "position": {
|
|
638 "left": 1945.5667114257812,
|
|
639 "top": 898.38333129882812
|
|
640 },
|
|
641 "post_job_actions": {},
|
|
642 "tool_errors": null,
|
|
643 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0",
|
|
644 "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"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}\", \"max_intron_len\": \"\\\"300000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"length_correction\": \"\\\"\\\"\", \"advanced_settings\": \"{\\\"__current_case__\\\": 0, \\\"use_advanced_settings\\\": \\\"No\\\"}\"}",
|
|
645 "tool_version": "2.2.1.0",
|
|
646 "type": "tool",
|
|
647 "user_outputs": [],
|
|
648 "uuid": "e7a08077-bf3f-4dc6-8e85-9efc6da9cfe7"
|
|
649 },
|
|
650 "17": {
|
|
651 "annotation": "",
|
|
652 "id": 17,
|
|
653 "input_connections": {
|
|
654 "input": {
|
|
655 "id": 13,
|
|
656 "output_name": "accepted_hits"
|
|
657 }
|
|
658 },
|
|
659 "inputs": [],
|
|
660 "label": null,
|
|
661 "name": "Cufflinks",
|
|
662 "outputs": [
|
|
663 {
|
|
664 "name": "genes_expression",
|
|
665 "type": "tabular"
|
|
666 },
|
|
667 {
|
|
668 "name": "transcripts_expression",
|
|
669 "type": "tabular"
|
|
670 },
|
|
671 {
|
|
672 "name": "assembled_isoforms",
|
|
673 "type": "gtf"
|
|
674 },
|
|
675 {
|
|
676 "name": "total_map_mass",
|
|
677 "type": "txt"
|
|
678 },
|
|
679 {
|
|
680 "name": "skipped",
|
|
681 "type": "gtf"
|
|
682 }
|
|
683 ],
|
|
684 "position": {
|
|
685 "left": 1952.5667114257812,
|
|
686 "top": 1218.3832702636719
|
|
687 },
|
|
688 "post_job_actions": {},
|
|
689 "tool_errors": null,
|
|
690 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0",
|
|
691 "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"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}\", \"max_intron_len\": \"\\\"300000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"length_correction\": \"\\\"\\\"\", \"advanced_settings\": \"{\\\"__current_case__\\\": 0, \\\"use_advanced_settings\\\": \\\"No\\\"}\"}",
|
|
692 "tool_version": "2.2.1.0",
|
|
693 "type": "tool",
|
|
694 "user_outputs": [],
|
|
695 "uuid": "0b10a303-8204-4a40-8b9a-7d74d3425f5a"
|
|
696 },
|
|
697 "18": {
|
|
698 "annotation": "",
|
|
699 "id": 18,
|
|
700 "input_connections": {
|
|
701 "inputs": [
|
|
702 {
|
|
703 "id": 14,
|
|
704 "output_name": "assembled_isoforms"
|
|
705 },
|
|
706 {
|
|
707 "id": 15,
|
|
708 "output_name": "assembled_isoforms"
|
|
709 },
|
|
710 {
|
|
711 "id": 16,
|
|
712 "output_name": "assembled_isoforms"
|
|
713 },
|
|
714 {
|
|
715 "id": 17,
|
|
716 "output_name": "assembled_isoforms"
|
|
717 }
|
|
718 ]
|
|
719 },
|
|
720 "inputs": [],
|
|
721 "label": null,
|
|
722 "name": "Cuffmerge",
|
|
723 "outputs": [
|
|
724 {
|
|
725 "name": "merged_transcripts",
|
|
726 "type": "gtf"
|
|
727 }
|
|
728 ],
|
|
729 "position": {
|
|
730 "left": 2599.566650390625,
|
|
731 "top": 590.38333129882812
|
|
732 },
|
|
733 "post_job_actions": {},
|
|
734 "tool_errors": null,
|
|
735 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0",
|
|
736 "tool_state": "{\"seq_data\": \"{\\\"use_seq_data\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"inputs\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"min_isoform_fraction\": \"\\\"0.05\\\"\", \"additional_inputs\": \"[]\", \"annotation\": \"{\\\"use_ref_annotation\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}",
|
|
737 "tool_version": "2.2.1.0",
|
|
738 "type": "tool",
|
|
739 "user_outputs": [],
|
|
740 "uuid": "19184e08-8f96-4adf-966f-dd2b726c0b23"
|
|
741 },
|
|
742 "19": {
|
|
743 "annotation": "",
|
|
744 "id": 19,
|
|
745 "input_connections": {
|
|
746 "genome": {
|
|
747 "id": 4,
|
|
748 "output_name": "output"
|
|
749 },
|
|
750 "gtf": {
|
|
751 "id": 18,
|
|
752 "output_name": "merged_transcripts"
|
|
753 }
|
|
754 },
|
|
755 "inputs": [],
|
|
756 "label": null,
|
|
757 "name": "gtf2fasta",
|
|
758 "outputs": [
|
|
759 {
|
|
760 "name": "fasta",
|
|
761 "type": "fasta"
|
|
762 }
|
|
763 ],
|
|
764 "position": {
|
|
765 "left": 1200.0000457763672,
|
|
766 "top": 557.81668090820312
|
|
767 },
|
|
768 "post_job_actions": {},
|
|
769 "tool_errors": null,
|
|
770 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/id_gtf2fasta/1.0",
|
|
771 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"genome\": \"null\", \"gtf\": \"null\"}",
|
|
772 "tool_version": "1.0",
|
|
773 "type": "tool",
|
|
774 "user_outputs": [],
|
|
775 "uuid": "01f889e0-dcba-4ed1-aa9b-6b447409a32b"
|
|
776 },
|
|
777 "20": {
|
|
778 "annotation": "",
|
|
779 "id": 20,
|
|
780 "input_connections": {
|
|
781 "reads|left_input": {
|
|
782 "id": 0,
|
|
783 "output_name": "output"
|
|
784 },
|
|
785 "reads|right_input": {
|
|
786 "id": 1,
|
|
787 "output_name": "output"
|
|
788 },
|
|
789 "transcripts": {
|
|
790 "id": 19,
|
|
791 "output_name": "fasta"
|
|
792 }
|
|
793 },
|
|
794 "inputs": [],
|
|
795 "label": null,
|
|
796 "name": "align_and_estimate_abundance",
|
|
797 "outputs": [
|
|
798 {
|
|
799 "name": "align_and_estimate_abundance_log",
|
|
800 "type": "txt"
|
|
801 },
|
|
802 {
|
|
803 "name": "bowtie_bam",
|
|
804 "type": "bam"
|
|
805 },
|
|
806 {
|
|
807 "name": "rsem_isoforms",
|
|
808 "type": "tabular"
|
|
809 },
|
|
810 {
|
|
811 "name": "rsem_genes",
|
|
812 "type": "tabular"
|
|
813 }
|
|
814 ],
|
|
815 "position": {
|
|
816 "left": 1323.1833801269531,
|
|
817 "top": 200
|
|
818 },
|
|
819 "post_job_actions": {},
|
|
820 "tool_errors": null,
|
|
821 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/id_align_and_estimate_abundance/1.0",
|
|
822 "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\"}",
|
|
823 "tool_version": "1.0",
|
|
824 "type": "tool",
|
|
825 "user_outputs": [],
|
|
826 "uuid": "dd4703c8-9da1-4756-aa32-ee3f1d45a4c9"
|
|
827 },
|
|
828 "21": {
|
|
829 "annotation": "",
|
|
830 "id": 21,
|
|
831 "input_connections": {
|
|
832 "reads|left_input": {
|
|
833 "id": 2,
|
|
834 "output_name": "output"
|
|
835 },
|
|
836 "reads|right_input": {
|
|
837 "id": 3,
|
|
838 "output_name": "output"
|
|
839 },
|
|
840 "transcripts": {
|
|
841 "id": 19,
|
|
842 "output_name": "fasta"
|
|
843 }
|
|
844 },
|
|
845 "inputs": [],
|
|
846 "label": null,
|
|
847 "name": "align_and_estimate_abundance",
|
|
848 "outputs": [
|
|
849 {
|
|
850 "name": "align_and_estimate_abundance_log",
|
|
851 "type": "txt"
|
|
852 },
|
|
853 {
|
|
854 "name": "bowtie_bam",
|
|
855 "type": "bam"
|
|
856 },
|
|
857 {
|
|
858 "name": "rsem_isoforms",
|
|
859 "type": "tabular"
|
|
860 },
|
|
861 {
|
|
862 "name": "rsem_genes",
|
|
863 "type": "tabular"
|
|
864 }
|
|
865 ],
|
|
866 "position": {
|
|
867 "left": 1563.1833801269531,
|
|
868 "top": 658.99996948242188
|
|
869 },
|
|
870 "post_job_actions": {},
|
|
871 "tool_errors": null,
|
|
872 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/id_align_and_estimate_abundance/1.0",
|
|
873 "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\"}",
|
|
874 "tool_version": "1.0",
|
|
875 "type": "tool",
|
|
876 "user_outputs": [],
|
|
877 "uuid": "a43e25a9-acc6-46a2-9c63-639fc68124c4"
|
|
878 },
|
|
879 "22": {
|
|
880 "annotation": "",
|
|
881 "id": 22,
|
|
882 "input_connections": {
|
|
883 "reads|left_input": {
|
|
884 "id": 6,
|
|
885 "output_name": "output"
|
|
886 },
|
|
887 "reads|right_input": {
|
|
888 "id": 7,
|
|
889 "output_name": "output"
|
|
890 },
|
|
891 "transcripts": {
|
|
892 "id": 19,
|
|
893 "output_name": "fasta"
|
|
894 }
|
|
895 },
|
|
896 "inputs": [],
|
|
897 "label": null,
|
|
898 "name": "align_and_estimate_abundance",
|
|
899 "outputs": [
|
|
900 {
|
|
901 "name": "align_and_estimate_abundance_log",
|
|
902 "type": "txt"
|
|
903 },
|
|
904 {
|
|
905 "name": "bowtie_bam",
|
|
906 "type": "bam"
|
|
907 },
|
|
908 {
|
|
909 "name": "rsem_isoforms",
|
|
910 "type": "tabular"
|
|
911 },
|
|
912 {
|
|
913 "name": "rsem_genes",
|
|
914 "type": "tabular"
|
|
915 }
|
|
916 ],
|
|
917 "position": {
|
|
918 "left": 1434.1833801269531,
|
|
919 "top": 1027.9999694824219
|
|
920 },
|
|
921 "post_job_actions": {},
|
|
922 "tool_errors": null,
|
|
923 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/id_align_and_estimate_abundance/1.0",
|
|
924 "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\"}",
|
|
925 "tool_version": "1.0",
|
|
926 "type": "tool",
|
|
927 "user_outputs": [],
|
|
928 "uuid": "b8bcc4bc-5eff-407e-a456-a63b474ef9d4"
|
|
929 },
|
|
930 "23": {
|
|
931 "annotation": "",
|
|
932 "id": 23,
|
|
933 "input_connections": {
|
|
934 "reads|left_input": {
|
|
935 "id": 8,
|
|
936 "output_name": "output"
|
|
937 },
|
|
938 "reads|right_input": {
|
|
939 "id": 9,
|
|
940 "output_name": "output"
|
|
941 },
|
|
942 "transcripts": {
|
|
943 "id": 19,
|
|
944 "output_name": "fasta"
|
|
945 }
|
|
946 },
|
|
947 "inputs": [],
|
|
948 "label": null,
|
|
949 "name": "align_and_estimate_abundance",
|
|
950 "outputs": [
|
|
951 {
|
|
952 "name": "align_and_estimate_abundance_log",
|
|
953 "type": "txt"
|
|
954 },
|
|
955 {
|
|
956 "name": "bowtie_bam",
|
|
957 "type": "bam"
|
|
958 },
|
|
959 {
|
|
960 "name": "rsem_isoforms",
|
|
961 "type": "tabular"
|
|
962 },
|
|
963 {
|
|
964 "name": "rsem_genes",
|
|
965 "type": "tabular"
|
|
966 }
|
|
967 ],
|
|
968 "position": {
|
|
969 "left": 1450.1833801269531,
|
|
970 "top": 1409.9999694824219
|
|
971 },
|
|
972 "post_job_actions": {},
|
|
973 "tool_errors": null,
|
|
974 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/id_align_and_estimate_abundance/1.0",
|
|
975 "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\"}",
|
|
976 "tool_version": "1.0",
|
|
977 "type": "tool",
|
|
978 "user_outputs": [],
|
|
979 "uuid": "05a6da48-9337-4ab0-a67b-bd97babfc0c3"
|
|
980 },
|
|
981 "24": {
|
|
982 "annotation": "",
|
|
983 "id": 24,
|
|
984 "input_connections": {
|
|
985 "transcript": {
|
|
986 "id": 19,
|
|
987 "output_name": "fasta"
|
|
988 }
|
|
989 },
|
|
990 "inputs": [],
|
|
991 "label": null,
|
|
992 "name": "transDecoder",
|
|
993 "outputs": [
|
|
994 {
|
|
995 "name": "transdecoder_pep",
|
|
996 "type": "fasta"
|
|
997 },
|
|
998 {
|
|
999 "name": "transdecoder_cds",
|
|
1000 "type": "fasta"
|
|
1001 },
|
|
1002 {
|
|
1003 "name": "transdecoder_bed",
|
|
1004 "type": "bed"
|
|
1005 },
|
|
1006 {
|
|
1007 "name": "transdecoder_gff3",
|
|
1008 "type": "tabular"
|
|
1009 },
|
|
1010 {
|
|
1011 "name": "transdecoder_mRNA",
|
|
1012 "type": "fasta"
|
|
1013 },
|
|
1014 {
|
|
1015 "name": "transdecoder_log",
|
|
1016 "type": "txt"
|
|
1017 }
|
|
1018 ],
|
|
1019 "position": {
|
|
1020 "left": 2701,
|
|
1021 "top": 1033.8166809082031
|
|
1022 },
|
|
1023 "post_job_actions": {},
|
|
1024 "tool_errors": null,
|
|
1025 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/id_transDecoder/1.0",
|
|
1026 "tool_state": "{\"pfam\": \"{\\\"options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"optional\": \"{\\\"parameters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"transcript\": \"null\", \"__page__\": 0}",
|
|
1027 "tool_version": "1.0",
|
|
1028 "type": "tool",
|
|
1029 "user_outputs": [],
|
|
1030 "uuid": "cd9576bd-5729-418d-808c-cba84fc4f597"
|
|
1031 },
|
|
1032 "25": {
|
|
1033 "annotation": "",
|
|
1034 "id": 25,
|
|
1035 "input_connections": {
|
|
1036 "isoform_sample_0|isoform_sample_matrix": {
|
|
1037 "id": 20,
|
|
1038 "output_name": "rsem_isoforms"
|
|
1039 },
|
|
1040 "isoform_sample_1|isoform_sample_matrix": {
|
|
1041 "id": 21,
|
|
1042 "output_name": "rsem_isoforms"
|
|
1043 },
|
|
1044 "isoform_sample_2|isoform_sample_matrix": {
|
|
1045 "id": 22,
|
|
1046 "output_name": "rsem_isoforms"
|
|
1047 },
|
|
1048 "isoform_sample_3|isoform_sample_matrix": {
|
|
1049 "id": 23,
|
|
1050 "output_name": "rsem_isoforms"
|
|
1051 }
|
|
1052 },
|
|
1053 "inputs": [],
|
|
1054 "label": null,
|
|
1055 "name": "Differential Expression",
|
|
1056 "outputs": [
|
|
1057 {
|
|
1058 "name": "de_output",
|
|
1059 "type": "zip"
|
|
1060 },
|
|
1061 {
|
|
1062 "name": "output_log",
|
|
1063 "type": "txt"
|
|
1064 }
|
|
1065 ],
|
|
1066 "position": {
|
|
1067 "left": 2924,
|
|
1068 "top": 675.81668090820312
|
|
1069 },
|
|
1070 "post_job_actions": {},
|
|
1071 "tool_errors": null,
|
|
1072 "tool_id": "toolshed.g2.bx.psu.edu/repos/lynngroup/testing11/differential_expression/1.0",
|
|
1073 "tool_state": "{\"isoform_sample\": \"[{\\\"__index__\\\": 0, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"s1\\\"}, {\\\"__index__\\\": 1, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"s2\\\"}, {\\\"__index__\\\": 2, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"s3\\\"}, {\\\"__index__\\\": 3, \\\"isoform_sample_matrix\\\": null, \\\"sample_name\\\": \\\"s4\\\"}]\", \"__page__\": 0, \"est_method\": \"\\\"RSEM\\\"\", \"__rerun_remap_job_id__\": null, \"method\": \"\\\"edgeR\\\"\"}",
|
|
1074 "tool_version": "1.0",
|
|
1075 "type": "tool",
|
|
1076 "user_outputs": [],
|
|
1077 "uuid": "f050b6ce-635b-429c-91b0-0fdd7a367895"
|
|
1078 },
|
|
1079 "26": {
|
|
1080 "annotation": "",
|
|
1081 "id": 26,
|
|
1082 "input_connections": {
|
|
1083 "query": {
|
|
1084 "id": 24,
|
|
1085 "output_name": "transdecoder_pep"
|
|
1086 }
|
|
1087 },
|
|
1088 "inputs": [],
|
|
1089 "label": null,
|
|
1090 "name": "NCBI BLAST+ blastp",
|
|
1091 "outputs": [
|
|
1092 {
|
|
1093 "name": "output1",
|
|
1094 "type": "tabular"
|
|
1095 }
|
|
1096 ],
|
|
1097 "position": {
|
|
1098 "left": 2827,
|
|
1099 "top": 439.81668090820312
|
|
1100 },
|
|
1101 "post_job_actions": {},
|
|
1102 "tool_errors": null,
|
|
1103 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.01",
|
|
1104 "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\"}",
|
|
1105 "tool_version": "0.1.01",
|
|
1106 "type": "tool",
|
|
1107 "user_outputs": [],
|
|
1108 "uuid": "66733833-c554-4f7f-bea2-5acbe7b0f039"
|
|
1109 }
|
|
1110 },
|
|
1111 "uuid": "26af851d-d14b-4065-85ca-ebd1e8f45f21"
|
|
1112 }
|