|
25
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "rapsosnp v1.15 -1x",
|
|
|
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,
|
|
|
21 "top": 319.48333740234375
|
|
|
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,
|
|
|
44 "top": 404.48333740234375
|
|
|
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,
|
|
|
67 "top": 489.48333740234375
|
|
|
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,
|
|
|
90 "top": 574.4833374023438
|
|
|
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,
|
|
|
118 "top": 319.48333740234375
|
|
|
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_read1_file": {
|
|
|
133 "id": 1,
|
|
|
134 "output_name": "output"
|
|
|
135 },
|
|
|
136 "input_read2_file": {
|
|
|
137 "id": 2,
|
|
|
138 "output_name": "output"
|
|
|
139 }
|
|
|
140 },
|
|
|
141 "inputs": [],
|
|
|
142 "name": "PrepareFastqLight",
|
|
|
143 "outputs": [
|
|
|
144 {
|
|
|
145 "name": "output_read1_file",
|
|
|
146 "type": "fastqsanger"
|
|
|
147 },
|
|
|
148 {
|
|
|
149 "name": "output_read2_file",
|
|
|
150 "type": "fastqsanger"
|
|
|
151 }
|
|
|
152 ],
|
|
|
153 "position": {
|
|
|
154 "left": 428,
|
|
|
155 "top": 450.48333740234375
|
|
|
156 },
|
|
|
157 "post_job_actions": {},
|
|
|
158 "tool_errors": null,
|
|
|
159 "tool_id": "PrepareFastqLight",
|
|
|
160 "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\"}",
|
|
|
161 "tool_version": "0.01",
|
|
|
162 "type": "tool",
|
|
|
163 "user_outputs": []
|
|
|
164 },
|
|
|
165 "6": {
|
|
|
166 "annotation": "",
|
|
|
167 "id": 6,
|
|
|
168 "input_connections": {
|
|
|
169 "input_file": {
|
|
|
170 "id": 4,
|
|
|
171 "output_name": "output_fasta"
|
|
|
172 }
|
|
|
173 },
|
|
|
174 "inputs": [],
|
|
|
175 "name": "NCBI BLAST+ makeblastdb",
|
|
|
176 "outputs": [
|
|
|
177 {
|
|
|
178 "name": "outfile",
|
|
|
179 "type": "data"
|
|
|
180 }
|
|
|
181 ],
|
|
|
182 "position": {
|
|
|
183 "left": 756,
|
|
|
184 "top": 319.48333740234375
|
|
|
185 },
|
|
|
186 "post_job_actions": {},
|
|
|
187 "tool_errors": null,
|
|
|
188 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.00",
|
|
|
189 "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\\\"\"}",
|
|
|
190 "tool_version": "0.1.00",
|
|
|
191 "type": "tool",
|
|
|
192 "user_outputs": []
|
|
|
193 },
|
|
|
194 "7": {
|
|
|
195 "annotation": "",
|
|
|
196 "id": 7,
|
|
|
197 "input_connections": {
|
|
|
198 "genomeSource|ownFile": {
|
|
|
199 "id": 0,
|
|
|
200 "output_name": "output"
|
|
|
201 },
|
|
|
202 "paired|input1": {
|
|
|
203 "id": 5,
|
|
|
204 "output_name": "output_read1_file"
|
|
|
205 },
|
|
|
206 "paired|input2": {
|
|
|
207 "id": 5,
|
|
|
208 "output_name": "output_read2_file"
|
|
|
209 }
|
|
|
210 },
|
|
|
211 "inputs": [],
|
|
|
212 "name": "Map with BWA for Illumina",
|
|
|
213 "outputs": [
|
|
|
214 {
|
|
|
215 "name": "output",
|
|
|
216 "type": "sam"
|
|
|
217 }
|
|
|
218 ],
|
|
|
219 "position": {
|
|
|
220 "left": 756,
|
|
|
221 "top": 477.48333740234375
|
|
|
222 },
|
|
|
223 "post_job_actions": {},
|
|
|
224 "tool_errors": null,
|
|
|
225 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
|
|
|
226 "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\\\"\"}",
|
|
|
227 "tool_version": "1.2.3",
|
|
|
228 "type": "tool",
|
|
|
229 "user_outputs": []
|
|
|
230 },
|
|
|
231 "8": {
|
|
|
232 "annotation": "",
|
|
|
233 "id": 8,
|
|
|
234 "input_connections": {
|
|
|
235 "input_sam_file": {
|
|
|
236 "id": 7,
|
|
|
237 "output_name": "output"
|
|
|
238 }
|
|
|
239 },
|
|
|
240 "inputs": [],
|
|
|
241 "name": "filtersam_mapped_and_unique",
|
|
|
242 "outputs": [
|
|
|
243 {
|
|
|
244 "name": "output_file",
|
|
|
245 "type": "sam"
|
|
|
246 }
|
|
|
247 ],
|
|
|
248 "position": {
|
|
|
249 "left": 1084,
|
|
|
250 "top": 319.48333740234375
|
|
|
251 },
|
|
|
252 "post_job_actions": {},
|
|
|
253 "tool_errors": null,
|
|
|
254 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/filtersam_mapped_and_unique/0.01",
|
|
|
255 "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\"}",
|
|
|
256 "tool_version": "0.01",
|
|
|
257 "type": "tool",
|
|
|
258 "user_outputs": []
|
|
|
259 },
|
|
|
260 "9": {
|
|
|
261 "annotation": "",
|
|
|
262 "id": 9,
|
|
|
263 "input_connections": {
|
|
|
264 "source|input1": {
|
|
|
265 "id": 8,
|
|
|
266 "output_name": "output_file"
|
|
|
267 },
|
|
|
268 "source|ref_file": {
|
|
|
269 "id": 0,
|
|
|
270 "output_name": "output"
|
|
|
271 }
|
|
|
272 },
|
|
|
273 "inputs": [],
|
|
|
274 "name": "SAM-to-BAM",
|
|
|
275 "outputs": [
|
|
|
276 {
|
|
|
277 "name": "output1",
|
|
|
278 "type": "bam"
|
|
|
279 }
|
|
|
280 ],
|
|
|
281 "position": {
|
|
|
282 "left": 1411.9998779296875,
|
|
|
283 "top": 319.48333740234375
|
|
|
284 },
|
|
|
285 "post_job_actions": {},
|
|
|
286 "tool_errors": null,
|
|
|
287 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4",
|
|
|
288 "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}",
|
|
|
289 "tool_version": "1.1.4",
|
|
|
290 "type": "tool",
|
|
|
291 "user_outputs": []
|
|
|
292 },
|
|
|
293 "10": {
|
|
|
294 "annotation": "",
|
|
|
295 "id": 10,
|
|
|
296 "input_connections": {
|
|
|
297 "reference_source|input_bams_0|input_bam": {
|
|
|
298 "id": 9,
|
|
|
299 "output_name": "output1"
|
|
|
300 },
|
|
|
301 "reference_source|ref_file": {
|
|
|
302 "id": 0,
|
|
|
303 "output_name": "output"
|
|
|
304 }
|
|
|
305 },
|
|
|
306 "inputs": [],
|
|
|
307 "name": "MPileup",
|
|
|
308 "outputs": [
|
|
|
309 {
|
|
|
310 "name": "output_mpileup",
|
|
|
311 "type": "pileup"
|
|
|
312 },
|
|
|
313 {
|
|
|
314 "name": "output_log",
|
|
|
315 "type": "txt"
|
|
|
316 }
|
|
|
317 ],
|
|
|
318 "position": {
|
|
|
319 "left": 1639.9998779296875,
|
|
|
320 "top": 319.48333740234375
|
|
|
321 },
|
|
|
322 "post_job_actions": {},
|
|
|
323 "tool_errors": null,
|
|
|
324 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3",
|
|
|
325 "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\\\"\"}",
|
|
|
326 "tool_version": "0.0.3",
|
|
|
327 "type": "tool",
|
|
|
328 "user_outputs": []
|
|
|
329 },
|
|
|
330 "11": {
|
|
|
331 "annotation": "",
|
|
|
332 "id": 11,
|
|
|
333 "input_connections": {
|
|
|
334 "input_file": {
|
|
|
335 "id": 10,
|
|
|
336 "output_name": "output_mpileup"
|
|
|
337 }
|
|
|
338 },
|
|
|
339 "inputs": [],
|
|
|
340 "name": "PileupVariant",
|
|
|
341 "outputs": [
|
|
|
342 {
|
|
|
343 "name": "output_file",
|
|
|
344 "type": "pileup"
|
|
|
345 }
|
|
|
346 ],
|
|
|
347 "position": {
|
|
|
348 "left": 1965.9998779296875,
|
|
|
349 "top": 319.48333740234375
|
|
|
350 },
|
|
|
351 "post_job_actions": {},
|
|
|
352 "tool_errors": null,
|
|
|
353 "tool_id": "PileupVariant",
|
|
|
354 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_file\": \"null\"}",
|
|
|
355 "tool_version": "0.01",
|
|
|
356 "type": "tool",
|
|
|
357 "user_outputs": []
|
|
|
358 },
|
|
|
359 "12": {
|
|
|
360 "annotation": "",
|
|
|
361 "id": 12,
|
|
|
362 "input_connections": {
|
|
|
363 "input_listA": {
|
|
|
364 "id": 11,
|
|
|
365 "output_name": "output_file"
|
|
|
366 },
|
|
|
367 "input_listB": {
|
|
|
368 "id": 3,
|
|
|
369 "output_name": "output"
|
|
|
370 }
|
|
|
371 },
|
|
|
372 "inputs": [],
|
|
|
373 "name": "listfiltering",
|
|
|
374 "outputs": [
|
|
|
375 {
|
|
|
376 "name": "output_file",
|
|
|
377 "type": "pileup"
|
|
|
378 }
|
|
|
379 ],
|
|
|
380 "position": {
|
|
|
381 "left": 2293.9999389648438,
|
|
|
382 "top": 319.48333740234375
|
|
|
383 },
|
|
|
384 "post_job_actions": {},
|
|
|
385 "tool_errors": null,
|
|
|
386 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/listfiltering/0.01",
|
|
|
387 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_listB\": \"null\", \"nb_col\": \"\\\"2\\\"\", \"input_listA\": \"null\"}",
|
|
|
388 "tool_version": "0.01",
|
|
|
389 "type": "tool",
|
|
|
390 "user_outputs": []
|
|
|
391 },
|
|
|
392 "13": {
|
|
|
393 "annotation": "",
|
|
|
394 "id": 13,
|
|
|
395 "input_connections": {
|
|
|
396 "input_assembly_file": {
|
|
|
397 "id": 0,
|
|
|
398 "output_name": "output"
|
|
|
399 },
|
|
|
400 "input_variant_file": {
|
|
|
401 "id": 12,
|
|
|
402 "output_name": "output_file"
|
|
|
403 }
|
|
|
404 },
|
|
|
405 "inputs": [],
|
|
|
406 "name": "extractseq",
|
|
|
407 "outputs": [
|
|
|
408 {
|
|
|
409 "name": "output_file",
|
|
|
410 "type": "fasta"
|
|
|
411 }
|
|
|
412 ],
|
|
|
413 "position": {
|
|
|
414 "left": 2621.9999389648438,
|
|
|
415 "top": 319.48333740234375
|
|
|
416 },
|
|
|
417 "post_job_actions": {},
|
|
|
418 "tool_errors": null,
|
|
|
419 "tool_id": "toolshed.g2.bx.psu.edu/repos/mcharles/rapsodyn/extractseq/0.03",
|
|
|
420 "tool_state": "{\"__page__\": 0, \"input_variant_file\": \"null\", \"__rerun_remap_job_id__\": null, \"window_length\": \"\\\"50\\\"\", \"input_assembly_file\": \"null\"}",
|
|
|
421 "tool_version": "0.03",
|
|
|
422 "type": "tool",
|
|
|
423 "user_outputs": []
|
|
|
424 },
|
|
|
425 "14": {
|
|
|
426 "annotation": "",
|
|
|
427 "id": 14,
|
|
|
428 "input_connections": {
|
|
|
429 "db_opts|histdb": {
|
|
|
430 "id": 6,
|
|
|
431 "output_name": "outfile"
|
|
|
432 },
|
|
|
433 "query": {
|
|
|
434 "id": 13,
|
|
|
435 "output_name": "output_file"
|
|
|
436 }
|
|
|
437 },
|
|
|
438 "inputs": [],
|
|
|
439 "name": "NCBI BLAST+ blastn",
|
|
|
440 "outputs": [
|
|
|
441 {
|
|
|
442 "name": "output1",
|
|
|
443 "type": "tabular"
|
|
|
444 }
|
|
|
445 ],
|
|
|
446 "position": {
|
|
|
447 "left": 2949.9999389648438,
|
|
|
448 "top": 319.48333740234375
|
|
|
449 },
|
|
|
450 "post_job_actions": {},
|
|
|
451 "tool_errors": null,
|
|
|
452 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00",
|
|
|
453 "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\"}",
|
|
|
454 "tool_version": "0.1.00",
|
|
|
455 "type": "tool",
|
|
|
456 "user_outputs": []
|
|
|
457 },
|
|
|
458 "15": {
|
|
|
459 "annotation": "",
|
|
|
460 "id": 15,
|
|
|
461 "input_connections": {
|
|
|
462 "input_blast_file": {
|
|
|
463 "id": 14,
|
|
|
464 "output_name": "output1"
|
|
|
465 },
|
|
|
466 "input_variant_file": {
|
|
|
467 "id": 12,
|
|
|
468 "output_name": "output_file"
|
|
|
469 }
|
|
|
470 },
|
|
|
471 "inputs": [],
|
|
|
472 "name": "ParseBlastForUniqueMatch",
|
|
|
473 "outputs": [
|
|
|
474 {
|
|
|
475 "name": "output_file",
|
|
|
476 "type": "pileup"
|
|
|
477 }
|
|
|
478 ],
|
|
|
479 "position": {
|
|
|
480 "left": 3251.9999237060547,
|
|
|
481 "top": 319.48333740234375
|
|
|
482 },
|
|
|
483 "post_job_actions": {},
|
|
|
484 "tool_errors": null,
|
|
|
485 "tool_id": "ParseBlastForUniqueMatch",
|
|
|
486 "tool_state": "{\"input_variant_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_blast_file\": \"null\", \"window_length\": \"\\\"50\\\"\", \"nb_mismatch_max\": \"\\\"3\\\"\"}",
|
|
|
487 "tool_version": "0.01",
|
|
|
488 "type": "tool",
|
|
|
489 "user_outputs": []
|
|
|
490 },
|
|
|
491 "16": {
|
|
|
492 "annotation": "",
|
|
|
493 "id": 16,
|
|
|
494 "input_connections": {
|
|
|
495 "input_file": {
|
|
|
496 "id": 15,
|
|
|
497 "output_name": "output_file"
|
|
|
498 }
|
|
|
499 },
|
|
|
500 "inputs": [],
|
|
|
501 "name": "mpileupfilterandstat",
|
|
|
502 "outputs": [
|
|
|
503 {
|
|
|
504 "name": "output_file",
|
|
|
505 "type": "pileup"
|
|
|
506 },
|
|
|
507 {
|
|
|
508 "name": "log_file",
|
|
|
509 "type": "txt"
|
|
|
510 }
|
|
|
511 ],
|
|
|
512 "position": {
|
|
|
513 "left": 3579.9999389648438,
|
|
|
514 "top": 319.48333740234375
|
|
|
515 },
|
|
|
516 "post_job_actions": {},
|
|
|
517 "tool_errors": null,
|
|
|
518 "tool_id": "mpileupfilterandstat",
|
|
|
519 "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\\\"\"}",
|
|
|
520 "tool_version": "0.08",
|
|
|
521 "type": "tool",
|
|
|
522 "user_outputs": []
|
|
|
523 },
|
|
|
524 "17": {
|
|
|
525 "annotation": "",
|
|
|
526 "id": 17,
|
|
|
527 "input_connections": {
|
|
|
528 "input_blast_filtered_file": {
|
|
|
529 "id": 15,
|
|
|
530 "output_name": "output_file"
|
|
|
531 },
|
|
|
532 "input_list_filtered_file": {
|
|
|
533 "id": 12,
|
|
|
534 "output_name": "output_file"
|
|
|
535 },
|
|
|
536 "input_mpileup_variant_file": {
|
|
|
537 "id": 11,
|
|
|
538 "output_name": "output_file"
|
|
|
539 },
|
|
|
540 "input_read1_row_file": {
|
|
|
541 "id": 1,
|
|
|
542 "output_name": "output"
|
|
|
543 },
|
|
|
544 "input_read1_trimmed_file": {
|
|
|
545 "id": 5,
|
|
|
546 "output_name": "output_read1_file"
|
|
|
547 },
|
|
|
548 "input_read2_row_file": {
|
|
|
549 "id": 2,
|
|
|
550 "output_name": "output"
|
|
|
551 },
|
|
|
552 "input_read2_trimmed_file": {
|
|
|
553 "id": 5,
|
|
|
554 "output_name": "output_read2_file"
|
|
|
555 },
|
|
|
556 "input_sam_filtered_file": {
|
|
|
557 "id": 8,
|
|
|
558 "output_name": "output_file"
|
|
|
559 },
|
|
|
560 "input_sam_row_file": {
|
|
|
561 "id": 7,
|
|
|
562 "output_name": "output"
|
|
|
563 },
|
|
|
564 "input_snp_selected_file": {
|
|
|
565 "id": 16,
|
|
|
566 "output_name": "output_file"
|
|
|
567 }
|
|
|
568 },
|
|
|
569 "inputs": [],
|
|
|
570 "name": "rapsosnp_stats",
|
|
|
571 "outputs": [
|
|
|
572 {
|
|
|
573 "name": "output_file",
|
|
|
574 "type": "txt"
|
|
|
575 }
|
|
|
576 ],
|
|
|
577 "position": {
|
|
|
578 "left": 3907.9999389648438,
|
|
|
579 "top": 319.48333740234375
|
|
|
580 },
|
|
|
581 "post_job_actions": {},
|
|
|
582 "tool_errors": null,
|
|
|
583 "tool_id": "rapsosnp_stats",
|
|
|
584 "tool_state": "{\"input_read1_trimmed_file\": \"null\", \"__page__\": 0, \"input_read2_trimmed_file\": \"null\", \"input_sam_row_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_read2_row_file\": \"null\", \"input_mpileup_variant_file\": \"null\", \"input_sam_filtered_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_snp_selected_file\": \"null\", \"input_list_filtered_file\": \"null\", \"input_blast_filtered_file\": \"null\"}",
|
|
|
585 "tool_version": "0.01",
|
|
|
586 "type": "tool",
|
|
|
587 "user_outputs": []
|
|
|
588 }
|
|
|
589 }
|
|
|
590 } |
