Mercurial > repos > urgi-team > gandalfworkflow
comparison Galaxy-Workflow-workflow_gandalf_2_sets.ga @ 6:7557b71a92e7 draft
Uploaded
author | urgi-team |
---|---|
date | Wed, 25 Nov 2015 09:34:17 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
5:33391dfcfc07 | 6:7557b71a92e7 |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "workflow gandalf 2 sets", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "Reference genome" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 248, | |
21 "top": 874 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"Reference genome\"}", | |
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": "genome 1 reads forward" | |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
41 "outputs": [], | |
42 "position": { | |
43 "left": 280, | |
44 "top": 979 | |
45 }, | |
46 "tool_errors": null, | |
47 "tool_id": null, | |
48 "tool_state": "{\"name\": \"genome 1 reads forward\"}", | |
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": "genome 1 reads reverse" | |
61 } | |
62 ], | |
63 "name": "Input dataset", | |
64 "outputs": [], | |
65 "position": { | |
66 "left": 288, | |
67 "top": 1048 | |
68 }, | |
69 "tool_errors": null, | |
70 "tool_id": null, | |
71 "tool_state": "{\"name\": \"genome 1 reads reverse\"}", | |
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": "genome 2 reads forward" | |
84 } | |
85 ], | |
86 "name": "Input dataset", | |
87 "outputs": [], | |
88 "position": { | |
89 "left": 346, | |
90 "top": 1206 | |
91 }, | |
92 "tool_errors": null, | |
93 "tool_id": null, | |
94 "tool_state": "{\"name\": \"genome 2 reads forward\"}", | |
95 "tool_version": null, | |
96 "type": "data_input", | |
97 "user_outputs": [] | |
98 }, | |
99 "4": { | |
100 "annotation": "", | |
101 "id": 4, | |
102 "input_connections": {}, | |
103 "inputs": [ | |
104 { | |
105 "description": "", | |
106 "name": "genome 2 reads reverse" | |
107 } | |
108 ], | |
109 "name": "Input dataset", | |
110 "outputs": [], | |
111 "position": { | |
112 "left": 344, | |
113 "top": 1277 | |
114 }, | |
115 "tool_errors": null, | |
116 "tool_id": null, | |
117 "tool_state": "{\"name\": \"genome 2 reads reverse\"}", | |
118 "tool_version": null, | |
119 "type": "data_input", | |
120 "user_outputs": [] | |
121 }, | |
122 "5": { | |
123 "annotation": "", | |
124 "id": 5, | |
125 "input_connections": { | |
126 "input_file": { | |
127 "id": 0, | |
128 "output_name": "output" | |
129 } | |
130 }, | |
131 "inputs": [], | |
132 "name": "mdust", | |
133 "outputs": [ | |
134 { | |
135 "name": "output_masked_fasta", | |
136 "type": "fasta" | |
137 }, | |
138 { | |
139 "name": "output_tab", | |
140 "type": "tabular" | |
141 }, | |
142 { | |
143 "name": "output_bed", | |
144 "type": "bed" | |
145 } | |
146 ], | |
147 "position": { | |
148 "left": 1419, | |
149 "top": 230 | |
150 }, | |
151 "post_job_actions": { | |
152 "HideDatasetActionoutput_bed": { | |
153 "action_arguments": {}, | |
154 "action_type": "HideDatasetAction", | |
155 "output_name": "output_bed" | |
156 }, | |
157 "HideDatasetActionoutput_masked_fasta": { | |
158 "action_arguments": {}, | |
159 "action_type": "HideDatasetAction", | |
160 "output_name": "output_masked_fasta" | |
161 }, | |
162 "HideDatasetActionoutput_tab": { | |
163 "action_arguments": {}, | |
164 "action_type": "HideDatasetAction", | |
165 "output_name": "output_tab" | |
166 }, | |
167 "RenameDatasetActionoutput_bed": { | |
168 "action_arguments": { | |
169 "newname": "#{input_file | basename}.bed" | |
170 }, | |
171 "action_type": "RenameDatasetAction", | |
172 "output_name": "output_bed" | |
173 } | |
174 }, | |
175 "tool_errors": null, | |
176 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mdust/mdust/1.0", | |
177 "tool_state": "{\"cutoff\": \"\\\"28\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"wsize\": \"\\\"3\\\"\", \"output_type\": \"{\\\"output_type_selector\\\": \\\"bed\\\", \\\"__current_case__\\\": 1}\", \"masking_letter\": \"{\\\"masking_letter_selector\\\": \\\"N\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
178 "tool_version": "1.0", | |
179 "type": "tool", | |
180 "user_outputs": [] | |
181 }, | |
182 "6": { | |
183 "annotation": "", | |
184 "id": 6, | |
185 "input_connections": { | |
186 "fastq_input|fastq_input1": { | |
187 "id": 1, | |
188 "output_name": "output" | |
189 }, | |
190 "fastq_input|fastq_input2": { | |
191 "id": 2, | |
192 "output_name": "output" | |
193 }, | |
194 "reference_source|ref_file": { | |
195 "id": 0, | |
196 "output_name": "output" | |
197 } | |
198 }, | |
199 "inputs": [], | |
200 "name": "Map with BWA-MEM", | |
201 "outputs": [ | |
202 { | |
203 "name": "bam_output", | |
204 "type": "bam" | |
205 } | |
206 ], | |
207 "position": { | |
208 "left": 758, | |
209 "top": 929 | |
210 }, | |
211 "post_job_actions": { | |
212 "HideDatasetActionbam_output": { | |
213 "action_arguments": {}, | |
214 "action_type": "HideDatasetAction", | |
215 "output_name": "bam_output" | |
216 }, | |
217 "RenameDatasetActionbam_output": { | |
218 "action_arguments": { | |
219 "newname": "#{fastq_input1 | basename}.bam" | |
220 }, | |
221 "action_type": "RenameDatasetAction", | |
222 "output_name": "bam_output" | |
223 } | |
224 }, | |
225 "tool_errors": null, | |
226 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", | |
227 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
228 "tool_version": "0.4.1", | |
229 "type": "tool", | |
230 "user_outputs": [] | |
231 }, | |
232 "7": { | |
233 "annotation": "", | |
234 "id": 7, | |
235 "input_connections": { | |
236 "fastq_input|fastq_input1": { | |
237 "id": 3, | |
238 "output_name": "output" | |
239 }, | |
240 "fastq_input|fastq_input2": { | |
241 "id": 4, | |
242 "output_name": "output" | |
243 }, | |
244 "reference_source|ref_file": { | |
245 "id": 0, | |
246 "output_name": "output" | |
247 } | |
248 }, | |
249 "inputs": [], | |
250 "name": "Map with BWA-MEM", | |
251 "outputs": [ | |
252 { | |
253 "name": "bam_output", | |
254 "type": "bam" | |
255 } | |
256 ], | |
257 "position": { | |
258 "left": 758, | |
259 "top": 1114 | |
260 }, | |
261 "post_job_actions": { | |
262 "HideDatasetActionbam_output": { | |
263 "action_arguments": {}, | |
264 "action_type": "HideDatasetAction", | |
265 "output_name": "bam_output" | |
266 }, | |
267 "RenameDatasetActionbam_output": { | |
268 "action_arguments": { | |
269 "newname": "#{fastq_input1 | basename}.bam" | |
270 }, | |
271 "action_type": "RenameDatasetAction", | |
272 "output_name": "bam_output" | |
273 } | |
274 }, | |
275 "tool_errors": null, | |
276 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.1", | |
277 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"SM\\\": \\\"SMstrand1\\\", \\\"__current_case__\\\": 1}, \\\"CN\\\": \\\"CNexemple\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"LB\\\": \\\"LB1\\\", \\\"__current_case__\\\": 1}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"False\\\", \\\"ID\\\": \\\"IDstrain1\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"full\\\", \\\"algorithmic_options\\\": {\\\"algorithmic_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}, \\\"io_options\\\": {\\\"a\\\": \\\"False\\\", \\\"C\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"h\\\": \\\"5\\\", \\\"M\\\": \\\"True\\\", \\\"T\\\": \\\"30\\\", \\\"io_options_selector\\\": \\\"set\\\", \\\"V\\\": \\\"False\\\", \\\"Y\\\": \\\"False\\\"}, \\\"__current_case__\\\": 2, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
278 "tool_version": "0.4.1", | |
279 "type": "tool", | |
280 "user_outputs": [] | |
281 }, | |
282 "8": { | |
283 "annotation": "", | |
284 "id": 8, | |
285 "input_connections": { | |
286 "input1": { | |
287 "id": 6, | |
288 "output_name": "bam_output" | |
289 } | |
290 }, | |
291 "inputs": [], | |
292 "name": "mapQfilter", | |
293 "outputs": [ | |
294 { | |
295 "name": "output1", | |
296 "type": "bam" | |
297 } | |
298 ], | |
299 "position": { | |
300 "left": 1086, | |
301 "top": 593 | |
302 }, | |
303 "post_job_actions": { | |
304 "HideDatasetActionoutput1": { | |
305 "action_arguments": {}, | |
306 "action_type": "HideDatasetAction", | |
307 "output_name": "output1" | |
308 }, | |
309 "RenameDatasetActionoutput1": { | |
310 "action_arguments": { | |
311 "newname": "#{input1 | basename}.filteredbam" | |
312 }, | |
313 "action_type": "RenameDatasetAction", | |
314 "output_name": "output1" | |
315 } | |
316 }, | |
317 "tool_errors": null, | |
318 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", | |
319 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
320 "tool_version": "1.0", | |
321 "type": "tool", | |
322 "user_outputs": [] | |
323 }, | |
324 "9": { | |
325 "annotation": "", | |
326 "id": 9, | |
327 "input_connections": { | |
328 "input1": { | |
329 "id": 7, | |
330 "output_name": "bam_output" | |
331 } | |
332 }, | |
333 "inputs": [], | |
334 "name": "mapQfilter", | |
335 "outputs": [ | |
336 { | |
337 "name": "output1", | |
338 "type": "bam" | |
339 } | |
340 ], | |
341 "position": { | |
342 "left": 1086, | |
343 "top": 706 | |
344 }, | |
345 "post_job_actions": { | |
346 "HideDatasetActionoutput1": { | |
347 "action_arguments": {}, | |
348 "action_type": "HideDatasetAction", | |
349 "output_name": "output1" | |
350 }, | |
351 "RenameDatasetActionoutput1": { | |
352 "action_arguments": { | |
353 "newname": "#{input1 | basename}.filteredbam" | |
354 }, | |
355 "action_type": "RenameDatasetAction", | |
356 "output_name": "output1" | |
357 } | |
358 }, | |
359 "tool_errors": null, | |
360 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/mapqfilter/mapQfilter/1.0", | |
361 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"mapQ\": \"\\\"30\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
362 "tool_version": "1.0", | |
363 "type": "tool", | |
364 "user_outputs": [] | |
365 }, | |
366 "10": { | |
367 "annotation": "", | |
368 "id": 10, | |
369 "input_connections": { | |
370 "inputFile": { | |
371 "id": 8, | |
372 "output_name": "output1" | |
373 } | |
374 }, | |
375 "inputs": [], | |
376 "name": "MarkDuplicates", | |
377 "outputs": [ | |
378 { | |
379 "name": "metrics_file", | |
380 "type": "txt" | |
381 }, | |
382 { | |
383 "name": "outFile", | |
384 "type": "bam" | |
385 } | |
386 ], | |
387 "position": { | |
388 "left": 1314, | |
389 "top": 593 | |
390 }, | |
391 "post_job_actions": { | |
392 "HideDatasetActionmetrics_file": { | |
393 "action_arguments": {}, | |
394 "action_type": "HideDatasetAction", | |
395 "output_name": "metrics_file" | |
396 }, | |
397 "HideDatasetActionoutFile": { | |
398 "action_arguments": {}, | |
399 "action_type": "HideDatasetAction", | |
400 "output_name": "outFile" | |
401 }, | |
402 "RenameDatasetActionoutFile": { | |
403 "action_arguments": { | |
404 "newname": "#{inputFile | basename}.markedBAM" | |
405 }, | |
406 "action_type": "RenameDatasetAction", | |
407 "output_name": "outFile" | |
408 } | |
409 }, | |
410 "tool_errors": null, | |
411 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", | |
412 "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", | |
413 "tool_version": "1.126.0", | |
414 "type": "tool", | |
415 "user_outputs": [] | |
416 }, | |
417 "11": { | |
418 "annotation": "", | |
419 "id": 11, | |
420 "input_connections": { | |
421 "inputFile": { | |
422 "id": 9, | |
423 "output_name": "output1" | |
424 } | |
425 }, | |
426 "inputs": [], | |
427 "name": "MarkDuplicates", | |
428 "outputs": [ | |
429 { | |
430 "name": "metrics_file", | |
431 "type": "txt" | |
432 }, | |
433 { | |
434 "name": "outFile", | |
435 "type": "bam" | |
436 } | |
437 ], | |
438 "position": { | |
439 "left": 1314, | |
440 "top": 751 | |
441 }, | |
442 "post_job_actions": { | |
443 "HideDatasetActionmetrics_file": { | |
444 "action_arguments": {}, | |
445 "action_type": "HideDatasetAction", | |
446 "output_name": "metrics_file" | |
447 }, | |
448 "HideDatasetActionoutFile": { | |
449 "action_arguments": {}, | |
450 "action_type": "HideDatasetAction", | |
451 "output_name": "outFile" | |
452 }, | |
453 "RenameDatasetActionoutFile": { | |
454 "action_arguments": { | |
455 "newname": "#{inputFile | basename}.markedBAM" | |
456 }, | |
457 "action_type": "RenameDatasetAction", | |
458 "output_name": "outFile" | |
459 } | |
460 }, | |
461 "tool_errors": null, | |
462 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0", | |
463 "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"True\\\"\", \"read_name_regex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"validation_stringency\": \"\\\"LENIENT\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", | |
464 "tool_version": "1.126.0", | |
465 "type": "tool", | |
466 "user_outputs": [] | |
467 }, | |
468 "12": { | |
469 "annotation": "", | |
470 "id": 12, | |
471 "input_connections": { | |
472 "input_bams_0|input_bam": { | |
473 "id": 10, | |
474 "output_name": "outFile" | |
475 }, | |
476 "reference_source|ref_file": { | |
477 "id": 0, | |
478 "output_name": "output" | |
479 } | |
480 }, | |
481 "inputs": [], | |
482 "name": "Freebayes4Workflow", | |
483 "outputs": [ | |
484 { | |
485 "name": "output_vcf_default", | |
486 "type": "vcf" | |
487 }, | |
488 { | |
489 "name": "output_vcf_firstBAM", | |
490 "type": "vcf" | |
491 }, | |
492 { | |
493 "name": "output_vcf_rename", | |
494 "type": "vcf" | |
495 }, | |
496 { | |
497 "name": "output_failed_alleles_bed", | |
498 "type": "bed" | |
499 }, | |
500 { | |
501 "name": "output_trace", | |
502 "type": "txt" | |
503 } | |
504 ], | |
505 "position": { | |
506 "left": 1642, | |
507 "top": 593 | |
508 }, | |
509 "post_job_actions": { | |
510 "HideDatasetActionoutput_failed_alleles_bed": { | |
511 "action_arguments": {}, | |
512 "action_type": "HideDatasetAction", | |
513 "output_name": "output_failed_alleles_bed" | |
514 }, | |
515 "HideDatasetActionoutput_trace": { | |
516 "action_arguments": {}, | |
517 "action_type": "HideDatasetAction", | |
518 "output_name": "output_trace" | |
519 }, | |
520 "HideDatasetActionoutput_vcf_default": { | |
521 "action_arguments": {}, | |
522 "action_type": "HideDatasetAction", | |
523 "output_name": "output_vcf_default" | |
524 }, | |
525 "HideDatasetActionoutput_vcf_firstBAM": { | |
526 "action_arguments": {}, | |
527 "action_type": "HideDatasetAction", | |
528 "output_name": "output_vcf_firstBAM" | |
529 }, | |
530 "HideDatasetActionoutput_vcf_rename": { | |
531 "action_arguments": {}, | |
532 "action_type": "HideDatasetAction", | |
533 "output_name": "output_vcf_rename" | |
534 } | |
535 }, | |
536 "tool_errors": null, | |
537 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", | |
538 "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", | |
539 "tool_version": "0.5", | |
540 "type": "tool", | |
541 "user_outputs": [] | |
542 }, | |
543 "13": { | |
544 "annotation": "", | |
545 "id": 13, | |
546 "input_connections": { | |
547 "input1": { | |
548 "id": 10, | |
549 "output_name": "outFile" | |
550 } | |
551 }, | |
552 "inputs": [], | |
553 "name": "flagstat", | |
554 "outputs": [ | |
555 { | |
556 "name": "output1", | |
557 "type": "txt" | |
558 } | |
559 ], | |
560 "position": { | |
561 "left": 1642, | |
562 "top": 1125 | |
563 }, | |
564 "post_job_actions": { | |
565 "HideDatasetActionoutput1": { | |
566 "action_arguments": {}, | |
567 "action_type": "HideDatasetAction", | |
568 "output_name": "output1" | |
569 }, | |
570 "RenameDatasetActionoutput1": { | |
571 "action_arguments": { | |
572 "newname": "#{inupt1| basename}.stats" | |
573 }, | |
574 "action_type": "RenameDatasetAction", | |
575 "output_name": "output1" | |
576 } | |
577 }, | |
578 "tool_errors": null, | |
579 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", | |
580 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\"}", | |
581 "tool_version": "1.0.1", | |
582 "type": "tool", | |
583 "user_outputs": [] | |
584 }, | |
585 "14": { | |
586 "annotation": "", | |
587 "id": 14, | |
588 "input_connections": { | |
589 "input_bams_0|input_bam": { | |
590 "id": 11, | |
591 "output_name": "outFile" | |
592 }, | |
593 "reference_source|ref_file": { | |
594 "id": 0, | |
595 "output_name": "output" | |
596 } | |
597 }, | |
598 "inputs": [], | |
599 "name": "Freebayes4Workflow", | |
600 "outputs": [ | |
601 { | |
602 "name": "output_vcf_default", | |
603 "type": "vcf" | |
604 }, | |
605 { | |
606 "name": "output_vcf_firstBAM", | |
607 "type": "vcf" | |
608 }, | |
609 { | |
610 "name": "output_vcf_rename", | |
611 "type": "vcf" | |
612 }, | |
613 { | |
614 "name": "output_failed_alleles_bed", | |
615 "type": "bed" | |
616 }, | |
617 { | |
618 "name": "output_trace", | |
619 "type": "txt" | |
620 } | |
621 ], | |
622 "position": { | |
623 "left": 1776, | |
624 "top": 1195 | |
625 }, | |
626 "post_job_actions": { | |
627 "HideDatasetActionoutput_failed_alleles_bed": { | |
628 "action_arguments": {}, | |
629 "action_type": "HideDatasetAction", | |
630 "output_name": "output_failed_alleles_bed" | |
631 }, | |
632 "HideDatasetActionoutput_trace": { | |
633 "action_arguments": {}, | |
634 "action_type": "HideDatasetAction", | |
635 "output_name": "output_trace" | |
636 }, | |
637 "HideDatasetActionoutput_vcf_default": { | |
638 "action_arguments": {}, | |
639 "action_type": "HideDatasetAction", | |
640 "output_name": "output_vcf_default" | |
641 }, | |
642 "HideDatasetActionoutput_vcf_firstBAM": { | |
643 "action_arguments": {}, | |
644 "action_type": "HideDatasetAction", | |
645 "output_name": "output_vcf_firstBAM" | |
646 }, | |
647 "HideDatasetActionoutput_vcf_rename": { | |
648 "action_arguments": {}, | |
649 "action_type": "HideDatasetAction", | |
650 "output_name": "output_vcf_rename" | |
651 } | |
652 }, | |
653 "tool_errors": null, | |
654 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/freebayes4workflow/freebayes4workflow/0.5", | |
655 "tool_state": "{\"__page__\": 0, \"input_bams\": \"[{\\\"__index__\\\": 0, \\\"input_bam\\\": null}]\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"rename_output\": \"{\\\"rename_output_selector\\\": \\\"firstBAM\\\", \\\"__current_case__\\\": 1}\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"full\\\", \\\"allele_scope\\\": {\\\"no_partial_observations\\\": \\\"False\\\", \\\"I\\\": \\\"False\\\", \\\"n\\\": \\\"0\\\", \\\"min_repeat_length\\\": \\\"5\\\", \\\"i\\\": \\\"False\\\", \\\"min_repeat_entropy\\\": \\\"0\\\", \\\"u\\\": \\\"True\\\", \\\"__current_case__\\\": 0, \\\"X\\\": \\\"True\\\", \\\"haplotype_length\\\": \\\"3\\\", \\\"allele_scope_selector\\\": \\\"True\\\"}, \\\"reporting\\\": {\\\"reporting_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"genotype_likelihoods\\\": {\\\"genotype_likelihoods_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"O\\\": \\\"False\\\", \\\"population_model\\\": {\\\"population_model_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"reference_allele\\\": {\\\"reference_allele_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"optional_inputs\\\": {\\\"A\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"populations\\\": null, \\\"optional_inputs_selector\\\": \\\"True\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_monomorphic\\\": \\\"True\\\", \\\"observation_bias\\\": null, \\\"contamination_estimates\\\": null, \\\"samples\\\": null, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"haplotype_basis_alleles\\\": null}, \\\"__current_case__\\\": 0, \\\"population_mappability_priors\\\": {\\\"population_mappability_priors_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"input_filters\\\": {\\\"input_filters_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"algorithmic_features\\\": {\\\"algorithmic_features_selector\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"target_limit_type\": \"{\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}\"}", | |
656 "tool_version": "0.5", | |
657 "type": "tool", | |
658 "user_outputs": [] | |
659 }, | |
660 "15": { | |
661 "annotation": "", | |
662 "id": 15, | |
663 "input_connections": { | |
664 "input1": { | |
665 "id": 11, | |
666 "output_name": "outFile" | |
667 } | |
668 }, | |
669 "inputs": [], | |
670 "name": "flagstat", | |
671 "outputs": [ | |
672 { | |
673 "name": "output1", | |
674 "type": "txt" | |
675 } | |
676 ], | |
677 "position": { | |
678 "left": 1642, | |
679 "top": 1770 | |
680 }, | |
681 "post_job_actions": { | |
682 "HideDatasetActionoutput1": { | |
683 "action_arguments": {}, | |
684 "action_type": "HideDatasetAction", | |
685 "output_name": "output1" | |
686 }, | |
687 "RenameDatasetActionoutput1": { | |
688 "action_arguments": { | |
689 "newname": "#{inupt1| basename}.stats" | |
690 }, | |
691 "action_type": "RenameDatasetAction", | |
692 "output_name": "output1" | |
693 } | |
694 }, | |
695 "tool_errors": null, | |
696 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1", | |
697 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\"}", | |
698 "tool_version": "1.0.1", | |
699 "type": "tool", | |
700 "user_outputs": [] | |
701 }, | |
702 "16": { | |
703 "annotation": "", | |
704 "id": 16, | |
705 "input_connections": { | |
706 "BedFile_List|BedFiles_0|inputBed": { | |
707 "id": 5, | |
708 "output_name": "output_bed" | |
709 }, | |
710 "inputVCF": { | |
711 "id": 12, | |
712 "output_name": "output_vcf_firstBAM" | |
713 } | |
714 }, | |
715 "inputs": [], | |
716 "name": "VCFFiltering", | |
717 "outputs": [ | |
718 { | |
719 "name": "outputVCF", | |
720 "type": "vcf" | |
721 }, | |
722 { | |
723 "name": "output_html", | |
724 "type": "html" | |
725 } | |
726 ], | |
727 "position": { | |
728 "left": 1970, | |
729 "top": 593 | |
730 }, | |
731 "post_job_actions": { | |
732 "HideDatasetActionoutputVCF": { | |
733 "action_arguments": {}, | |
734 "action_type": "HideDatasetAction", | |
735 "output_name": "outputVCF" | |
736 }, | |
737 "HideDatasetActionoutput_html": { | |
738 "action_arguments": {}, | |
739 "action_type": "HideDatasetAction", | |
740 "output_name": "output_html" | |
741 }, | |
742 "RenameDatasetActionoutputVCF": { | |
743 "action_arguments": { | |
744 "newname": "#{inputVCF | basename}.filteredVCF" | |
745 }, | |
746 "action_type": "RenameDatasetAction", | |
747 "output_name": "outputVCF" | |
748 }, | |
749 "RenameDatasetActionoutput_html": { | |
750 "action_arguments": { | |
751 "newname": "#{inputVCF | basename}.VCFFiltering.graphs" | |
752 }, | |
753 "action_type": "RenameDatasetAction", | |
754 "output_name": "output_html" | |
755 } | |
756 }, | |
757 "tool_errors": null, | |
758 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", | |
759 "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
760 "tool_version": "0.01", | |
761 "type": "tool", | |
762 "user_outputs": [] | |
763 }, | |
764 "17": { | |
765 "annotation": "", | |
766 "id": 17, | |
767 "input_connections": { | |
768 "BedFile_List|BedFiles_0|inputBed": { | |
769 "id": 5, | |
770 "output_name": "output_bed" | |
771 }, | |
772 "inputVCF": { | |
773 "id": 14, | |
774 "output_name": "output_vcf_firstBAM" | |
775 } | |
776 }, | |
777 "inputs": [], | |
778 "name": "VCFFiltering", | |
779 "outputs": [ | |
780 { | |
781 "name": "outputVCF", | |
782 "type": "vcf" | |
783 }, | |
784 { | |
785 "name": "output_html", | |
786 "type": "html" | |
787 } | |
788 ], | |
789 "position": { | |
790 "left": 1970, | |
791 "top": 778 | |
792 }, | |
793 "post_job_actions": { | |
794 "HideDatasetActionoutputVCF": { | |
795 "action_arguments": {}, | |
796 "action_type": "HideDatasetAction", | |
797 "output_name": "outputVCF" | |
798 }, | |
799 "HideDatasetActionoutput_html": { | |
800 "action_arguments": {}, | |
801 "action_type": "HideDatasetAction", | |
802 "output_name": "output_html" | |
803 }, | |
804 "RenameDatasetActionoutputVCF": { | |
805 "action_arguments": { | |
806 "newname": "#{inputVCF | basename}.filteredVCF" | |
807 }, | |
808 "action_type": "RenameDatasetAction", | |
809 "output_name": "outputVCF" | |
810 }, | |
811 "RenameDatasetActionoutput_html": { | |
812 "action_arguments": { | |
813 "newname": "#{inputVCF | basename}.VCFFiltering.graphs" | |
814 }, | |
815 "action_type": "RenameDatasetAction", | |
816 "output_name": "output_html" | |
817 } | |
818 }, | |
819 "tool_errors": null, | |
820 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", | |
821 "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", | |
822 "tool_version": "0.01", | |
823 "type": "tool", | |
824 "user_outputs": [] | |
825 }, | |
826 "18": { | |
827 "annotation": "", | |
828 "id": 18, | |
829 "input_connections": { | |
830 "VCFFile_0|inputStrainVCF": { | |
831 "id": 16, | |
832 "output_name": "outputVCF" | |
833 }, | |
834 "VCFFile_1|inputStrainVCF": { | |
835 "id": 17, | |
836 "output_name": "outputVCF" | |
837 }, | |
838 "inputFasta": { | |
839 "id": 0, | |
840 "output_name": "output" | |
841 } | |
842 }, | |
843 "inputs": [], | |
844 "name": "VCFStorage", | |
845 "outputs": [ | |
846 { | |
847 "name": "outputVCFStorage", | |
848 "type": "tabular" | |
849 } | |
850 ], | |
851 "position": { | |
852 "left": 2298, | |
853 "top": 593 | |
854 }, | |
855 "post_job_actions": { | |
856 "HideDatasetActionoutputVCFStorage": { | |
857 "action_arguments": {}, | |
858 "action_type": "HideDatasetAction", | |
859 "output_name": "outputVCFStorage" | |
860 }, | |
861 "RenameDatasetActionoutputVCFStorage": { | |
862 "action_arguments": { | |
863 "newname": "#{inputFasta | basename}.matrix" | |
864 }, | |
865 "action_type": "RenameDatasetAction", | |
866 "output_name": "outputVCFStorage" | |
867 } | |
868 }, | |
869 "tool_errors": null, | |
870 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01", | |
871 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"VCFFile\": \"[{\\\"strainName\\\": \\\"strain1\\\", \\\"__index__\\\": 0, \\\"inputStrainVCF\\\": null}, {\\\"strainName\\\": \\\"strain2\\\", \\\"__index__\\\": 1, \\\"inputStrainVCF\\\": null}]\", \"inputFasta\": \"null\"}", | |
872 "tool_version": "0.01", | |
873 "type": "tool", | |
874 "user_outputs": [] | |
875 }, | |
876 "19": { | |
877 "annotation": "", | |
878 "id": 19, | |
879 "input_connections": { | |
880 "inputTabular": { | |
881 "id": 18, | |
882 "output_name": "outputVCFStorage" | |
883 } | |
884 }, | |
885 "inputs": [], | |
886 "name": "VCFCarto", | |
887 "outputs": [ | |
888 { | |
889 "name": "outputVCFCarto", | |
890 "type": "tabular" | |
891 }, | |
892 { | |
893 "name": "output_html", | |
894 "type": "html" | |
895 }, | |
896 { | |
897 "name": "output_bed", | |
898 "type": "bed" | |
899 } | |
900 ], | |
901 "position": { | |
902 "left": 2618, | |
903 "top": 593 | |
904 }, | |
905 "post_job_actions": { | |
906 "HideDatasetActionoutput_bed": { | |
907 "action_arguments": {}, | |
908 "action_type": "HideDatasetAction", | |
909 "output_name": "output_bed" | |
910 }, | |
911 "HideDatasetActionoutput_html": { | |
912 "action_arguments": {}, | |
913 "action_type": "HideDatasetAction", | |
914 "output_name": "output_html" | |
915 }, | |
916 "RenameDatasetActionoutputVCFCarto": { | |
917 "action_arguments": { | |
918 "newname": "#{inputTabular | basename}.red" | |
919 }, | |
920 "action_type": "RenameDatasetAction", | |
921 "output_name": "outputVCFCarto" | |
922 } | |
923 }, | |
924 "tool_errors": null, | |
925 "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFCarto/0.01", | |
926 "tool_state": "{\"__page__\": 0, \"parentA\": \"\\\"strain1\\\"\", \"__rerun_remap_job_id__\": null, \"outputType\": \"\\\"raw\\\"\", \"parentH\": \"\\\"strain2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputTabular\": \"null\"}", | |
927 "tool_version": "0.01", | |
928 "type": "tool", | |
929 "user_outputs": [] | |
930 } | |
931 }, | |
932 "uuid": "f217cc60-5c89-442b-80ee-3d055e407367" | |
933 } |