Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.R @ 6:61e45c111ef7 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, 03 Feb 2016 12:37:47 -0500
parents 7e078d4e40f8
children b83a4002aab1
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1 #!/usr/bin/env Rscript
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3 initial.options <- commandArgs(trailingOnly = FALSE)
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4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
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6 ## begin warning handler
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7 withCallingHandlers({
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9 library(methods) # Because Rscript does not always do this
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11 options('useFancyQuotes' = FALSE)
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13 suppressPackageStartupMessages(library("optparse"))
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14 suppressPackageStartupMessages(library("RGalaxy"))
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17 option_list <- list()
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19 option_list$bam <- make_option('--bam', type='character')
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20 option_list$bai <- make_option('--bai', type='character')
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21 option_list$vcf <- make_option('--vcf', type='character')
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22 option_list$exon_anno <- make_option('--exon_anno', type='character')
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23 option_list$proteinseq <- make_option('--proteinseq', type='character')
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24 option_list$procodingseq <- make_option('--procodingseq', type='character')
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25 option_list$ids <- make_option('--ids', type='character')
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26 option_list$outputFile <- make_option('--outputFile', type='character')
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29 opt <- parse_args(OptionParser(option_list=option_list))
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32 customProDB <- function(
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33 bam_file = GalaxyInputFile(required=TRUE),
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34 bai_file = GalaxyInputFile(required=TRUE),
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35 vcf_file = GalaxyInputFile(required=TRUE),
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36 exon_anno_file = GalaxyInputFile(required=TRUE),
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37 proteinseq_file = GalaxyInputFile(required=TRUE),
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38 procodingseq_file = GalaxyInputFile(required=TRUE),
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39 ids_file = GalaxyInputFile(required=TRUE),
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40 outputFile = GalaxyOutput("FASTA","fasta"))
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41 {
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42 file.symlink(exon_anno_file, paste(dirname(exon_anno_file), "exon_anno.RData", sep="/"))
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43 file.symlink(proteinseq_file, paste(dirname(exon_anno_file), "proseq.RData", sep="/"))
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44 file.symlink(procodingseq_file, paste(dirname(exon_anno_file), "procodingseq.RData", sep="/"))
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45 file.symlink(ids_file, paste(dirname(exon_anno_file), "ids.RData", sep="/"))
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47 bamLink = paste(dirname(bam_file), "input.bam", sep="/")
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48 file.symlink(bam_file, bamLink)
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49 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
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51 suppressPackageStartupMessages(library(customProDB))
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53 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file),
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54 outfile_path=".", outfile_name="output",
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55 nov_junction=F, INDEL=T, lablersid=F, COSMIC=F)
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56 }
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59 params <- list()
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60 for(param in names(opt))
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61 {
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62 if (!param == "help")
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63 params[param] <- opt[param]
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64 }
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66 setClass("GalaxyRemoteError", contains="character")
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67 wrappedFunction <- function(f)
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68 {
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69 tryCatch(do.call(f, params),
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70 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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71 }
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74 suppressPackageStartupMessages(library(RGalaxy))
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75 do.call(customProDB, params)
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77 ## end warning handler
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78 }, warning = function(w) {
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79 cat(paste("Warning:", conditionMessage(w), "\n"))
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80 invokeRestart("muffleWarning")
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81 })