Mercurial > repos > jjohnson > mmuflr

comparison Galaxy-Workflow-MMuFLR_Human_from_MPileup_v1.4.ga @ 0:4f70b23c497a

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author jjohnson
date Tue, 04 Jun 2013 09:51:17 -0400
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-1:000000000000 0:4f70b23c497a
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "MMuFLR_Human_from_MPileup_v1.4",
6 "steps": {
7 "0": {
8 "annotation": "Tabular output from SAMtools mpileup",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "Tabular output from SAMtools mpileup",
14 "name": "Output from SAMtools MPileup"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
20 "left": 200,
21 "top": 273
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Output from SAMtools MPileup\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "Known SNPs - dbSNP.vcf",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "Known SNPs - dbSNP.vcf",
37 "name": "VCF file of known variants (dbSNP)"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 432,
44 "top": 403
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}",
49 "tool_version": null,
50 "type": "data_input",
51 "user_outputs": []
52 },
53 "2": {
54 "annotation": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)",
55 "id": 2,
56 "input_connections": {},
57 "inputs": [
58 {
59 "description": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)",
60 "name": "VCF file of additional known variants "
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
65 "position": {
66 "left": 818,
67 "top": 453
68 },
69 "tool_errors": null,
70 "tool_id": null,
71 "tool_state": "{\"name\": \"VCF file of additional known variants \"}",
72 "tool_version": null,
73 "type": "data_input",
74 "user_outputs": []
75 },
76 "3": {
77 "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nLeave VCF_ID blank for tumor sample",
78 "id": 3,
79 "input_connections": {
80 "input_file": {
81 "id": 0,
82 "output_name": "output"
83 }
84 },
85 "inputs": [
86 {
87 "description": "runtime parameter for tool Pileup to VCF",
88 "name": "min_base_qual"
89 }
90 ],
91 "name": "Pileup to VCF",
92 "outputs": [
93 {
94 "name": "output_file",
95 "type": "vcf"
96 }
97 ],
98 "position": {
99 "left": 459,
100 "top": 200
101 },
102 "post_job_actions": {},
103 "tool_errors": null,
104 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0",
105 "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}",
106 "tool_version": "2.0",
107 "type": "tool",
108 "user_outputs": []
109 },
110 "4": {
111 "annotation": "Annotate the ID field with dbSNP IDs.",
112 "id": 4,
113 "input_connections": {
114 "dbSnp": {
115 "id": 1,
116 "output_name": "output"
117 },
118 "input": {
119 "id": 3,
120 "output_name": "output_file"
121 }
122 },
123 "inputs": [],
124 "name": "SnpSift Annotate",
125 "outputs": [
126 {
127 "name": "output",
128 "type": "vcf"
129 }
130 ],
131 "position": {
132 "left": 751,
133 "top": 256
134 },
135 "post_job_actions": {
136 "HideDatasetActionoutput": {
137 "action_arguments": {},
138 "action_type": "HideDatasetAction",
139 "output_name": "output"
140 }
141 },
142 "tool_errors": null,
143 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2",
144 "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}",
145 "tool_version": "3.2",
146 "type": "tool",
147 "user_outputs": []
148 },
149 "5": {
150 "annotation": "Annotate the ID field with users known variant IDs.",
151 "id": 5,
152 "input_connections": {
153 "dbSnp": {
154 "id": 2,
155 "output_name": "output"
156 },
157 "input": {
158 "id": 4,
159 "output_name": "output"
160 }
161 },
162 "inputs": [],
163 "name": "SnpSift Annotate",
164 "outputs": [
165 {
166 "name": "output",
167 "type": "vcf"
168 }
169 ],
170 "position": {
171 "left": 1134,
172 "top": 284
173 },
174 "post_job_actions": {
175 "HideDatasetActionoutput": {
176 "action_arguments": {},
177 "action_type": "HideDatasetAction",
178 "output_name": "output"
179 }
180 },
181 "tool_errors": null,
182 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_annotate/3.2",
183 "tool_state": "{\"annotate\": \"{\\\"id\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"dbSnp\": \"null\", \"annotate_cmd\": \"\\\"False\\\"\", \"__page__\": 0}",
184 "tool_version": "3.2",
185 "type": "tool",
186 "user_outputs": []
187 },
188 "6": {
189 "annotation": "Filter out chrM variations and any variant with an annotated ID",
190 "id": 6,
191 "input_connections": {
192 "input": {
193 "id": 5,
194 "output_name": "output"
195 }
196 },
197 "inputs": [],
198 "name": "SnpSift Filter",
199 "outputs": [
200 {
201 "name": "output",
202 "type": "vcf"
203 }
204 ],
205 "position": {
206 "left": 1488,
207 "top": 378
208 },
209 "post_job_actions": {},
210 "tool_errors": null,
211 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2",
212 "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"(CHROM !~ 'chrM') & (ID = '')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}",
213 "tool_version": "3.2",
214 "type": "tool",
215 "user_outputs": []
216 },
217 "7": {
218 "annotation": "",
219 "id": 7,
220 "input_connections": {
221 "input": {
222 "id": 6,
223 "output_name": "output"
224 }
225 },
226 "inputs": [],
227 "name": "SnpEff",
228 "outputs": [
229 {
230 "name": "snpeff_output",
231 "type": "vcf"
232 },
233 {
234 "name": "statsFile",
235 "type": "html"
236 }
237 ],
238 "position": {
239 "left": 1728,
240 "top": 310
241 },
242 "post_job_actions": {},
243 "tool_errors": null,
244 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpEff/3.2",
245 "tool_state": "{\"spliceSiteSize\": \"\\\"2\\\"\", \"filterHomHet\": \"\\\"no_filter\\\"\", \"outputFormat\": \"\\\"vcf\\\"\", \"udLength\": \"\\\"0\\\"\", \"inputFormat\": \"\\\"vcf\\\"\", \"filterIn\": \"\\\"no_filter\\\"\", \"__page__\": 0, \"filterOut\": \"[\\\"no-downstream\\\", \\\"no-intergenic\\\", \\\"no-intron\\\", \\\"no-upstream\\\", \\\"no-utr\\\"]\", \"genomeVersion\": \"\\\"GRCh37.68\\\"\", \"regulation\": \"null\", \"generate_stats\": \"\\\"True\\\"\", \"noLog\": \"\\\"True\\\"\", \"chr\": \"\\\"\\\"\", \"intervals\": \"null\", \"offset\": \"\\\"\\\"\", \"input\": \"null\", \"transcripts\": \"null\", \"annotations\": \"[\\\"hgvs\\\", \\\"lof\\\"]\"}",
246 "tool_version": "3.2",
247 "type": "tool",
248 "user_outputs": []
249 },
250 "8": {
251 "annotation": "Filter SnpEffects keeping FRAME_SHIFT \nvariants",
252 "id": 8,
253 "input_connections": {
254 "input": {
255 "id": 7,
256 "output_name": "snpeff_output"
257 }
258 },
259 "inputs": [],
260 "name": "SnpSift Filter",
261 "outputs": [
262 {
263 "name": "output",
264 "type": "vcf"
265 }
266 ],
267 "position": {
268 "left": 2061,
269 "top": 310
270 },
271 "post_job_actions": {},
272 "tool_errors": null,
273 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2",
274 "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'FRAME_SHIFT' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}",
275 "tool_version": "3.2",
276 "type": "tool",
277 "user_outputs": []
278 },
279 "9": {
280 "annotation": "Filter SnpEffects keeping NON_SYNONYMOUS_CODING variants",
281 "id": 9,
282 "input_connections": {
283 "input": {
284 "id": 7,
285 "output_name": "snpeff_output"
286 }
287 },
288 "inputs": [],
289 "name": "SnpSift Filter",
290 "outputs": [
291 {
292 "name": "output",
293 "type": "vcf"
294 }
295 ],
296 "position": {
297 "left": 2058,
298 "top": 475
299 },
300 "post_job_actions": {},
301 "tool_errors": null,
302 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2",
303 "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"False\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[*].EFFECT = 'NON_SYNONYMOUS_CODING')\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}",
304 "tool_version": "3.2",
305 "type": "tool",
306 "user_outputs": []
307 },
308 "10": {
309 "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence",
310 "id": 10,
311 "input_connections": {
312 "snp_effect_vcf": {
313 "id": 8,
314 "output_name": "output"
315 }
316 },
317 "inputs": [],
318 "name": "SnpEff Ensembl CDS",
319 "outputs": [
320 {
321 "name": "html_report",
322 "type": "html"
323 },
324 {
325 "name": "tsv_report",
326 "type": "tabular"
327 },
328 {
329 "name": "text_report",
330 "type": "text"
331 }
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335 "top": 226
336 },
337 "post_job_actions": {
338 "HideDatasetActiontext_report": {
339 "action_arguments": {},
340 "action_type": "HideDatasetAction",
341 "output_name": "text_report"
342 }
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344 "tool_errors": null,
345 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2",
346 "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"FRAME_SHIFT\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}",
347 "tool_version": "1.2",
348 "type": "tool",
349 "user_outputs": []
350 },
351 "11": {
352 "annotation": "Ignore variations in SPLICE donor/acceptor regions",
353 "id": 11,
354 "input_connections": {
355 "input": {
356 "id": 9,
357 "output_name": "output"
358 }
359 },
360 "inputs": [],
361 "name": "SnpSift Filter",
362 "outputs": [
363 {
364 "name": "output",
365 "type": "vcf"
366 }
367 ],
368 "position": {
369 "left": 2281,
370 "top": 409
371 },
372 "post_job_actions": {},
373 "tool_errors": null,
374 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff/snpSift_filter/3.2",
375 "tool_state": "{\"__page__\": 0, \"inverse\": \"\\\"True\\\"\", \"addFilter\": \"\\\"\\\"\", \"rmFilter\": \"\\\"\\\"\", \"expr\": \"\\\"( EFF[ANY].EFFECT =~ 'SPLICE' )\\\"\", \"filterId\": \"\\\"\\\"\", \"pass\": \"\\\"False\\\"\", \"input\": \"null\"}",
376 "tool_version": "3.2",
377 "type": "tool",
378 "user_outputs": []
379 },
380 "12": {
381 "annotation": "Query biomart for the coding sequence for the Ensembl Transcripts associated with the variation and report the variation in the coding sequence",
382 "id": 12,
383 "input_connections": {
384 "snp_effect_vcf": {
385 "id": 11,
386 "output_name": "output"
387 }
388 },
389 "inputs": [],
390 "name": "SnpEff Ensembl CDS",
391 "outputs": [
392 {
393 "name": "html_report",
394 "type": "html"
395 },
396 {
397 "name": "tsv_report",
398 "type": "tabular"
399 },
400 {
401 "name": "text_report",
402 "type": "text"
403 }
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407 "top": 381
408 },
409 "post_job_actions": {
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411 "action_arguments": {},
412 "action_type": "HideDatasetAction",
413 "output_name": "text_report"
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416 "tool_errors": null,
417 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/snpeff_cds_report/SnpEff-cds-report/1.2",
418 "tool_state": "{\"ensembl_host\": \"\\\"feb2012\\\"\", \"report_format\": \"[\\\"html\\\", \\\"tsv\\\"]\", \"ensembl_dataset\": \"\\\"hsapiens_gene_ensembl\\\"\", \"__page__\": 0, \"effects_filter\": \"\\\"NON_SYNONYMOUS_CODING\\\"\", \"polya\": \"\\\"5\\\"\", \"all_effects\": \"\\\"False\\\"\", \"snpeff_aa_change\": \"\\\"False\\\"\", \"snp_effect_vcf\": \"null\", \"with_ccds\": \"\\\"False\\\"\"}",
419 "tool_version": "1.2",
420 "type": "tool",
421 "user_outputs": []
422 }
423 }
424 }