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comparison Galaxy-Workflow-MMuFF.ga @ 5:60a6f2d92058

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Adding Galaxy-Workflow-MMuFF.ga (version 1.4 updated for SnpEff v3.2 and snpeff_cds_report v1.2)
author Jim Johnson <jj@umn.edu>
date Sun, 26 May 2013 08:17:53 -0500
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4:6c284cb55352 5:60a6f2d92058
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "MMuFF_Human_v1.4",
6 "steps": {
7 "0": {
8 "annotation": "Human RNA-seq paired reads left mates",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "Human RNA-seq paired reads left mates",
14 "name": "Forward reads fastq"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
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20 "left": 240,
21 "top": 314
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Forward reads fastq\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "Human RNA-seq paired reads right mates",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "Human RNA-seq paired reads right mates",
37 "name": "Reverse reads fastq"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
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44 "top": 410
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"Reverse reads fastq\"}",
49 "tool_version": null,
50 "type": "data_input",
51 "user_outputs": []
52 },
53 "2": {
54 "annotation": "Known SNPs - dbSNP.vcf",
55 "id": 2,
56 "input_connections": {},
57 "inputs": [
58 {
59 "description": "Known SNPs - dbSNP.vcf",
60 "name": "VCF file of known variants (dbSNP)"
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
65 "position": {
66 "left": 2362,
67 "top": 745
68 },
69 "tool_errors": null,
70 "tool_id": null,
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72 "tool_version": null,
73 "type": "data_input",
74 "user_outputs": []
75 },
76 "3": {
77 "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)",
78 "id": 3,
79 "input_connections": {},
80 "inputs": [
81 {
82 "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)",
83 "name": "VCF file of additional known variants "
84 }
85 ],
86 "name": "Input dataset",
87 "outputs": [],
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90 "top": 576
91 },
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93 "tool_id": null,
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96 "type": "data_input",
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98 },
99 "4": {
100 "annotation": "Convert quality scores to sanger scale",
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102 "input_connections": {
103 "input_file": {
104 "id": 0,
105 "output_name": "output"
106 }
107 },
108 "inputs": [
109 {
110 "description": "runtime parameter for tool FASTQ Groomer",
111 "name": "input_type"
112 }
113 ],
114 "name": "FASTQ Groomer",
115 "outputs": [
116 {
117 "name": "output_file",
118 "type": "fastqsanger"
119 }
120 ],
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124 },
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129 "tool_version": "1.0.4",
130 "type": "tool",
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132 },
133 "5": {
134 "annotation": "Convert quality scores to sanger scale",
135 "id": 5,
136 "input_connections": {
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138 "id": 1,
139 "output_name": "output"
140 }
141 },
142 "inputs": [
143 {
144 "description": "runtime parameter for tool FASTQ Groomer",
145 "name": "input_type"
146 }
147 ],
148 "name": "FASTQ Groomer",
149 "outputs": [
150 {
151 "name": "output_file",
152 "type": "fastqsanger"
153 }
154 ],
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157 "top": 431
158 },
159 "post_job_actions": {},
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163 "tool_version": "1.0.4",
164 "type": "tool",
165 "user_outputs": []
166 },
167 "6": {
168 "annotation": "Map paired reads to reference genome",
169 "id": 6,
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174 },
175 "singlePaired|input2": {
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177 "output_name": "output_file"
178 }
179 },
180 "inputs": [
181 {
182 "description": "runtime parameter for tool Tophat for Illumina",
183 "name": "singlePaired"
184 }
185 ],
186 "name": "Tophat for Illumina",
187 "outputs": [
188 {
189 "name": "insertions",
190 "type": "bed"
191 },
192 {
193 "name": "deletions",
194 "type": "bed"
195 },
196 {
197 "name": "junctions",
198 "type": "bed"
199 },
200 {
201 "name": "accepted_hits",
202 "type": "bam"
203 }
204 ],
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208 },
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229 "tool_version": "1.5.0",
230 "type": "tool",
231 "user_outputs": []
232 },
233 "7": {
234 "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)",
235 "id": 7,
236 "input_connections": {
237 "input1": {
238 "id": 6,
239 "output_name": "accepted_hits"
240 }
241 },
242 "inputs": [],
243 "name": "Filter SAM or BAM",
244 "outputs": [
245 {
246 "name": "output1",
247 "type": "sam"
248 }
249 ],
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252 "top": 366
253 },
254 "post_job_actions": {
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264 "tool_version": "1.1.0",
265 "type": "tool",
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267 },
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271 "input_connections": {
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274 "output_name": "output1"
275 }
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277 "inputs": [],
278 "name": "flagstat",
279 "outputs": [
280 {
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282 "type": "txt"
283 }
284 ],
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293 "tool_version": "1.0.0",
294 "type": "tool",
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296 },
297 "9": {
298 "annotation": "Add Read Group info required by GATK tools",
299 "id": 9,
300 "input_connections": {
301 "inputFile": {
302 "id": 7,
303 "output_name": "output1"
304 }
305 },
306 "inputs": [],
307 "name": "Add or Replace Groups",
308 "outputs": [
309 {
310 "name": "outFile",
311 "type": "bam"
312 }
313 ],
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316 "top": 503
317 },
318 "post_job_actions": {},
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322 "tool_version": "1.56.0",
323 "type": "tool",
324 "user_outputs": []
325 },
326 "10": {
327 "annotation": "Synchronize paired reads",
328 "id": 10,
329 "input_connections": {
330 "input_file": {
331 "id": 9,
332 "output_name": "outFile"
333 }
334 },
335 "inputs": [],
336 "name": "Paired Read Mate Fixer",
337 "outputs": [
338 {
339 "name": "out_file",
340 "type": "bam"
341 }
342 ],
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347 "post_job_actions": {
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357 "tool_version": "1.56.0",
358 "type": "tool",
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360 },
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362 "annotation": "Remove duplicate reads",
363 "id": 11,
364 "input_connections": {
365 "input_file": {
366 "id": 10,
367 "output_name": "out_file"
368 }
369 },
370 "inputs": [],
371 "name": "Mark Duplicate reads",
372 "outputs": [
373 {
374 "name": "out_file",
375 "type": "bam"
376 },
377 {
378 "name": "html_file",
379 "type": "html"
380 }
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385 },
386 "post_job_actions": {},
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390 "tool_version": "1.56.0",
391 "type": "tool",
392 "user_outputs": []
393 },
394 "12": {
395 "annotation": "Reorder BAM for GATK tools",
396 "id": 12,
397 "input_connections": {
398 "inputFile": {
399 "id": 11,
400 "output_name": "out_file"
401 }
402 },
403 "inputs": [],
404 "name": "Reorder SAM/BAM",
405 "outputs": [
406 {
407 "name": "outFile",
408 "type": "bam"
409 }
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420 "type": "tool",
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433 "output_name": "output"
434 }
435 },
436 "inputs": [],
437 "name": "Realigner Target Creator",
438 "outputs": [
439 {
440 "name": "output_interval",
441 "type": "gatk_interval"
442 },
443 {
444 "name": "output_log",
445 "type": "txt"
446 }
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463 "type": "tool",
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523 "type": "bam"
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