diff preprocess.R @ 4:3fcbb8030fcc draft

"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"

--- 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")