Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.R @ 9:328a1e3b5261 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 08 Jun 2016 14:04:54 -0400
parents fa6aa0d5a27c
children 982fb2cde6c5
comparison
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8:fa6aa0d5a27c 9:328a1e3b5261
21 option_list$vcf <- make_option('--vcf', type='character') 21 option_list$vcf <- make_option('--vcf', type='character')
22 option_list$exon_anno <- make_option('--exon_anno', type='character') 22 option_list$exon_anno <- make_option('--exon_anno', type='character')
23 option_list$proteinseq <- make_option('--proteinseq', type='character') 23 option_list$proteinseq <- make_option('--proteinseq', type='character')
24 option_list$procodingseq <- make_option('--procodingseq', type='character') 24 option_list$procodingseq <- make_option('--procodingseq', type='character')
25 option_list$ids <- make_option('--ids', type='character') 25 option_list$ids <- make_option('--ids', type='character')
26 option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
27 option_list$cosmic <- make_option('--cosmic', type='character')
28 option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
26 option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') 29 option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
30 #option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
31 #option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
27 option_list$outputFile <- make_option('--outputFile', type='character') 32 option_list$outputFile <- make_option('--outputFile', type='character')
28 33
29 34
30 opt <- parse_args(OptionParser(option_list=option_list)) 35 opt <- parse_args(OptionParser(option_list=option_list))
31 36
35 bai_file = GalaxyInputFile(required=TRUE), 40 bai_file = GalaxyInputFile(required=TRUE),
36 vcf_file = GalaxyInputFile(required=TRUE), 41 vcf_file = GalaxyInputFile(required=TRUE),
37 exon_anno_file = GalaxyInputFile(required=TRUE), 42 exon_anno_file = GalaxyInputFile(required=TRUE),
38 proteinseq_file = GalaxyInputFile(required=TRUE), 43 proteinseq_file = GalaxyInputFile(required=TRUE),
39 procodingseq_file = GalaxyInputFile(required=TRUE), 44 procodingseq_file = GalaxyInputFile(required=TRUE),
45 ids_file = GalaxyInputFile(required=TRUE),
46 dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
47 cosmic_file = GalaxyInputFile(required=FALSE),
48 annotationFromHistory = GalaxyLogicalParam(required=FALSE),
40 rpkmCutoff = GalaxyNumericParam(required=TRUE), 49 rpkmCutoff = GalaxyNumericParam(required=TRUE),
41 ids_file = GalaxyInputFile(required=TRUE), 50 #outputIndels = GalaxyLogicalParam(required=FALSE),
51 #outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
42 outputFile = GalaxyOutput("FASTA","fasta")) 52 outputFile = GalaxyOutput("FASTA","fasta"))
43 { 53 {
44 file.symlink(exon_anno_file, "exon_anno.RData") 54 file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
45 file.symlink(proteinseq_file, "proseq.RData") 55 file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
46 file.symlink(procodingseq_file, "procodingseq.RData") 56 file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
47 file.symlink(ids_file, "ids.RData") 57 file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
58
59 if (length(dbsnpinCoding_file) > 0)
60 {
61 file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
62 labelrsid = T
63 }
64 else
65 {
66 labelrsid = F
67 }
68
69 if (length(cosmic_file) > 0)
70 {
71 file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
72 cosmic = T
73 }
74 else
75 {
76 cosmic = F
77 }
48 78
49 bamLink = "input.bam" 79 bamLink = "input.bam"
50 file.symlink(bam_file, bamLink) 80 file.symlink(bam_file, bamLink)
51 file.symlink(bai_file, paste(bamLink, ".bai", sep="")) 81 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
52 82
53 suppressPackageStartupMessages(library(customProDB)) 83 suppressPackageStartupMessages(library(customProDB))
54 84
55 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file), 85 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
56 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", 86 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
57 nov_junction=F, INDEL=T, lablersid=F, COSMIC=F) 87 nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
58 } 88 }
59 89
60 90
61 params <- list() 91 params <- list()
62 for(param in names(opt)) 92 for(param in names(opt))