diff ipo4xcmsSet.r @ 1:ae8de756dfcf draft

"planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"

--- a/ipo4xcmsSet.r	Thu Aug 03 06:00:00 2017 -0400
+++ b/ipo4xcmsSet.r	Mon Dec 16 05:26:42 2019 -0500
@@ -2,143 +2,56 @@
 #Authors Gildas Le Corguille and Yann Guitton
 
 
-# ----- LOG FILE -----
-log_file=file("log.txt", open = "wt")
-sink(log_file)
-sink(log_file, type = "output")
-
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
 
-# ----- PACKAGE -----
-options(bitmapType='cairo')
-cat("\tPACKAGE INFO\n")
-#pkgs=c("xcms","batch")
-pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch")
-for(pkg in pkgs) {
-  suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
-  cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
-}
-source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
-cat("\n\n"); 
+#Import the different functions
+source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+source_local("lib.r")
 
-
-
+pkgs <- c("IPO","batch")
+loadAndDisplayPackages(pkgs)
+cat("\n\n");
 
 
 # ----- ARGUMENTS -----
 cat("\tARGUMENTS INFO\n")
-listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
-write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
+args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
 
 cat("\n\n");
 
-
-# ----- ARGUMENTS PROCESSING -----
-cat("\tINFILE PROCESSING INFO\n")
-
-
-#Import the different functions
-source_local("lib.r")
-
-cat("\n\n")
-
-#Import the different functions
-
 # ----- PROCESSING INFILE -----
 cat("\tARGUMENTS PROCESSING INFO\n")
-
-xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".")
-if (!is.null(listArguments[["xsetRdataOutput"]])){
-  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
-}
-
-parametersOutput = "parametersOutput.tsv"
-if (!is.null(listArguments[["parametersOutput"]])){
-  parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL
-}
+options(bitmapType='cairo')
 
 samplebyclass = 2
-if (!is.null(listArguments[["samplebyclass"]])){
-  samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL
-}
-
-#necessary to unzip .zip file uploaded to Galaxy
-#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
-
-
-if (!is.null(listArguments[["zipfile"]])){
-  zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
-}
-
-
-if (!is.null(listArguments[["singlefile_galaxyPath"]])){
-    singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL
-    singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL
+if (!is.null(args$samplebyclass)){
+  samplebyclass = args$samplebyclass; args$samplebyclass=NULL
 }
 
-# single file case
-#@TODO: need to be refactoring
-if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
-    if(!file.exists(singlefile_galaxyPath)){
-        error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
-        print(error_message); stop(error_message)
-    }
-    
-    cwd=getwd()
-    dir.create("raw")
-    setwd("raw")
-    file.symlink(singlefile_galaxyPath,singlefile_sampleName)
-    setwd(cwd)
-    
-    directory = "raw"
-    
-}
-
-# We unzip automatically the chromatograms from the zip files.
-if(exists("zipfile") && (zipfile!="")) {
-    if(!file.exists(zipfile)){
-        error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
-        print(error_message)
-        stop(error_message)
-    }
+# ----- INFILE PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
 
-    #list all file in the zip file
-    #zip_files=unzip(zipfile,list=T)[,"Name"]
-
-    # Because IPO only want raw data in its working directory
-    dir.create("ipoworkingdir")
-    setwd("ipoworkingdir")
-
-    #unzip
-    suppressWarnings(unzip(zipfile, unzip="unzip"))
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
+singlefile <- rawFilePath$singlefile
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL)
 
-    #get the directory name
-    filesInZip=unzip(zipfile, list=T);
-    directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
-    directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
-    directory = "."
-    if (length(directories) == 1) directory = directories
-
-    cat("files_root_directory\t",directory,"\n")
-
-
-}
-
-#addition of the directory to the list of arguments in the first position
+# Check some character issues
 checkXmlStructure(directory)
-checkFilesCompatibilityWithXcms(directory)
 
 cat("\n\n")
 
 
 
 
-
-
 # ----- MAIN PROCESSING INFO -----
 cat("\tMAIN PROCESSING INFO\n")
 
 
-xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass)
+xset = ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
 
 
 
@@ -153,8 +66,8 @@
 
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save = c("xset","zipfile")
-save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
+objects2save = c("xset", "singlefile")
+save(list=objects2save[objects2save %in% ls()], file="ipo4xcmsSet.RData")
 
 cat("\n\n")