Mercurial > repos > galaxyp > custom_pro_db
diff customProDB.R @ 3:7e078d4e40f8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author | galaxyp |
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date | Fri, 29 Jan 2016 14:26:25 -0500 |
parents | |
children | 61e45c111ef7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customProDB.R Fri Jan 29 14:26:25 2016 -0500 @@ -0,0 +1,87 @@ +#!/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$bam <- make_option('--bam', type='character') +option_list$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$procodingseq <- make_option('--procodingseq', type='character') +option_list$outputFile <- make_option('--outputFile', type='character') + + +opt <- parse_args(OptionParser(option_list=option_list)) + + +customProDB <- function( + bam_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), + outputFile = GalaxyOutput("FASTA","fasta")) +{ + if (dirname(exon_anno_file) != dirname(proteinseq_file) || + dirname(exon_anno_file) != dirname(procodingseq_file)) + { + gstop("parent directory of annotation files must all be the same") + } + + if (file.exists(outputFile)) + { + if (file.info(outputFile)$size > 0) { gstop("output file already exists") } + else + { + tryCatch( + { + file.remove(outputFile) + }, error=function(err) + { + gstop("failed to remove empty existing file") + }) + } + } + + suppressPackageStartupMessages(library(customProDB)) + + easyRun(bamFile=bamFile, vcfFile=vcfFile, annotation_path=dirname(exon_anno_file), outfile_path=dirname(outputFile), outfile_name=basename(outputFile)) +} + + +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") +})