|
1
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "SNiPlay Workflow",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "id": 0,
|
|
|
10 "input_connections": {},
|
|
|
11 "inputs": [
|
|
|
12 {
|
|
|
13 "description": "",
|
|
|
14 "name": "Input Dataset"
|
|
|
15 }
|
|
|
16 ],
|
|
|
17 "label": null,
|
|
|
18 "name": "Input dataset",
|
|
|
19 "outputs": [],
|
|
|
20 "position": {
|
|
|
21 "left": 200,
|
|
|
22 "top": 200
|
|
|
23 },
|
|
|
24 "tool_errors": null,
|
|
|
25 "tool_id": null,
|
|
|
26 "tool_state": "{\"name\": \"Input Dataset\"}",
|
|
|
27 "tool_version": null,
|
|
|
28 "type": "data_input",
|
|
|
29 "user_outputs": [],
|
|
|
30 "uuid": "156cb9d1-fff4-4c22-8eb8-6c7e8b6f891c"
|
|
|
31 },
|
|
|
32 "1": {
|
|
|
33 "annotation": "",
|
|
|
34 "id": 1,
|
|
|
35 "input_connections": {},
|
|
|
36 "inputs": [
|
|
|
37 {
|
|
|
38 "description": "",
|
|
|
39 "name": "Input Dataset"
|
|
|
40 }
|
|
|
41 ],
|
|
|
42 "label": null,
|
|
|
43 "name": "Input dataset",
|
|
|
44 "outputs": [],
|
|
|
45 "position": {
|
|
|
46 "left": 200,
|
|
|
47 "top": 320
|
|
|
48 },
|
|
|
49 "tool_errors": null,
|
|
|
50 "tool_id": null,
|
|
|
51 "tool_state": "{\"name\": \"Input Dataset\"}",
|
|
|
52 "tool_version": null,
|
|
|
53 "type": "data_input",
|
|
|
54 "user_outputs": [],
|
|
|
55 "uuid": "4005036f-e5fd-4f8b-8eac-68d0872a77e4"
|
|
|
56 },
|
|
|
57 "2": {
|
|
|
58 "annotation": "",
|
|
|
59 "id": 2,
|
|
|
60 "input_connections": {},
|
|
|
61 "inputs": [
|
|
|
62 {
|
|
|
63 "description": "",
|
|
|
64 "name": "Input Dataset"
|
|
|
65 }
|
|
|
66 ],
|
|
|
67 "label": null,
|
|
|
68 "name": "Input dataset",
|
|
|
69 "outputs": [],
|
|
|
70 "position": {
|
|
|
71 "left": 200,
|
|
|
72 "top": 440
|
|
|
73 },
|
|
|
74 "tool_errors": null,
|
|
|
75 "tool_id": null,
|
|
|
76 "tool_state": "{\"name\": \"Input Dataset\"}",
|
|
|
77 "tool_version": null,
|
|
|
78 "type": "data_input",
|
|
|
79 "user_outputs": [],
|
|
|
80 "uuid": "6088050b-e81a-4f1a-8e38-192974d0c711"
|
|
|
81 },
|
|
|
82 "3": {
|
|
|
83 "annotation": "",
|
|
|
84 "id": 3,
|
|
|
85 "input_connections": {
|
|
|
86 "genome": {
|
|
|
87 "id": 1,
|
|
|
88 "output_name": "output"
|
|
|
89 },
|
|
|
90 "gff": {
|
|
|
91 "id": 2,
|
|
|
92 "output_name": "output"
|
|
|
93 },
|
|
|
94 "vcf": {
|
|
|
95 "id": 0,
|
|
|
96 "output_name": "output"
|
|
|
97 }
|
|
|
98 },
|
|
|
99 "inputs": [],
|
|
|
100 "label": null,
|
|
|
101 "name": "SnpEff",
|
|
|
102 "outputs": [
|
|
|
103 {
|
|
|
104 "name": "output",
|
|
|
105 "type": "vcf"
|
|
|
106 },
|
|
|
107 {
|
|
|
108 "name": "statsFile",
|
|
|
109 "type": "html"
|
|
|
110 },
|
|
|
111 {
|
|
|
112 "name": "log",
|
|
|
113 "type": "txt"
|
|
|
114 }
|
|
|
115 ],
|
|
|
116 "position": {
|
|
|
117 "left": 424,
|
|
|
118 "top": 111
|
|
|
119 },
|
|
|
120 "post_job_actions": {},
|
|
|
121 "tool_errors": null,
|
|
|
122 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/4.0",
|
|
|
123 "tool_state": "{\"__page__\": 0, \"vcf\": \"null\", \"gff\": \"null\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"genome\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
124 "tool_version": "4.0",
|
|
|
125 "type": "tool",
|
|
|
126 "user_outputs": [],
|
|
|
127 "uuid": "84ba0275-3db8-4106-b725-9626f5f78c2e"
|
|
|
128 },
|
|
|
129 "4": {
|
|
|
130 "annotation": "",
|
|
|
131 "id": 4,
|
|
|
132 "input_connections": {
|
|
|
133 "input": {
|
|
|
134 "id": 3,
|
|
|
135 "output_name": "output"
|
|
|
136 }
|
|
|
137 },
|
|
|
138 "inputs": [],
|
|
|
139 "label": null,
|
|
|
140 "name": "SnpSift Filter",
|
|
|
141 "outputs": [
|
|
|
142 {
|
|
|
143 "name": "output",
|
|
|
144 "type": "vcf"
|
|
|
145 }
|
|
|
146 ],
|
|
|
147 "position": {
|
|
|
148 "left": 640,
|
|
|
149 "top": 200
|
|
|
150 },
|
|
|
151 "post_job_actions": {},
|
|
|
152 "tool_errors": null,
|
|
|
153 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.0.0",
|
|
|
154 "tool_state": "{\"__page__\": 0, \"filtering\": \"{\\\"mode\\\": \\\"entries\\\", \\\"__current_case__\\\": 0}\", \"expr\": \"\\\"( QUAL > 3 )\\\"\", \"__rerun_remap_job_id__\": null, \"inverse\": \"\\\"False\\\"\", \"input\": \"null\"}",
|
|
|
155 "tool_version": "4.0.0",
|
|
|
156 "type": "tool",
|
|
|
157 "user_outputs": [],
|
|
|
158 "uuid": "5139c1e1-6155-4881-9257-136c8ea9213a"
|
|
|
159 },
|
|
|
160 "5": {
|
|
|
161 "annotation": "",
|
|
|
162 "id": 5,
|
|
|
163 "input_connections": {
|
|
|
164 "filein": {
|
|
|
165 "id": 4,
|
|
|
166 "output_name": "output"
|
|
|
167 }
|
|
|
168 },
|
|
|
169 "inputs": [],
|
|
|
170 "label": null,
|
|
|
171 "name": "VCFtools Filter",
|
|
|
172 "outputs": [
|
|
|
173 {
|
|
|
174 "name": "fileout",
|
|
|
175 "type": "vcf"
|
|
|
176 },
|
|
|
177 {
|
|
|
178 "name": "fileout_map",
|
|
|
179 "type": "txt"
|
|
|
180 },
|
|
|
181 {
|
|
|
182 "name": "filelog",
|
|
|
183 "type": "txt"
|
|
|
184 }
|
|
|
185 ],
|
|
|
186 "position": {
|
|
|
187 "left": 860,
|
|
|
188 "top": 200
|
|
|
189 },
|
|
|
190 "post_job_actions": {},
|
|
|
191 "tool_errors": null,
|
|
|
192 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1",
|
|
|
193 "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"None\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"export\": \"\\\"VCF\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"filein\": \"null\", \"samples\": \"\\\"None\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}",
|
|
|
194 "tool_version": "1.1.1",
|
|
|
195 "type": "tool",
|
|
|
196 "user_outputs": [],
|
|
|
197 "uuid": "f4296cba-1369-4e44-97c9-2e1c1f4955cb"
|
|
|
198 },
|
|
|
199 "6": {
|
|
|
200 "annotation": "",
|
|
|
201 "id": 6,
|
|
|
202 "input_connections": {
|
|
|
203 "filein": {
|
|
|
204 "id": 5,
|
|
|
205 "output_name": "fileout"
|
|
|
206 }
|
|
|
207 },
|
|
|
208 "inputs": [],
|
|
|
209 "label": null,
|
|
|
210 "name": "VCFtools Filter",
|
|
|
211 "outputs": [
|
|
|
212 {
|
|
|
213 "name": "fileout",
|
|
|
214 "type": "vcf"
|
|
|
215 },
|
|
|
216 {
|
|
|
217 "name": "fileout_map",
|
|
|
218 "type": "txt"
|
|
|
219 },
|
|
|
220 {
|
|
|
221 "name": "filelog",
|
|
|
222 "type": "txt"
|
|
|
223 }
|
|
|
224 ],
|
|
|
225 "position": {
|
|
|
226 "left": 1080,
|
|
|
227 "top": 200
|
|
|
228 },
|
|
|
229 "post_job_actions": {},
|
|
|
230 "tool_errors": null,
|
|
|
231 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/1.1.1",
|
|
|
232 "tool_state": "{\"__page__\": 0, \"chromosomes\": \"\\\"\\\"\", \"nb_alleles_max\": \"\\\"2\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"export\": \"\\\"plink\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"filein\": \"null\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"nb_alleles_min\": \"\\\"2\\\"\", \"max_freq\": \"\\\"0.5\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}",
|
|
|
233 "tool_version": "1.1.1",
|
|
|
234 "type": "tool",
|
|
|
235 "user_outputs": [],
|
|
|
236 "uuid": "8e4bd231-e134-42dc-9457-5c0738b8c46a"
|
|
|
237 },
|
|
|
238 "7": {
|
|
|
239 "annotation": "",
|
|
|
240 "id": 7,
|
|
|
241 "input_connections": {
|
|
|
242 "filein": {
|
|
|
243 "id": 5,
|
|
|
244 "output_name": "fileout"
|
|
|
245 }
|
|
|
246 },
|
|
|
247 "inputs": [],
|
|
|
248 "label": null,
|
|
|
249 "name": "VCFtools Stats",
|
|
|
250 "outputs": [
|
|
|
251 {
|
|
|
252 "name": "fileout_annot",
|
|
|
253 "type": "txt"
|
|
|
254 },
|
|
|
255 {
|
|
|
256 "name": "fileout_het",
|
|
|
257 "type": "txt"
|
|
|
258 },
|
|
|
259 {
|
|
|
260 "name": "fileout_imiss",
|
|
|
261 "type": "txt"
|
|
|
262 },
|
|
|
263 {
|
|
|
264 "name": "fileout_sum",
|
|
|
265 "type": "txt"
|
|
|
266 },
|
|
|
267 {
|
|
|
268 "name": "filelog",
|
|
|
269 "type": "txt"
|
|
|
270 }
|
|
|
271 ],
|
|
|
272 "position": {
|
|
|
273 "left": 1080,
|
|
|
274 "top": 320
|
|
|
275 },
|
|
|
276 "post_job_actions": {},
|
|
|
277 "tool_errors": null,
|
|
|
278 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsstats/1.0.0",
|
|
|
279 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"vcf_stats\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
280 "tool_version": "1.0.0",
|
|
|
281 "type": "tool",
|
|
|
282 "user_outputs": [],
|
|
|
283 "uuid": "32da698d-fcab-4da7-a0c2-deace884d47e"
|
|
|
284 },
|
|
|
285 "8": {
|
|
|
286 "annotation": "",
|
|
|
287 "id": 8,
|
|
|
288 "input_connections": {
|
|
|
289 "filein": {
|
|
|
290 "id": 5,
|
|
|
291 "output_name": "fileout"
|
|
|
292 }
|
|
|
293 },
|
|
|
294 "inputs": [],
|
|
|
295 "label": null,
|
|
|
296 "name": "VCF tools SlidingWindow",
|
|
|
297 "outputs": [
|
|
|
298 {
|
|
|
299 "name": "fileout_snp",
|
|
|
300 "type": "tabular"
|
|
|
301 },
|
|
|
302 {
|
|
|
303 "name": "fileout_taj",
|
|
|
304 "type": "tabular"
|
|
|
305 },
|
|
|
306 {
|
|
|
307 "name": "fileout_tstv",
|
|
|
308 "type": "tabular"
|
|
|
309 },
|
|
|
310 {
|
|
|
311 "name": "fileout_windowed",
|
|
|
312 "type": "tabular"
|
|
|
313 },
|
|
|
314 {
|
|
|
315 "name": "filelog",
|
|
|
316 "type": "txt"
|
|
|
317 }
|
|
|
318 ],
|
|
|
319 "position": {
|
|
|
320 "left": 1080,
|
|
|
321 "top": 440
|
|
|
322 },
|
|
|
323 "post_job_actions": {},
|
|
|
324 "tool_errors": null,
|
|
|
325 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/vcftools_filter_stats_diversity/sniplay_vcftoolsslidingwindow/1.0.0",
|
|
|
326 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"step\": \"\\\"50000\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"snp_density\\\"\", \"window\": \"\\\"200000\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
327 "tool_version": "1.0.0",
|
|
|
328 "type": "tool",
|
|
|
329 "user_outputs": [],
|
|
|
330 "uuid": "25ee9e9a-00f0-484b-bf48-685193d95882"
|
|
|
331 },
|
|
|
332 "9": {
|
|
|
333 "annotation": "",
|
|
|
334 "id": 9,
|
|
|
335 "input_connections": {
|
|
|
336 "filein": {
|
|
|
337 "id": 5,
|
|
|
338 "output_name": "fileout"
|
|
|
339 },
|
|
|
340 "optional|filefasta": {
|
|
|
341 "id": 1,
|
|
|
342 "output_name": "output"
|
|
|
343 },
|
|
|
344 "optional|filegff": {
|
|
|
345 "id": 2,
|
|
|
346 "output_name": "output"
|
|
|
347 }
|
|
|
348 },
|
|
|
349 "inputs": [],
|
|
|
350 "label": null,
|
|
|
351 "name": "VCF to Hapmap",
|
|
|
352 "outputs": [
|
|
|
353 {
|
|
|
354 "name": "fileout",
|
|
|
355 "type": "txt"
|
|
|
356 },
|
|
|
357 {
|
|
|
358 "name": "fileout_seq",
|
|
|
359 "type": "txt"
|
|
|
360 },
|
|
|
361 {
|
|
|
362 "name": "fileout_fa1",
|
|
|
363 "type": "fasta"
|
|
|
364 }
|
|
|
365 ],
|
|
|
366 "position": {
|
|
|
367 "left": 1080,
|
|
|
368 "top": 560
|
|
|
369 },
|
|
|
370 "post_job_actions": {},
|
|
|
371 "tool_errors": null,
|
|
|
372 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_vcf2fastaandhapmap/1.1.0",
|
|
|
373 "tool_state": "{\"__page__\": 0, \"optional\": \"{\\\"file_opt\\\": \\\"fasta_gff\\\", \\\"filefasta\\\": null, \\\"filegff\\\": null, \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"input\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
374 "tool_version": "1.1.0",
|
|
|
375 "type": "tool",
|
|
|
376 "user_outputs": [],
|
|
|
377 "uuid": "123f77f8-3fd2-4579-9d0f-74b0aab7a5ae"
|
|
|
378 },
|
|
|
379 "10": {
|
|
|
380 "annotation": "",
|
|
|
381 "id": 10,
|
|
|
382 "input_connections": {
|
|
|
383 "map": {
|
|
|
384 "id": 6,
|
|
|
385 "output_name": "fileout_map"
|
|
|
386 },
|
|
|
387 "ped": {
|
|
|
388 "id": 6,
|
|
|
389 "output_name": "fileout"
|
|
|
390 }
|
|
|
391 },
|
|
|
392 "inputs": [],
|
|
|
393 "label": null,
|
|
|
394 "name": "plink: ped2bed",
|
|
|
395 "outputs": [
|
|
|
396 {
|
|
|
397 "name": "bed",
|
|
|
398 "type": "txt"
|
|
|
399 },
|
|
|
400 {
|
|
|
401 "name": "fam",
|
|
|
402 "type": "txt"
|
|
|
403 },
|
|
|
404 {
|
|
|
405 "name": "bim",
|
|
|
406 "type": "txt"
|
|
|
407 },
|
|
|
408 {
|
|
|
409 "name": "logs",
|
|
|
410 "type": "txt"
|
|
|
411 }
|
|
|
412 ],
|
|
|
413 "position": {
|
|
|
414 "left": 1300,
|
|
|
415 "top": 200
|
|
|
416 },
|
|
|
417 "post_job_actions": {},
|
|
|
418 "tool_errors": null,
|
|
|
419 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/ped2bed/1.24",
|
|
|
420 "tool_state": "{\"map\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"ped\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
421 "tool_version": "1.24",
|
|
|
422 "type": "tool",
|
|
|
423 "user_outputs": [],
|
|
|
424 "uuid": "30c86fbf-9815-4d5a-b5ee-ae8ea9a67cec"
|
|
|
425 },
|
|
|
426 "11": {
|
|
|
427 "annotation": "",
|
|
|
428 "id": 11,
|
|
|
429 "input_connections": {
|
|
|
430 "filein": {
|
|
|
431 "id": 6,
|
|
|
432 "output_name": "fileout"
|
|
|
433 }
|
|
|
434 },
|
|
|
435 "inputs": [],
|
|
|
436 "label": null,
|
|
|
437 "name": "Ped2Fasta",
|
|
|
438 "outputs": [
|
|
|
439 {
|
|
|
440 "name": "fileout",
|
|
|
441 "type": "fasta"
|
|
|
442 }
|
|
|
443 ],
|
|
|
444 "position": {
|
|
|
445 "left": 1300,
|
|
|
446 "top": 320
|
|
|
447 },
|
|
|
448 "post_job_actions": {},
|
|
|
449 "tool_errors": null,
|
|
|
450 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_pedToFasta/1.0.0",
|
|
|
451 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
452 "tool_version": "1.0.0",
|
|
|
453 "type": "tool",
|
|
|
454 "user_outputs": [],
|
|
|
455 "uuid": "ba6bfbda-00b1-41fa-b731-b416db10f9dd"
|
|
|
456 },
|
|
|
457 "12": {
|
|
|
458 "annotation": "",
|
|
|
459 "id": 12,
|
|
|
460 "input_connections": {
|
|
|
461 "filemap": {
|
|
|
462 "id": 6,
|
|
|
463 "output_name": "fileout_map"
|
|
|
464 },
|
|
|
465 "fileped": {
|
|
|
466 "id": 6,
|
|
|
467 "output_name": "fileout"
|
|
|
468 }
|
|
|
469 },
|
|
|
470 "inputs": [],
|
|
|
471 "label": null,
|
|
|
472 "name": "MDS plot",
|
|
|
473 "outputs": [
|
|
|
474 {
|
|
|
475 "name": "fileout_matrix",
|
|
|
476 "type": "tabular"
|
|
|
477 },
|
|
|
478 {
|
|
|
479 "name": "fileout_plot",
|
|
|
480 "type": "tabular"
|
|
|
481 },
|
|
|
482 {
|
|
|
483 "name": "fileout_log",
|
|
|
484 "type": "txt"
|
|
|
485 }
|
|
|
486 ],
|
|
|
487 "position": {
|
|
|
488 "left": 1300,
|
|
|
489 "top": 680
|
|
|
490 },
|
|
|
491 "post_job_actions": {},
|
|
|
492 "tool_errors": null,
|
|
|
493 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_mdsplot/1.1.1",
|
|
|
494 "tool_state": "{\"__page__\": 0, \"fileped\": \"null\", \"filemap\": \"null\", \"__rerun_remap_job_id__\": null, \"fileout_label\": \"\\\"mdsplot\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
495 "tool_version": "1.1.1",
|
|
|
496 "type": "tool",
|
|
|
497 "user_outputs": [],
|
|
|
498 "uuid": "c912f3bf-23e5-4bb0-9a0f-516828c9d4db"
|
|
|
499 },
|
|
|
500 "13": {
|
|
|
501 "annotation": "",
|
|
|
502 "id": 13,
|
|
|
503 "input_connections": {
|
|
|
504 "filein": {
|
|
|
505 "id": 9,
|
|
|
506 "output_name": "fileout"
|
|
|
507 }
|
|
|
508 },
|
|
|
509 "inputs": [],
|
|
|
510 "label": null,
|
|
|
511 "name": "SNP density",
|
|
|
512 "outputs": [
|
|
|
513 {
|
|
|
514 "name": "fileout",
|
|
|
515 "type": "tabular"
|
|
|
516 },
|
|
|
517 {
|
|
|
518 "name": "fileout_bysample",
|
|
|
519 "type": "tabular"
|
|
|
520 }
|
|
|
521 ],
|
|
|
522 "position": {
|
|
|
523 "left": 1300,
|
|
|
524 "top": 440
|
|
|
525 },
|
|
|
526 "post_job_actions": {},
|
|
|
527 "tool_errors": null,
|
|
|
528 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_density/1.2.0",
|
|
|
529 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"densities\\\"\", \"step\": \"\\\"200000\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
530 "tool_version": "1.2.0",
|
|
|
531 "type": "tool",
|
|
|
532 "user_outputs": [],
|
|
|
533 "uuid": "a7524249-d521-42b8-bf9e-953a4807b46b"
|
|
|
534 },
|
|
|
535 "14": {
|
|
|
536 "annotation": "",
|
|
|
537 "id": 14,
|
|
|
538 "input_connections": {
|
|
|
539 "input": {
|
|
|
540 "id": 9,
|
|
|
541 "output_name": "fileout_fa1"
|
|
|
542 }
|
|
|
543 },
|
|
|
544 "inputs": [],
|
|
|
545 "label": null,
|
|
|
546 "name": "Diversity by gene",
|
|
|
547 "outputs": [
|
|
|
548 {
|
|
|
549 "name": "output",
|
|
|
550 "type": "txt"
|
|
|
551 },
|
|
|
552 {
|
|
|
553 "name": "log",
|
|
|
554 "type": "txt"
|
|
|
555 }
|
|
|
556 ],
|
|
|
557 "position": {
|
|
|
558 "left": 1300,
|
|
|
559 "top": 560
|
|
|
560 },
|
|
|
561 "post_job_actions": {},
|
|
|
562 "tool_errors": null,
|
|
|
563 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/calculate_diversity/2.1.6",
|
|
|
564 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"__page__\": 0}",
|
|
|
565 "tool_version": "2.1.6",
|
|
|
566 "type": "tool",
|
|
|
567 "user_outputs": [],
|
|
|
568 "uuid": "f1b611d0-ae04-4ee0-ba80-e7d5154b77db"
|
|
|
569 },
|
|
|
570 "15": {
|
|
|
571 "annotation": "",
|
|
|
572 "id": 15,
|
|
|
573 "input_connections": {
|
|
|
574 "bed": {
|
|
|
575 "id": 10,
|
|
|
576 "output_name": "bed"
|
|
|
577 },
|
|
|
578 "bim": {
|
|
|
579 "id": 10,
|
|
|
580 "output_name": "bim"
|
|
|
581 },
|
|
|
582 "fam": {
|
|
|
583 "id": 10,
|
|
|
584 "output_name": "fam"
|
|
|
585 }
|
|
|
586 },
|
|
|
587 "inputs": [],
|
|
|
588 "label": null,
|
|
|
589 "name": "Admixture",
|
|
|
590 "outputs": [
|
|
|
591 {
|
|
|
592 "name": "best_k_output",
|
|
|
593 "type": "txt"
|
|
|
594 },
|
|
|
595 {
|
|
|
596 "name": "best_k_logfile",
|
|
|
597 "type": "txt"
|
|
|
598 },
|
|
|
599 {
|
|
|
600 "name": "outputs",
|
|
|
601 "type": "txt"
|
|
|
602 },
|
|
|
603 {
|
|
|
604 "name": "logs",
|
|
|
605 "type": "txt"
|
|
|
606 }
|
|
|
607 ],
|
|
|
608 "position": {
|
|
|
609 "left": 1520,
|
|
|
610 "top": 200
|
|
|
611 },
|
|
|
612 "post_job_actions": {},
|
|
|
613 "tool_errors": null,
|
|
|
614 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/admixture/admixture/1.23",
|
|
|
615 "tool_state": "{\"__page__\": 0, \"bim\": \"null\", \"__rerun_remap_job_id__\": null, \"kmin\": \"\\\"1\\\"\", \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"kmax\": \"\\\"5\\\"\", \"bed\": \"null\", \"fam\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
616 "tool_version": "1.23",
|
|
|
617 "type": "tool",
|
|
|
618 "user_outputs": [],
|
|
|
619 "uuid": "3fcde6c6-747d-416b-9594-d4f5e3ed565e"
|
|
|
620 },
|
|
|
621 "16": {
|
|
|
622 "annotation": "",
|
|
|
623 "id": 16,
|
|
|
624 "input_connections": {
|
|
|
625 "filein": {
|
|
|
626 "id": 11,
|
|
|
627 "output_name": "fileout"
|
|
|
628 }
|
|
|
629 },
|
|
|
630 "inputs": [],
|
|
|
631 "label": null,
|
|
|
632 "name": "Readseq",
|
|
|
633 "outputs": [
|
|
|
634 {
|
|
|
635 "name": "fileout_log",
|
|
|
636 "type": "txt"
|
|
|
637 },
|
|
|
638 {
|
|
|
639 "name": "fileout",
|
|
|
640 "type": "txt"
|
|
|
641 }
|
|
|
642 ],
|
|
|
643 "position": {
|
|
|
644 "left": 1520,
|
|
|
645 "top": 320
|
|
|
646 },
|
|
|
647 "post_job_actions": {},
|
|
|
648 "tool_errors": null,
|
|
|
649 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/readseq/sniplay_readseq/1.0.2",
|
|
|
650 "tool_state": "{\"__page__\": 0, \"format\": \"\\\"12\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"phylip conversion\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
651 "tool_version": "1.0.2",
|
|
|
652 "type": "tool",
|
|
|
653 "user_outputs": [],
|
|
|
654 "uuid": "b9dff56a-5a08-47e3-9f89-1cffb294230c"
|
|
|
655 },
|
|
|
656 "17": {
|
|
|
657 "annotation": "",
|
|
|
658 "id": 17,
|
|
|
659 "input_connections": {
|
|
|
660 "input_data": {
|
|
|
661 "id": 16,
|
|
|
662 "output_name": "fileout_log"
|
|
|
663 }
|
|
|
664 },
|
|
|
665 "inputs": [],
|
|
|
666 "label": null,
|
|
|
667 "name": "FastME",
|
|
|
668 "outputs": [
|
|
|
669 {
|
|
|
670 "name": "fileout_log",
|
|
|
671 "type": "txt"
|
|
|
672 },
|
|
|
673 {
|
|
|
674 "name": "fileout",
|
|
|
675 "type": "txt"
|
|
|
676 }
|
|
|
677 ],
|
|
|
678 "position": {
|
|
|
679 "left": 1740,
|
|
|
680 "top": 200
|
|
|
681 },
|
|
|
682 "post_job_actions": {},
|
|
|
683 "tool_errors": null,
|
|
|
684 "tool_id": "toolshed.g2.bx.psu.edu/repos/gandres/fastme/sniplay_fastme/1.0.2",
|
|
|
685 "tool_state": "{\"distance\": \"\\\"I\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"Newick tree\\\"\", \"input_data\": \"null\", \"model\": \"\\\"4\\\"\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
686 "tool_version": "1.0.2",
|
|
|
687 "type": "tool",
|
|
|
688 "user_outputs": [],
|
|
|
689 "uuid": "0fd8a01b-9dd4-4347-a68c-6c7c4c6c077b"
|
|
|
690 },
|
|
|
691 "18": {
|
|
|
692 "annotation": "",
|
|
|
693 "id": 18,
|
|
|
694 "input_connections": {
|
|
|
695 "filein": {
|
|
|
696 "id": 17,
|
|
|
697 "output_name": "fileout"
|
|
|
698 }
|
|
|
699 },
|
|
|
700 "inputs": [],
|
|
|
701 "label": null,
|
|
|
702 "name": "Rooting",
|
|
|
703 "outputs": [
|
|
|
704 {
|
|
|
705 "name": "fileout_log",
|
|
|
706 "type": "txt"
|
|
|
707 },
|
|
|
708 {
|
|
|
709 "name": "fileout",
|
|
|
710 "type": "txt"
|
|
|
711 }
|
|
|
712 ],
|
|
|
713 "position": {
|
|
|
714 "left": 1960,
|
|
|
715 "top": 200
|
|
|
716 },
|
|
|
717 "post_job_actions": {},
|
|
|
718 "tool_errors": null,
|
|
|
719 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/1.0.2",
|
|
|
720 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"c1041690638511e584e3005056887438\\\"\", \"fileout_label\": \"\\\"out tree\\\"\", \"filein\": \"null\", \"chromInfo\": \"\\\"/w/galaxy/galaxy4gwen/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
|
|
|
721 "tool_version": "1.0.2",
|
|
|
722 "type": "tool",
|
|
|
723 "user_outputs": [],
|
|
|
724 "uuid": "a3bf63b2-f630-438c-8bdb-4800dbf0c84d"
|
|
|
725 }
|
|
|
726 },
|
|
|
727 "uuid": "787a27ea-111f-4e9b-b3e9-a649b0d41af8"
|
|
|
728 } |
