Mercurial > repos > jjohnson > mmuff

comparison Galaxy-Workflow-MMuFF_v1.2.ga @ 0:8b008a3c3ccb

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author jjohnson
date Tue, 12 Mar 2013 14:59:40 -0400
parents
children 6e49aa2461bd
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-1:000000000000 0:8b008a3c3ccb
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "MMuFF_v1.2",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Forward reads fastq"
15 }
16 ],
17 "name": "Input dataset",
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21 "top": 313
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": "",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "",
37 "name": "Reverse reads fastq"
38 }
39 ],
40 "name": "Input dataset",
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43 "left": 242,
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": "dbSNP.vcf",
55 "id": 2,
56 "input_connections": {},
57 "inputs": [
58 {
59 "description": "dbSNP.vcf",
60 "name": "VCF file of known variants (dbSNP)"
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
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67 "top": 532
68 },
69 "tool_errors": null,
70 "tool_id": null,
71 "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}",
72 "tool_version": null,
73 "type": "data_input",
74 "user_outputs": []
75 },
76 "3": {
77 "annotation": "These are locations other than those in dbSNP. The 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) even if it is a bogus value at position 1",
78 "id": 3,
79 "input_connections": {},
80 "inputs": [
81 {
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83 "name": "VCF file of additional known variants "
84 }
85 ],
86 "name": "Input dataset",
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90 "top": 573
91 },
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93 "tool_id": null,
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98 },
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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 },
125 "post_job_actions": {},
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145 "name": "input_type"
146 }
147 ],
148 "name": "FASTQ Groomer",
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150 {
151 "name": "output_file",
152 "type": "fastqsanger"
153 }
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158 },
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164 "type": "tool",
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166 },
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173 "output_name": "output_file"
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": "refGenomeSource"
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 }
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208 },
209 "post_job_actions": {
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240 }
241 },
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243 "name": "Filter SAM or BAM",
244 "outputs": [
245 {
246 "name": "output1",
247 "type": "sam"
248 }
249 ],
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282 "type": "txt"
283 }
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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 }
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316 "top": 500
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336 "name": "Paired Read Mate Fixer",
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339 "name": "out_file",
340 "type": "bam"
341 }
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367 "output_name": "out_file"
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370 "inputs": [],
371 "name": "Mark Duplicate reads",
372 "outputs": [
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374 "name": "out_file",
375 "type": "bam"
376 },
377 {
378 "name": "html_file",
379 "type": "html"
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391 "type": "tool",
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403 "inputs": [
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406 "name": "source"
407 }
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409 "name": "Reorder SAM/BAM",
410 "outputs": [
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412 "name": "outFile",
413 "type": "bam"
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437 "inputs": [
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439 "description": "runtime parameter for tool Realigner Target Creator",
440 "name": "reference_source"
441 }
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443 "name": "Realigner Target Creator",
444 "outputs": [
445 {
446 "name": "output_interval",
447 "type": "gatk_interval"
448 },
449 {
450 "name": "output_log",
451 "type": "txt"
452 }
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491 "name": "Indel Realigner",
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533 "name": "out_file",
534 "type": "bam"
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536 {
537 "name": "html_file",
538 "type": "html"
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576 "name": "reference_source"
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586 "name": "output_log",
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