Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.R @ 7:b83a4002aab1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Fri, 06 May 2016 15:56:07 -0400
parents 61e45c111ef7
children fa6aa0d5a27c
comparison
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6:61e45c111ef7 7:b83a4002aab1
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$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
26 option_list$outputFile <- make_option('--outputFile', type='character') 27 option_list$outputFile <- make_option('--outputFile', type='character')
27 28
28 29
29 opt <- parse_args(OptionParser(option_list=option_list)) 30 opt <- parse_args(OptionParser(option_list=option_list))
30 31
34 bai_file = GalaxyInputFile(required=TRUE), 35 bai_file = GalaxyInputFile(required=TRUE),
35 vcf_file = GalaxyInputFile(required=TRUE), 36 vcf_file = GalaxyInputFile(required=TRUE),
36 exon_anno_file = GalaxyInputFile(required=TRUE), 37 exon_anno_file = GalaxyInputFile(required=TRUE),
37 proteinseq_file = GalaxyInputFile(required=TRUE), 38 proteinseq_file = GalaxyInputFile(required=TRUE),
38 procodingseq_file = GalaxyInputFile(required=TRUE), 39 procodingseq_file = GalaxyInputFile(required=TRUE),
40 rpkmCutoff = GalaxyNumericParam(required=TRUE),
39 ids_file = GalaxyInputFile(required=TRUE), 41 ids_file = GalaxyInputFile(required=TRUE),
40 outputFile = GalaxyOutput("FASTA","fasta")) 42 outputFile = GalaxyOutput("FASTA","fasta"))
41 { 43 {
42 file.symlink(exon_anno_file, paste(dirname(exon_anno_file), "exon_anno.RData", sep="/")) 44 file.symlink(exon_anno_file, paste(dirname(exon_anno_file), "exon_anno.RData", sep="/"))
43 file.symlink(proteinseq_file, paste(dirname(exon_anno_file), "proseq.RData", sep="/")) 45 file.symlink(proteinseq_file, paste(dirname(exon_anno_file), "proseq.RData", sep="/"))
49 file.symlink(bai_file, paste(bamLink, ".bai", sep="")) 51 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
50 52
51 suppressPackageStartupMessages(library(customProDB)) 53 suppressPackageStartupMessages(library(customProDB))
52 54
53 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file), 55 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file),
54 outfile_path=".", outfile_name="output", 56 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
55 nov_junction=F, INDEL=T, lablersid=F, COSMIC=F) 57 nov_junction=F, INDEL=T, lablersid=F, COSMIC=F)
56 } 58 }
57 59
58 60
59 params <- list() 61 params <- list()