Mercurial > repos > sblanck > mpagenomics
diff preprocess.R @ 4:3fcbb8030fcc draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author | sblanck |
---|---|
date | Mon, 12 Apr 2021 14:47:09 +0000 |
parents | 4d539083cf7f |
children |
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--- a/preprocess.R Tue Jun 16 04:34:09 2020 -0400 +++ b/preprocess.R Mon Apr 12 14:47:09 2021 +0000 @@ -3,7 +3,7 @@ options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) # we need that to not crash galaxy with an UTF8 error on German LC settings. -loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +#loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") library("optparse") @@ -24,6 +24,7 @@ make_option("--settingsType",type="character",default=NULL, dest="settingsType"), make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"), make_option("--zipfigures",type="character",default=NULL, dest="zipfigures"), + make_option("--zipresults",type="character",default=NULL, dest="zipresults"), make_option("--outputlog",type="character",default=NULL, dest="outputlog"), make_option("--log",type="character",default=NULL, dest="log"), make_option("--user_id",type="character",default=NULL, dest="user_id"), @@ -55,6 +56,7 @@ settingsType=opt$settingsType outputGraph=opt$outputgraph zipfigures=opt$zipfigures +zipresults=opt$zipresults outputlog=opt$outputlog log=opt$log userId=opt$user_id @@ -129,6 +131,9 @@ library(MPAgenomics) +library(R.utils) +library(aroma.affymetrix) + setwd(workdir) if (outputlog){ @@ -143,13 +148,27 @@ } else { signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, normalTumorArray=tumor, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) } +setwd(mpagenomicsDir) +library(zip) +zipr(zipresults,files=".") setwd(abs_fig_dir) +#abs_fig_dir files2zip <- dir(abs_fig_dir) -zip(zipfile = "figures.zip", files = files2zip) -file.rename("figures.zip",zipfigures) +zipr(zipfigures, files = files2zip) + summarydf=data.frame(celFileNameList,rep(dataSetName,length(celFileNameList)),rep(chipType,length(celFileNameList))) write.table(summarydf,file=summary,quote=FALSE,row.names=FALSE,col.names=FALSE,sep="\t") +if (dir.exists(mpagenomicsDir)) { + system(paste0("rm -r ", mpagenomicsDir)) + dir.create(mpagenomicsDir, showWarnings = TRUE, recursive = TRUE) + } + +if (dir.exists(dataDir)) { + system(paste0("rm -r ", dataDir)) + dir.create(dataDir, showWarnings = TRUE, recursive = TRUE) + } + if (outputlog){ sink(type="output") sink(type="message")