Mercurial > repos > jjohnson > mmuflr

comparison Galaxy-Workflow-MMuFLR_Human_germline_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_germline_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 }
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21 "top": 287
22 },
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24 "tool_id": null,
25 "tool_state": "{\"name\": \"Forward reads fastq\"}",
26 "tool_version": null,
27 "type": "data_input",
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29 },
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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",
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44 "top": 383
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",
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67 "top": 758
68 },
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73 "type": "data_input",
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75 },
76 "3": {
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82 "output_name": "output"
83 }
84 },
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88 "name": "input_type"
89 }
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96 }
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109 },
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122 "name": "input_type"
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135 },
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140 "tool_version": "1.0.4",
141 "type": "tool",
142 "user_outputs": []
143 },
144 "5": {
145 "annotation": "Map paired reads to reference genome",
146 "id": 5,
147 "input_connections": {
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150 "output_name": "output_file"
151 },
152 "singlePaired|input2": {
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154 "output_name": "output_file"
155 }
156 },
157 "inputs": [
158 {
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160 "name": "singlePaired"
161 }
162 ],
163 "name": "Tophat for Illumina",
164 "outputs": [
165 {
166 "name": "insertions",
167 "type": "bed"
168 },
169 {
170 "name": "deletions",
171 "type": "bed"
172 },
173 {
174 "name": "junctions",
175 "type": "bed"
176 },
177 {
178 "name": "accepted_hits",
179 "type": "bam"
180 }
181 ],
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185 },
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189 "action_type": "HideDatasetAction",
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191 },
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200 "output_name": "junctions"
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207 "type": "tool",
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209 },
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213 "input_connections": {
214 "input1": {
215 "id": 5,
216 "output_name": "accepted_hits"
217 }
218 },
219 "inputs": [],
220 "name": "Filter SAM or BAM",
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225 }
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241 "tool_version": "1.1.0",
242 "type": "tool",
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244 },
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251 "output_name": "output1"
252 }
253 },
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255 "name": "flagstat",
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259 "type": "txt"
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270 "tool_version": "1.0.0",
271 "type": "tool",
272 "user_outputs": []
273 },
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275 "annotation": "Add Read Group info required by GATK tools",
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277 "input_connections": {
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281 }
282 },
283 "inputs": [],
284 "name": "Add or Replace Groups",
285 "outputs": [
286 {
287 "name": "outFile",
288 "type": "bam"
289 }
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294 },
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299 "tool_version": "1.56.0",
300 "type": "tool",
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302 },
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309 "output_name": "outFile"
310 }
311 },
312 "inputs": [],
313 "name": "Paired Read Mate Fixer",
314 "outputs": [
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317 "type": "bam"
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334 "tool_version": "1.56.0",
335 "type": "tool",
336 "user_outputs": []
337 },
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340 "id": 10,
341 "input_connections": {
342 "input_file": {
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344 "output_name": "out_file"
345 }
346 },
347 "inputs": [],
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352 "type": "bam"
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354 {
355 "name": "html_file",
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367 "tool_version": "1.56.0",
368 "type": "tool",
369 "user_outputs": []
370 },
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379 },
380 "inputs": [],
381 "name": "Reorder SAM/BAM",
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385 "type": "bam"
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397 "type": "tool",
398 "user_outputs": []
399 },
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406 "output_name": "outFile"
407 },
408 "rod_bind_0|rod_bind_type|input_rod": {
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410 "output_name": "output"
411 }
412 },
413 "inputs": [],
414 "name": "Realigner Target Creator",
415 "outputs": [
416 {
417 "name": "output_interval",
418 "type": "gatk_interval"
419 },
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421 "name": "output_log",
422 "type": "txt"
423 }
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439 "tool_version": "0.0.4",
440 "type": "tool",
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442 },
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451 "target_intervals": {
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482 "tool_version": "0.0.6",
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492 "output_name": "output_bam"
493 }
494 },
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500 "type": "bam"
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504 "type": "html"
505 }
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527 "type": "tool",
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536 "output_name": "out_file"
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571 "type": "tool",
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593 "type": "vcf"
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600 "post_job_actions": {},
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602 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0",
603 "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"germline\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}",
604 "tool_version": "2.0",
605 "type": "tool",
606 "user_outputs": []
607 }
608 }
609 }