|
0
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "rapsosnp v1.15 - 2x",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "id": 0,
|
|
|
10 "input_connections": {},
|
|
|
11 "inputs": [
|
|
|
12 {
|
|
|
13 "description": "",
|
|
|
14 "name": "ASSEMBLY"
|
|
|
15 }
|
|
|
16 ],
|
|
|
17 "name": "Input dataset",
|
|
|
18 "outputs": [],
|
|
|
19 "position": {
|
|
|
20 "left": 200.000244140625,
|
|
|
21 "top": 211
|
|
|
22 },
|
|
|
23 "tool_errors": null,
|
|
|
24 "tool_id": null,
|
|
|
25 "tool_state": "{\"name\": \"ASSEMBLY\"}",
|
|
|
26 "tool_version": null,
|
|
|
27 "type": "data_input",
|
|
|
28 "user_outputs": []
|
|
|
29 },
|
|
|
30 "1": {
|
|
|
31 "annotation": "",
|
|
|
32 "id": 1,
|
|
|
33 "input_connections": {},
|
|
|
34 "inputs": [
|
|
|
35 {
|
|
|
36 "description": "",
|
|
|
37 "name": "READ1"
|
|
|
38 }
|
|
|
39 ],
|
|
|
40 "name": "Input dataset",
|
|
|
41 "outputs": [],
|
|
|
42 "position": {
|
|
|
43 "left": 200.000244140625,
|
|
|
44 "top": 296
|
|
|
45 },
|
|
|
46 "tool_errors": null,
|
|
|
47 "tool_id": null,
|
|
|
48 "tool_state": "{\"name\": \"READ1\"}",
|
|
|
49 "tool_version": null,
|
|
|
50 "type": "data_input",
|
|
|
51 "user_outputs": []
|
|
|
52 },
|
|
|
53 "2": {
|
|
|
54 "annotation": "",
|
|
|
55 "id": 2,
|
|
|
56 "input_connections": {},
|
|
|
57 "inputs": [
|
|
|
58 {
|
|
|
59 "description": "",
|
|
|
60 "name": "READ2"
|
|
|
61 }
|
|
|
62 ],
|
|
|
63 "name": "Input dataset",
|
|
|
64 "outputs": [],
|
|
|
65 "position": {
|
|
|
66 "left": 200.000244140625,
|
|
|
67 "top": 381
|
|
|
68 },
|
|
|
69 "tool_errors": null,
|
|
|
70 "tool_id": null,
|
|
|
71 "tool_state": "{\"name\": \"READ2\"}",
|
|
|
72 "tool_version": null,
|
|
|
73 "type": "data_input",
|
|
|
74 "user_outputs": []
|
|
|
75 },
|
|
|
76 "3": {
|
|
|
77 "annotation": "",
|
|
|
78 "id": 3,
|
|
|
79 "input_connections": {},
|
|
|
80 "inputs": [
|
|
|
81 {
|
|
|
82 "description": "",
|
|
|
83 "name": "DUBIOUS"
|
|
|
84 }
|
|
|
85 ],
|
|
|
86 "name": "Input dataset",
|
|
|
87 "outputs": [],
|
|
|
88 "position": {
|
|
|
89 "left": 200.000244140625,
|
|
|
90 "top": 466
|
|
|
91 },
|
|
|
92 "tool_errors": null,
|
|
|
93 "tool_id": null,
|
|
|
94 "tool_state": "{\"name\": \"DUBIOUS\"}",
|
|
|
95 "tool_version": null,
|
|
|
96 "type": "data_input",
|
|
|
97 "user_outputs": []
|
|
|
98 },
|
|
|
99 "4": {
|
|
|
100 "annotation": "",
|
|
|
101 "id": 4,
|
|
|
102 "input_connections": {
|
|
|
103 "input_fasta": {
|
|
|
104 "id": 0,
|
|
|
105 "output_name": "output"
|
|
|
106 }
|
|
|
107 },
|
|
|
108 "inputs": [],
|
|
|
109 "name": "fastaGroomerForMakeBlastdb",
|
|
|
110 "outputs": [
|
|
|
111 {
|
|
|
112 "name": "output_fasta",
|
|
|
113 "type": "fasta"
|
|
|
114 }
|
|
|
115 ],
|
|
|
116 "position": {
|
|
|
117 "left": 428.000244140625,
|
|
|
118 "top": 211
|
|
|
119 },
|
|
|
120 "post_job_actions": {},
|
|
|
121 "tool_errors": null,
|
|
|
122 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/genephys/fastaGroomerForMakeBlastdb/0.01",
|
|
|
123 "tool_state": "{\"input_fasta\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
|
|
|
124 "tool_version": "0.01",
|
|
|
125 "type": "tool",
|
|
|
126 "user_outputs": []
|
|
|
127 },
|
|
|
128 "5": {
|
|
|
129 "annotation": "",
|
|
|
130 "id": 5,
|
|
|
131 "input_connections": {
|
|
|
132 "input_file": {
|
|
|
133 "id": 1,
|
|
|
134 "output_name": "output"
|
|
|
135 }
|
|
|
136 },
|
|
|
137 "inputs": [],
|
|
|
138 "name": "SplitFile2x",
|
|
|
139 "outputs": [
|
|
|
140 {
|
|
|
141 "name": "output_file1",
|
|
|
142 "type": "txt"
|
|
|
143 },
|
|
|
144 {
|
|
|
145 "name": "output_file2",
|
|
|
146 "type": "txt"
|
|
|
147 }
|
|
|
148 ],
|
|
|
149 "position": {
|
|
|
150 "left": 428.000244140625,
|
|
|
151 "top": 342
|
|
|
152 },
|
|
|
153 "post_job_actions": {},
|
|
|
154 "tool_errors": null,
|
|
|
155 "tool_id": "SplitFile2x",
|
|
|
156 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
|
|
|
157 "tool_version": "0.01",
|
|
|
158 "type": "tool",
|
|
|
159 "user_outputs": []
|
|
|
160 },
|
|
|
161 "6": {
|
|
|
162 "annotation": "",
|
|
|
163 "id": 6,
|
|
|
164 "input_connections": {
|
|
|
165 "input_file": {
|
|
|
166 "id": 2,
|
|
|
167 "output_name": "output"
|
|
|
168 }
|
|
|
169 },
|
|
|
170 "inputs": [],
|
|
|
171 "name": "SplitFile2x",
|
|
|
172 "outputs": [
|
|
|
173 {
|
|
|
174 "name": "output_file1",
|
|
|
175 "type": "txt"
|
|
|
176 },
|
|
|
177 {
|
|
|
178 "name": "output_file2",
|
|
|
179 "type": "txt"
|
|
|
180 }
|
|
|
181 ],
|
|
|
182 "position": {
|
|
|
183 "left": 428.000244140625,
|
|
|
184 "top": 534
|
|
|
185 },
|
|
|
186 "post_job_actions": {},
|
|
|
187 "tool_errors": null,
|
|
|
188 "tool_id": "SplitFile2x",
|
|
|
189 "tool_state": "{\"out_format\": \"\\\"fastq\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
|
|
|
190 "tool_version": "0.01",
|
|
|
191 "type": "tool",
|
|
|
192 "user_outputs": []
|
|
|
193 },
|
|
|
194 "7": {
|
|
|
195 "annotation": "",
|
|
|
196 "id": 7,
|
|
|
197 "input_connections": {
|
|
|
198 "input_file": {
|
|
|
199 "id": 4,
|
|
|
200 "output_name": "output_fasta"
|
|
|
201 }
|
|
|
202 },
|
|
|
203 "inputs": [],
|
|
|
204 "name": "NCBI BLAST+ makeblastdb",
|
|
|
205 "outputs": [
|
|
|
206 {
|
|
|
207 "name": "outfile",
|
|
|
208 "type": "data"
|
|
|
209 }
|
|
|
210 ],
|
|
|
211 "position": {
|
|
|
212 "left": 756.000244140625,
|
|
|
213 "top": 615.0000305175781
|
|
|
214 },
|
|
|
215 "post_job_actions": {},
|
|
|
216 "tool_errors": null,
|
|
|
217 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
|
|
|
218 "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}",
|
|
|
219 "tool_version": "0.1.00",
|
|
|
220 "type": "tool",
|
|
|
221 "user_outputs": []
|
|
|
222 },
|
|
|
223 "8": {
|
|
|
224 "annotation": "",
|
|
|
225 "id": 8,
|
|
|
226 "input_connections": {
|
|
|
227 "input_read1_file": {
|
|
|
228 "id": 5,
|
|
|
229 "output_name": "output_file1"
|
|
|
230 },
|
|
|
231 "input_read2_file": {
|
|
|
232 "id": 6,
|
|
|
233 "output_name": "output_file1"
|
|
|
234 }
|
|
|
235 },
|
|
|
236 "inputs": [],
|
|
|
237 "name": "PrepareFastqLight",
|
|
|
238 "outputs": [
|
|
|
239 {
|
|
|
240 "name": "output_read1_file",
|
|
|
241 "type": "fastqsanger"
|
|
|
242 },
|
|
|
243 {
|
|
|
244 "name": "output_read2_file",
|
|
|
245 "type": "fastqsanger"
|
|
|
246 }
|
|
|
247 ],
|
|
|
248 "position": {
|
|
|
249 "left": 756.000244140625,
|
|
|
250 "top": 211
|
|
|
251 },
|
|
|
252 "post_job_actions": {},
|
|
|
253 "tool_errors": null,
|
|
|
254 "tool_id": "PrepareFastqLight",
|
|
|
255 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
|
|
|
256 "tool_version": "0.01",
|
|
|
257 "type": "tool",
|
|
|
258 "user_outputs": []
|
|
|
259 },
|
|
|
260 "9": {
|
|
|
261 "annotation": "",
|
|
|
262 "id": 9,
|
|
|
263 "input_connections": {
|
|
|
264 "input_read1_file": {
|
|
|
265 "id": 5,
|
|
|
266 "output_name": "output_file2"
|
|
|
267 },
|
|
|
268 "input_read2_file": {
|
|
|
269 "id": 6,
|
|
|
270 "output_name": "output_file2"
|
|
|
271 }
|
|
|
272 },
|
|
|
273 "inputs": [],
|
|
|
274 "name": "PrepareFastqLight",
|
|
|
275 "outputs": [
|
|
|
276 {
|
|
|
277 "name": "output_read1_file",
|
|
|
278 "type": "fastqsanger"
|
|
|
279 },
|
|
|
280 {
|
|
|
281 "name": "output_read2_file",
|
|
|
282 "type": "fastqsanger"
|
|
|
283 }
|
|
|
284 ],
|
|
|
285 "position": {
|
|
|
286 "left": 756.000244140625,
|
|
|
287 "top": 413
|
|
|
288 },
|
|
|
289 "post_job_actions": {},
|
|
|
290 "tool_errors": null,
|
|
|
291 "tool_id": "PrepareFastqLight",
|
|
|
292 "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}",
|
|
|
293 "tool_version": "0.01",
|
|
|
294 "type": "tool",
|
|
|
295 "user_outputs": []
|
|
|
296 },
|
|
|
297 "10": {
|
|
|
298 "annotation": "",
|
|
|
299 "id": 10,
|
|
|
300 "input_connections": {
|
|
|
301 "genomeSource|ownFile": {
|
|
|
302 "id": 0,
|
|
|
303 "output_name": "output"
|
|
|
304 },
|
|
|
305 "paired|input1": {
|
|
|
306 "id": 8,
|
|
|
307 "output_name": "output_read1_file"
|
|
|
308 },
|
|
|
309 "paired|input2": {
|
|
|
310 "id": 8,
|
|
|
311 "output_name": "output_read2_file"
|
|
|
312 }
|
|
|
313 },
|
|
|
314 "inputs": [],
|
|
|
315 "name": "Map with BWA for Illumina",
|
|
|
316 "outputs": [
|
|
|
317 {
|
|
|
318 "name": "output",
|
|
|
319 "type": "sam"
|
|
|
320 }
|
|
|
321 ],
|
|
|
322 "position": {
|
|
|
323 "left": 1084.000244140625,
|
|
|
324 "top": 211
|
|
|
325 },
|
|
|
326 "post_job_actions": {},
|
|
|
327 "tool_errors": null,
|
|
|
328 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
329 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
330 "tool_version": "1.2.3",
|
|
|
331 "type": "tool",
|
|
|
332 "user_outputs": []
|
|
|
333 },
|
|
|
334 "11": {
|
|
|
335 "annotation": "",
|
|
|
336 "id": 11,
|
|
|
337 "input_connections": {
|
|
|
338 "genomeSource|ownFile": {
|
|
|
339 "id": 0,
|
|
|
340 "output_name": "output"
|
|
|
341 },
|
|
|
342 "paired|input1": {
|
|
|
343 "id": 9,
|
|
|
344 "output_name": "output_read1_file"
|
|
|
345 },
|
|
|
346 "paired|input2": {
|
|
|
347 "id": 9,
|
|
|
348 "output_name": "output_read2_file"
|
|
|
349 }
|
|
|
350 },
|
|
|
351 "inputs": [],
|
|
|
352 "name": "Map with BWA for Illumina",
|
|
|
353 "outputs": [
|
|
|
354 {
|
|
|
355 "name": "output",
|
|
|
356 "type": "sam"
|
|
|
357 }
|
|
|
358 ],
|
|
|
359 "position": {
|
|
|
360 "left": 1084.000244140625,
|
|
|
361 "top": 396
|
|
|
362 },
|
|
|
363 "post_job_actions": {},
|
|
|
364 "tool_errors": null,
|
|
|
365 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
366 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"__current_case__\\\": 0, \\\"source_select\\\": \\\"pre_set\\\"}\", \"suppressHeader\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
367 "tool_version": "1.2.3",
|
|
|
368 "type": "tool",
|
|
|
369 "user_outputs": []
|
|
|
370 },
|
|
|
371 "12": {
|
|
|
372 "annotation": "",
|
|
|
373 "id": 12,
|
|
|
374 "input_connections": {
|
|
|
375 "input_sam_file": {
|
|
|
376 "id": 10,
|
|
|
377 "output_name": "output"
|
|
|
378 }
|
|
|
379 },
|
|
|
380 "inputs": [],
|
|
|
381 "name": "filtersam_mapped_and_unique",
|
|
|
382 "outputs": [
|
|
|
383 {
|
|
|
384 "name": "output_file",
|
|
|
385 "type": "sam"
|
|
|
386 }
|
|
|
387 ],
|
|
|
388 "position": {
|
|
|
389 "left": 1348.000244140625,
|
|
|
390 "top": 211
|
|
|
391 },
|
|
|
392 "post_job_actions": {},
|
|
|
393 "tool_errors": null,
|
|
|
394 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/filtersam_mapped_and_unique/0.01",
|
|
|
395 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}",
|
|
|
396 "tool_version": "0.01",
|
|
|
397 "type": "tool",
|
|
|
398 "user_outputs": []
|
|
|
399 },
|
|
|
400 "13": {
|
|
|
401 "annotation": "",
|
|
|
402 "id": 13,
|
|
|
403 "input_connections": {
|
|
|
404 "input_sam_file": {
|
|
|
405 "id": 11,
|
|
|
406 "output_name": "output"
|
|
|
407 }
|
|
|
408 },
|
|
|
409 "inputs": [],
|
|
|
410 "name": "filtersam_mapped_and_unique",
|
|
|
411 "outputs": [
|
|
|
412 {
|
|
|
413 "name": "output_file",
|
|
|
414 "type": "sam"
|
|
|
415 }
|
|
|
416 ],
|
|
|
417 "position": {
|
|
|
418 "left": 1348.000244140625,
|
|
|
419 "top": 342
|
|
|
420 },
|
|
|
421 "post_job_actions": {},
|
|
|
422 "tool_errors": null,
|
|
|
423 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/filtersam_mapped_and_unique/0.01",
|
|
|
424 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input_sam_file\": \"null\"}",
|
|
|
425 "tool_version": "0.01",
|
|
|
426 "type": "tool",
|
|
|
427 "user_outputs": []
|
|
|
428 },
|
|
|
429 "14": {
|
|
|
430 "annotation": "",
|
|
|
431 "id": 14,
|
|
|
432 "input_connections": {
|
|
|
433 "source|input1": {
|
|
|
434 "id": 12,
|
|
|
435 "output_name": "output_file"
|
|
|
436 },
|
|
|
437 "source|ref_file": {
|
|
|
438 "id": 0,
|
|
|
439 "output_name": "output"
|
|
|
440 }
|
|
|
441 },
|
|
|
442 "inputs": [],
|
|
|
443 "name": "SAM-to-BAM",
|
|
|
444 "outputs": [
|
|
|
445 {
|
|
|
446 "name": "output1",
|
|
|
447 "type": "bam"
|
|
|
448 }
|
|
|
449 ],
|
|
|
450 "position": {
|
|
|
451 "left": 1676.000244140625,
|
|
|
452 "top": 211
|
|
|
453 },
|
|
|
454 "post_job_actions": {},
|
|
|
455 "tool_errors": null,
|
|
|
456 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
457 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
|
|
|
458 "tool_version": "1.1.4",
|
|
|
459 "type": "tool",
|
|
|
460 "user_outputs": []
|
|
|
461 },
|
|
|
462 "15": {
|
|
|
463 "annotation": "",
|
|
|
464 "id": 15,
|
|
|
465 "input_connections": {
|
|
|
466 "source|input1": {
|
|
|
467 "id": 13,
|
|
|
468 "output_name": "output_file"
|
|
|
469 },
|
|
|
470 "source|ref_file": {
|
|
|
471 "id": 0,
|
|
|
472 "output_name": "output"
|
|
|
473 }
|
|
|
474 },
|
|
|
475 "inputs": [],
|
|
|
476 "name": "SAM-to-BAM",
|
|
|
477 "outputs": [
|
|
|
478 {
|
|
|
479 "name": "output1",
|
|
|
480 "type": "bam"
|
|
|
481 }
|
|
|
482 ],
|
|
|
483 "position": {
|
|
|
484 "left": 1676.000244140625,
|
|
|
485 "top": 352
|
|
|
486 },
|
|
|
487 "post_job_actions": {},
|
|
|
488 "tool_errors": null,
|
|
|
489 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
490 "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
|
|
|
491 "tool_version": "1.1.4",
|
|
|
492 "type": "tool",
|
|
|
493 "user_outputs": []
|
|
|
494 },
|
|
|
495 "16": {
|
|
|
496 "annotation": "",
|
|
|
497 "id": 16,
|
|
|
498 "input_connections": {
|
|
|
499 "input1": {
|
|
|
500 "id": 14,
|
|
|
501 "output_name": "output1"
|
|
|
502 },
|
|
|
503 "input2": {
|
|
|
504 "id": 15,
|
|
|
505 "output_name": "output1"
|
|
|
506 }
|
|
|
507 },
|
|
|
508 "inputs": [],
|
|
|
509 "name": "Merge BAM Files",
|
|
|
510 "outputs": [
|
|
|
511 {
|
|
|
512 "name": "output1",
|
|
|
513 "type": "bam"
|
|
|
514 },
|
|
|
515 {
|
|
|
516 "name": "outlog",
|
|
|
517 "type": "txt"
|
|
|
518 }
|
|
|
519 ],
|
|
|
520 "position": {
|
|
|
521 "left": 1904.000244140625,
|
|
|
522 "top": 211
|
|
|
523 },
|
|
|
524 "post_job_actions": {},
|
|
|
525 "tool_errors": null,
|
|
|
526 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2",
|
|
|
527 "tool_state": "{\"input2\": \"null\", \"inputs\": \"[]\", \"input1\": \"null\", \"title\": \"\\\"merge bam\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mergeSD\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
528 "tool_version": "1.1.2",
|
|
|
529 "type": "tool",
|
|
|
530 "user_outputs": []
|
|
|
531 },
|
|
|
532 "17": {
|
|
|
533 "annotation": "",
|
|
|
534 "id": 17,
|
|
|
535 "input_connections": {
|
|
|
536 "reference_source|input_bams_0|input_bam": {
|
|
|
537 "id": 16,
|
|
|
538 "output_name": "output1"
|
|
|
539 },
|
|
|
540 "reference_source|ref_file": {
|
|
|
541 "id": 0,
|
|
|
542 "output_name": "output"
|
|
|
543 }
|
|
|
544 },
|
|
|
545 "inputs": [],
|
|
|
546 "name": "MPileup",
|
|
|
547 "outputs": [
|
|
|
548 {
|
|
|
549 "name": "output_mpileup",
|
|
|
550 "type": "pileup"
|
|
|
551 },
|
|
|
552 {
|
|
|
553 "name": "output_log",
|
|
|
554 "type": "txt"
|
|
|
555 }
|
|
|
556 ],
|
|
|
557 "position": {
|
|
|
558 "left": 2132.000244140625,
|
|
|
559 "top": 211
|
|
|
560 },
|
|
|
561 "post_job_actions": {},
|
|
|
562 "tool_errors": null,
|
|
|
563 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
|
|
|
564 "tool_state": "{\"__page__\": 0, \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"250\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"30\\\", \\\"disable_probabilistic_realignment\\\": \\\"False\\\", \\\"skip_anomalous_read_pairs\\\": \\\"False\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
565 "tool_version": "0.0.3",
|
|
|
566 "type": "tool",
|
|
|
567 "user_outputs": []
|
|
|
568 },
|
|
|
569 "18": {
|
|
|
570 "annotation": "",
|
|
|
571 "id": 18,
|
|
|
572 "input_connections": {
|
|
|
573 "input_file": {
|
|
|
574 "id": 17,
|
|
|
575 "output_name": "output_mpileup"
|
|
|
576 }
|
|
|
577 },
|
|
|
578 "inputs": [],
|
|
|
579 "name": "PileupVariant",
|
|
|
580 "outputs": [
|
|
|
581 {
|
|
|
582 "name": "output_file",
|
|
|
583 "type": "pileup"
|
|
|
584 }
|
|
|
585 ],
|
|
|
586 "position": {
|
|
|
587 "left": 2458.000244140625,
|
|
|
588 "top": 211
|
|
|
589 },
|
|
|
590 "post_job_actions": {},
|
|
|
591 "tool_errors": null,
|
|
|
592 "tool_id": "PileupVariant",
|
|
|
593 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
|
|
|
594 "tool_version": "0.01",
|
|
|
595 "type": "tool",
|
|
|
596 "user_outputs": []
|
|
|
597 },
|
|
|
598 "19": {
|
|
|
599 "annotation": "",
|
|
|
600 "id": 19,
|
|
|
601 "input_connections": {
|
|
|
602 "input_listA": {
|
|
|
603 "id": 18,
|
|
|
604 "output_name": "output_file"
|
|
|
605 },
|
|
|
606 "input_listB": {
|
|
|
607 "id": 3,
|
|
|
608 "output_name": "output"
|
|
|
609 }
|
|
|
610 },
|
|
|
611 "inputs": [],
|
|
|
612 "name": "listfiltering",
|
|
|
613 "outputs": [
|
|
|
614 {
|
|
|
615 "name": "output_file",
|
|
|
616 "type": "pileup"
|
|
|
617 }
|
|
|
618 ],
|
|
|
619 "position": {
|
|
|
620 "left": 2786.000244140625,
|
|
|
621 "top": 211
|
|
|
622 },
|
|
|
623 "post_job_actions": {},
|
|
|
624 "tool_errors": null,
|
|
|
625 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/listfiltering/0.01",
|
|
|
626 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}",
|
|
|
627 "tool_version": "0.01",
|
|
|
628 "type": "tool",
|
|
|
629 "user_outputs": []
|
|
|
630 },
|
|
|
631 "20": {
|
|
|
632 "annotation": "",
|
|
|
633 "id": 20,
|
|
|
634 "input_connections": {
|
|
|
635 "input_file": {
|
|
|
636 "id": 19,
|
|
|
637 "output_name": "output_file"
|
|
|
638 }
|
|
|
639 },
|
|
|
640 "inputs": [],
|
|
|
641 "name": "SplitFile2x",
|
|
|
642 "outputs": [
|
|
|
643 {
|
|
|
644 "name": "output_file1",
|
|
|
645 "type": "txt"
|
|
|
646 },
|
|
|
647 {
|
|
|
648 "name": "output_file2",
|
|
|
649 "type": "txt"
|
|
|
650 }
|
|
|
651 ],
|
|
|
652 "position": {
|
|
|
653 "left": 3114.000244140625,
|
|
|
654 "top": 211
|
|
|
655 },
|
|
|
656 "post_job_actions": {},
|
|
|
657 "tool_errors": null,
|
|
|
658 "tool_id": "SplitFile2x",
|
|
|
659 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"line_number\": \"\\\"4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
|
|
|
660 "tool_version": "0.01",
|
|
|
661 "type": "tool",
|
|
|
662 "user_outputs": []
|
|
|
663 },
|
|
|
664 "21": {
|
|
|
665 "annotation": "",
|
|
|
666 "id": 21,
|
|
|
667 "input_connections": {
|
|
|
668 "input_assembly_file": {
|
|
|
669 "id": 0,
|
|
|
670 "output_name": "output"
|
|
|
671 },
|
|
|
672 "input_variant_file": {
|
|
|
673 "id": 20,
|
|
|
674 "output_name": "output_file1"
|
|
|
675 }
|
|
|
676 },
|
|
|
677 "inputs": [],
|
|
|
678 "name": "extractseq",
|
|
|
679 "outputs": [
|
|
|
680 {
|
|
|
681 "name": "output_file",
|
|
|
682 "type": "fasta"
|
|
|
683 }
|
|
|
684 ],
|
|
|
685 "position": {
|
|
|
686 "left": 3442.000244140625,
|
|
|
687 "top": 211
|
|
|
688 },
|
|
|
689 "post_job_actions": {},
|
|
|
690 "tool_errors": null,
|
|
|
691 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/extractseq/0.03",
|
|
|
692 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
|
|
|
693 "tool_version": "0.03",
|
|
|
694 "type": "tool",
|
|
|
695 "user_outputs": []
|
|
|
696 },
|
|
|
697 "22": {
|
|
|
698 "annotation": "",
|
|
|
699 "id": 22,
|
|
|
700 "input_connections": {
|
|
|
701 "input_assembly_file": {
|
|
|
702 "id": 0,
|
|
|
703 "output_name": "output"
|
|
|
704 },
|
|
|
705 "input_variant_file": {
|
|
|
706 "id": 20,
|
|
|
707 "output_name": "output_file2"
|
|
|
708 }
|
|
|
709 },
|
|
|
710 "inputs": [],
|
|
|
711 "name": "extractseq",
|
|
|
712 "outputs": [
|
|
|
713 {
|
|
|
714 "name": "output_file",
|
|
|
715 "type": "fasta"
|
|
|
716 }
|
|
|
717 ],
|
|
|
718 "position": {
|
|
|
719 "left": 3442.000244140625,
|
|
|
720 "top": 386
|
|
|
721 },
|
|
|
722 "post_job_actions": {},
|
|
|
723 "tool_errors": null,
|
|
|
724 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/extractseq/0.03",
|
|
|
725 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
|
|
|
726 "tool_version": "0.03",
|
|
|
727 "type": "tool",
|
|
|
728 "user_outputs": []
|
|
|
729 },
|
|
|
730 "23": {
|
|
|
731 "annotation": "",
|
|
|
732 "id": 23,
|
|
|
733 "input_connections": {
|
|
|
734 "db_opts|histdb": {
|
|
|
735 "id": 7,
|
|
|
736 "output_name": "outfile"
|
|
|
737 },
|
|
|
738 "query": {
|
|
|
739 "id": 21,
|
|
|
740 "output_name": "output_file"
|
|
|
741 }
|
|
|
742 },
|
|
|
743 "inputs": [],
|
|
|
744 "name": "NCBI BLAST+ blastn",
|
|
|
745 "outputs": [
|
|
|
746 {
|
|
|
747 "name": "output1",
|
|
|
748 "type": "tabular"
|
|
|
749 }
|
|
|
750 ],
|
|
|
751 "position": {
|
|
|
752 "left": 3770.000244140625,
|
|
|
753 "top": 211
|
|
|
754 },
|
|
|
755 "post_job_actions": {},
|
|
|
756 "tool_errors": null,
|
|
|
757 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
|
|
|
758 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
|
|
|
759 "tool_version": "0.1.00",
|
|
|
760 "type": "tool",
|
|
|
761 "user_outputs": []
|
|
|
762 },
|
|
|
763 "24": {
|
|
|
764 "annotation": "",
|
|
|
765 "id": 24,
|
|
|
766 "input_connections": {
|
|
|
767 "db_opts|histdb": {
|
|
|
768 "id": 7,
|
|
|
769 "output_name": "outfile"
|
|
|
770 },
|
|
|
771 "query": {
|
|
|
772 "id": 22,
|
|
|
773 "output_name": "output_file"
|
|
|
774 }
|
|
|
775 },
|
|
|
776 "inputs": [],
|
|
|
777 "name": "NCBI BLAST+ blastn",
|
|
|
778 "outputs": [
|
|
|
779 {
|
|
|
780 "name": "output1",
|
|
|
781 "type": "tabular"
|
|
|
782 }
|
|
|
783 ],
|
|
|
784 "position": {
|
|
|
785 "left": 3770.000244140625,
|
|
|
786 "top": 352
|
|
|
787 },
|
|
|
788 "post_job_actions": {},
|
|
|
789 "tool_errors": null,
|
|
|
790 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
|
|
|
791 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"False\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"megablast\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"qstart\\\", \\\"qend\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"qseq\\\", \\\"sseq\\\"]}\", \"query\": \"null\"}",
|
|
|
792 "tool_version": "0.1.00",
|
|
|
793 "type": "tool",
|
|
|
794 "user_outputs": []
|
|
|
795 },
|
|
|
796 "25": {
|
|
|
797 "annotation": "",
|
|
|
798 "id": 25,
|
|
|
799 "input_connections": {
|
|
|
800 "input_blast_file": {
|
|
|
801 "id": 23,
|
|
|
802 "output_name": "output1"
|
|
|
803 },
|
|
|
804 "input_variant_file": {
|
|
|
805 "id": 20,
|
|
|
806 "output_name": "output_file1"
|
|
|
807 }
|
|
|
808 },
|
|
|
809 "inputs": [],
|
|
|
810 "name": "ParseBlastForUniqueMatch",
|
|
|
811 "outputs": [
|
|
|
812 {
|
|
|
813 "name": "output_file",
|
|
|
814 "type": "pileup"
|
|
|
815 }
|
|
|
816 ],
|
|
|
817 "position": {
|
|
|
818 "left": 4072.000228881836,
|
|
|
819 "top": 211
|
|
|
820 },
|
|
|
821 "post_job_actions": {},
|
|
|
822 "tool_errors": null,
|
|
|
823 "tool_id": "ParseBlastForUniqueMatch",
|
|
|
824 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
|
|
|
825 "tool_version": "0.01",
|
|
|
826 "type": "tool",
|
|
|
827 "user_outputs": []
|
|
|
828 },
|
|
|
829 "26": {
|
|
|
830 "annotation": "",
|
|
|
831 "id": 26,
|
|
|
832 "input_connections": {
|
|
|
833 "input_blast_file": {
|
|
|
834 "id": 24,
|
|
|
835 "output_name": "output1"
|
|
|
836 },
|
|
|
837 "input_variant_file": {
|
|
|
838 "id": 20,
|
|
|
839 "output_name": "output_file2"
|
|
|
840 }
|
|
|
841 },
|
|
|
842 "inputs": [],
|
|
|
843 "name": "ParseBlastForUniqueMatch",
|
|
|
844 "outputs": [
|
|
|
845 {
|
|
|
846 "name": "output_file",
|
|
|
847 "type": "pileup"
|
|
|
848 }
|
|
|
849 ],
|
|
|
850 "position": {
|
|
|
851 "left": 4072.000228881836,
|
|
|
852 "top": 420
|
|
|
853 },
|
|
|
854 "post_job_actions": {},
|
|
|
855 "tool_errors": null,
|
|
|
856 "tool_id": "ParseBlastForUniqueMatch",
|
|
|
857 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
|
|
|
858 "tool_version": "0.01",
|
|
|
859 "type": "tool",
|
|
|
860 "user_outputs": []
|
|
|
861 },
|
|
|
862 "27": {
|
|
|
863 "annotation": "",
|
|
|
864 "id": 27,
|
|
|
865 "input_connections": {
|
|
|
866 "input_file1": {
|
|
|
867 "id": 25,
|
|
|
868 "output_name": "output_file"
|
|
|
869 },
|
|
|
870 "input_file2": {
|
|
|
871 "id": 26,
|
|
|
872 "output_name": "output_file"
|
|
|
873 }
|
|
|
874 },
|
|
|
875 "inputs": [],
|
|
|
876 "name": "MergeFile2x",
|
|
|
877 "outputs": [
|
|
|
878 {
|
|
|
879 "name": "output_file",
|
|
|
880 "type": "txt"
|
|
|
881 }
|
|
|
882 ],
|
|
|
883 "position": {
|
|
|
884 "left": 4400.000228881836,
|
|
|
885 "top": 211
|
|
|
886 },
|
|
|
887 "post_job_actions": {},
|
|
|
888 "tool_errors": null,
|
|
|
889 "tool_id": "MergeFile2x",
|
|
|
890 "tool_state": "{\"out_format\": \"\\\"pileup\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file1\": \"null\", \"input_file2\": \"null\"}",
|
|
|
891 "tool_version": "0.01",
|
|
|
892 "type": "tool",
|
|
|
893 "user_outputs": []
|
|
|
894 },
|
|
|
895 "28": {
|
|
|
896 "annotation": "",
|
|
|
897 "id": 28,
|
|
|
898 "input_connections": {
|
|
|
899 "input_file": {
|
|
|
900 "id": 27,
|
|
|
901 "output_name": "output_file"
|
|
|
902 }
|
|
|
903 },
|
|
|
904 "inputs": [],
|
|
|
905 "name": "mpileupfilterandstat",
|
|
|
906 "outputs": [
|
|
|
907 {
|
|
|
908 "name": "output_file",
|
|
|
909 "type": "pileup"
|
|
|
910 },
|
|
|
911 {
|
|
|
912 "name": "log_file",
|
|
|
913 "type": "txt"
|
|
|
914 }
|
|
|
915 ],
|
|
|
916 "position": {
|
|
|
917 "left": 4728.000244140625,
|
|
|
918 "top": 211
|
|
|
919 },
|
|
|
920 "post_job_actions": {},
|
|
|
921 "tool_errors": null,
|
|
|
922 "tool_id": "mpileupfilterandstat",
|
|
|
923 "tool_state": "{\"__page__\": 0, \"stat\": \"{\\\"stat_dist_step\\\": \\\"50\\\", \\\"stat_min_depth_step\\\": \\\"2\\\", \\\"stat_max_depth_max\\\": \\\"200\\\", \\\"stat_min_depth_max\\\": \\\"10\\\", \\\"stat_freq_max\\\": \\\"1.0\\\", \\\"stat_min_depth_min\\\": \\\"2\\\", \\\"stat_max_depth_min\\\": \\\"100\\\", \\\"do_stat\\\": \\\"YES\\\", \\\"stat_dist_min\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"stat_max_depth_step\\\": \\\"100\\\", \\\"stat_dist_max\\\": \\\"50\\\", \\\"stat_freq_step\\\": \\\"0.1\\\", \\\"stat_freq_min\\\": \\\"0.8\\\"}\", \"input_file\": \"null\", \"min_frequency\": \"\\\"0.8\\\"\", \"do_stat\": \"\\\"YES\\\"\", \"min_depth\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"min_forward_and_reverse\": \"\\\"0\\\"\", \"max_depth\": \"\\\"100\\\"\", \"min_distance\": \"\\\"0\\\"\"}",
|
|
|
924 "tool_version": "0.08",
|
|
|
925 "type": "tool",
|
|
|
926 "user_outputs": []
|
|
|
927 },
|
|
|
928 "29": {
|
|
|
929 "annotation": "",
|
|
|
930 "id": 29,
|
|
|
931 "input_connections": {
|
|
|
932 "input_blast_filtered_part1_file": {
|
|
|
933 "id": 25,
|
|
|
934 "output_name": "output_file"
|
|
|
935 },
|
|
|
936 "input_blast_filtered_part2_file": {
|
|
|
937 "id": 26,
|
|
|
938 "output_name": "output_file"
|
|
|
939 },
|
|
|
940 "input_list_filtered_file": {
|
|
|
941 "id": 19,
|
|
|
942 "output_name": "output_file"
|
|
|
943 },
|
|
|
944 "input_mpileup_variant_file": {
|
|
|
945 "id": 18,
|
|
|
946 "output_name": "output_file"
|
|
|
947 },
|
|
|
948 "input_read1_part1_trimmed_file": {
|
|
|
949 "id": 8,
|
|
|
950 "output_name": "output_read1_file"
|
|
|
951 },
|
|
|
952 "input_read1_part2_trimmed_file": {
|
|
|
953 "id": 9,
|
|
|
954 "output_name": "output_read1_file"
|
|
|
955 },
|
|
|
956 "input_read1_row_file": {
|
|
|
957 "id": 1,
|
|
|
958 "output_name": "output"
|
|
|
959 },
|
|
|
960 "input_read2_part1_trimmed_file": {
|
|
|
961 "id": 8,
|
|
|
962 "output_name": "output_read2_file"
|
|
|
963 },
|
|
|
964 "input_read2_part2_trimmed_file": {
|
|
|
965 "id": 9,
|
|
|
966 "output_name": "output_read2_file"
|
|
|
967 },
|
|
|
968 "input_read2_row_file": {
|
|
|
969 "id": 2,
|
|
|
970 "output_name": "output"
|
|
|
971 },
|
|
|
972 "input_sam_filtered_part1_file": {
|
|
|
973 "id": 12,
|
|
|
974 "output_name": "output_file"
|
|
|
975 },
|
|
|
976 "input_sam_filtered_part2_file": {
|
|
|
977 "id": 13,
|
|
|
978 "output_name": "output_file"
|
|
|
979 },
|
|
|
980 "input_sam_row_part1_file": {
|
|
|
981 "id": 10,
|
|
|
982 "output_name": "output"
|
|
|
983 },
|
|
|
984 "input_sam_row_part2_file": {
|
|
|
985 "id": 11,
|
|
|
986 "output_name": "output"
|
|
|
987 },
|
|
|
988 "input_snp_selected_file": {
|
|
|
989 "id": 28,
|
|
|
990 "output_name": "output_file"
|
|
|
991 }
|
|
|
992 },
|
|
|
993 "inputs": [],
|
|
|
994 "name": "rapsosnp_stats2x",
|
|
|
995 "outputs": [
|
|
|
996 {
|
|
|
997 "name": "output_file",
|
|
|
998 "type": "txt"
|
|
|
999 }
|
|
|
1000 ],
|
|
|
1001 "position": {
|
|
|
1002 "left": 5056.000244140625,
|
|
|
1003 "top": 211
|
|
|
1004 },
|
|
|
1005 "post_job_actions": {},
|
|
|
1006 "tool_errors": null,
|
|
|
1007 "tool_id": "rapsosnp_stats2x",
|
|
|
1008 "tool_state": "{\"input_blast_filtered_part1_file\": \"null\", \"input_blast_filtered_part2_file\": \"null\", \"input_sam_row_part2_file\": \"null\", \"input_read1_part1_trimmed_file\": \"null\", \"__page__\": 0, \"input_list_filtered_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_read2_row_file\": \"null\", \"input_mpileup_variant_file\": \"null\", \"input_read2_part1_trimmed_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_sam_row_part1_file\": \"null\", \"input_sam_filtered_part2_file\": \"null\", \"input_read2_part2_trimmed_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_read1_part2_trimmed_file\": \"null\", \"input_sam_filtered_part1_file\": \"null\"}",
|
|
|
1009 "tool_version": "0.01",
|
|
|
1010 "type": "tool",
|
|
|
1011 "user_outputs": []
|
|
|
1012 }
|
|
|
1013 }
|
|
|
1014 } |
