Mercurial > repos > galaxyp > custom_pro_db
view customProDB.R @ 8:fa6aa0d5a27c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author | galaxyp |
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date | Mon, 09 May 2016 12:55:26 -0400 |
parents | b83a4002aab1 |
children | 328a1e3b5261 |
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#!/usr/bin/env Rscript initial.options <- commandArgs(trailingOnly = FALSE) script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)])) ## begin warning handler withCallingHandlers({ library(methods) # Because Rscript does not always do this options('useFancyQuotes' = FALSE) suppressPackageStartupMessages(library("optparse")) suppressPackageStartupMessages(library("RGalaxy")) option_list <- list() option_list$bam <- make_option('--bam', type='character') option_list$bai <- make_option('--bai', type='character') option_list$vcf <- make_option('--vcf', type='character') option_list$exon_anno <- make_option('--exon_anno', type='character') option_list$proteinseq <- make_option('--proteinseq', type='character') option_list$procodingseq <- make_option('--procodingseq', type='character') option_list$ids <- make_option('--ids', type='character') option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') option_list$outputFile <- make_option('--outputFile', type='character') opt <- parse_args(OptionParser(option_list=option_list)) customProDB <- function( bam_file = GalaxyInputFile(required=TRUE), bai_file = GalaxyInputFile(required=TRUE), vcf_file = GalaxyInputFile(required=TRUE), exon_anno_file = GalaxyInputFile(required=TRUE), proteinseq_file = GalaxyInputFile(required=TRUE), procodingseq_file = GalaxyInputFile(required=TRUE), rpkmCutoff = GalaxyNumericParam(required=TRUE), ids_file = GalaxyInputFile(required=TRUE), outputFile = GalaxyOutput("FASTA","fasta")) { file.symlink(exon_anno_file, "exon_anno.RData") file.symlink(proteinseq_file, "proseq.RData") file.symlink(procodingseq_file, "procodingseq.RData") file.symlink(ids_file, "ids.RData") bamLink = "input.bam" file.symlink(bam_file, bamLink) file.symlink(bai_file, paste(bamLink, ".bai", sep="")) suppressPackageStartupMessages(library(customProDB)) easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file), rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", nov_junction=F, INDEL=T, lablersid=F, COSMIC=F) } params <- list() for(param in names(opt)) { if (!param == "help") params[param] <- opt[param] } setClass("GalaxyRemoteError", contains="character") wrappedFunction <- function(f) { tryCatch(do.call(f, params), error=function(e) new("GalaxyRemoteError", conditionMessage(e))) } suppressPackageStartupMessages(library(RGalaxy)) do.call(customProDB, params) ## end warning handler }, warning = function(w) { cat(paste("Warning:", conditionMessage(w), "\n")) invokeRestart("muffleWarning") })