diff lib.r @ 0:728ebc7ae7dd draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib.r	Tue Sep 18 16:04:51 2018 -0400
@@ -0,0 +1,510 @@
+#@authors ABiMS TEAM, Y. Guitton
+# lib.r for Galaxy Workflow4Metabolomics xcms tools
+
+#@author G. Le Corguille
+# solve an issue with batch if arguments are logical TRUE/FALSE
+parseCommandArgs <- function(...) {
+    args <- batch::parseCommandArgs(...)
+    for (key in names(args)) {
+        if (args[key] %in% c("TRUE","FALSE"))
+            args[key] = as.logical(args[key])
+    }
+    return(args)
+}
+
+#@author G. Le Corguille
+# This function will
+# - load the packages
+# - display the sessionInfo
+loadAndDisplayPackages <- function(pkgs) {
+    for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+
+    sessioninfo = sessionInfo()
+    cat(sessioninfo$R.version$version.string,"\n")
+    cat("Main packages:\n")
+    for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+    cat("Other loaded packages:\n")
+    for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+}
+
+#@author G. Le Corguille
+# This function merge several chromBPI or chromTIC into one.
+mergeChrom <- function(chrom_merged, chrom) {
+    if (is.null(chrom_merged)) return(NULL)
+    chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
+    return(chrom_merged)
+}
+
+#@author G. Le Corguille
+# This function merge several xdata into one.
+mergeXData <- function(args) {
+    chromTIC <- NULL
+    chromBPI <- NULL
+    chromTIC_adjusted <- NULL
+    chromBPI_adjusted <- NULL
+    for(image in args$images) {
+
+        load(image)
+        # Handle infiles
+        if (!exists("singlefile")) singlefile <- NULL
+        if (!exists("zipfile")) zipfile <- NULL
+        rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+        zipfile <- rawFilePath$zipfile
+        singlefile <- rawFilePath$singlefile
+        retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+        if (exists("raw_data")) xdata <- raw_data
+        if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+        cat(sampleNamesList$sampleNamesOrigin,"\n")
+
+        if (!exists("xdata_merged")) {
+            xdata_merged <- xdata
+            singlefile_merged <- singlefile
+            md5sumList_merged <- md5sumList
+            sampleNamesList_merged <- sampleNamesList
+            chromTIC_merged <- chromTIC
+            chromBPI_merged <- chromBPI
+            chromTIC_adjusted_merged <- chromTIC_adjusted
+            chromBPI_adjusted_merged <- chromBPI_adjusted
+        } else {
+            if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
+            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
+            else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
+
+            singlefile_merged <- c(singlefile_merged,singlefile)
+            md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
+            sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
+            sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
+            chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
+            chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
+            chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
+            chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
+        }
+    }
+    rm(image)
+    xdata <- xdata_merged; rm(xdata_merged)
+    singlefile <- singlefile_merged; rm(singlefile_merged)
+    md5sumList <- md5sumList_merged; rm(md5sumList_merged)
+    sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
+
+    if (!is.null(args$sampleMetadata)) {
+        cat("\tXSET PHENODATA SETTING...\n")
+        sampleMetadataFile <- args$sampleMetadata
+        sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
+        xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
+
+        if (any(is.na(pData(xdata)$sample_group))) {
+            sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
+            error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
+            print(error_message)
+            stop(error_message)
+        }
+    }
+
+    if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
+    if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
+    if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
+    if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
+
+    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
+}
+
+#@author G. Le Corguille
+# This function convert if it is required the Retention Time in minutes
+RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
+    if (convertRTMinute){
+        #converting the retention times (seconds) into minutes
+        print("converting the retention times into minutes in the variableMetadata")
+        variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
+        variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
+        variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
+    }
+    return (variableMetadata)
+}
+
+#@author G. Le Corguille
+# This function format ions identifiers
+formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
+    splitDeco <- strsplit(as.character(variableMetadata$name),"_")
+    idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
+    namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
+    variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
+    return(variableMetadata)
+}
+
+#@author G. Le Corguille
+# This function convert the remain NA to 0 in the dataMatrix
+naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
+    if (naTOzero){
+        dataMatrix[is.na(dataMatrix)] <- 0
+    }
+    return (dataMatrix)
+}
+
+#@author G. Le Corguille
+# Draw the plotChromPeakDensity 3 per page in a pdf file
+getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
+    pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
+
+    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
+
+    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
+    names(group_colors) <- unique(xdata$sample_group)
+
+    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
+    for (i in 1:nrow(featureDefinitions(xdata))) {
+        mzmin = featureDefinitions(xdata)[i,]$mzmin
+        mzmax = featureDefinitions(xdata)[i,]$mzmax
+        plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
+        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    }
+
+    dev.off()
+}
+
+#@author G. Le Corguille
+# Draw the plotChromPeakDensity 3 per page in a pdf file
+getPlotAdjustedRtime <- function(xdata) {
+
+    pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
+
+    # Color by group
+    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
+    if (length(group_colors) > 1) {
+        names(group_colors) <- unique(xdata$sample_group)
+        plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
+        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    }
+
+    # Color by sample
+    plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
+    legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
+
+    dev.off()
+}
+
+#@author G. Le Corguille
+# value: intensity values to be used into, maxo or intb
+getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) {
+    dataMatrix <- featureValues(xdata, method="medret", value=intval)
+    colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
+    dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
+    variableMetadata <- featureDefinitions(xdata)
+    colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
+    variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
+
+    variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
+    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
+    dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
+
+    write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
+    write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
+
+}
+
+#@author G. Le Corguille
+# It allow different of field separators
+getDataFrameFromFile <- function(filename, header=T) {
+    myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
+    if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
+    if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
+    if (ncol(myDataFrame) < 2) {
+        error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
+        print(error_message)
+        stop(error_message)
+    }
+    return(myDataFrame)
+}
+
+#@author G. Le Corguille
+# Draw the BPI and TIC graphics
+# colored by sample names or class names
+getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
+
+    if (aggregationFun == "sum")
+        type="Total Ion Chromatograms"
+    else
+        type="Base Peak Intensity Chromatograms"
+
+    adjusted="Raw"
+    if (hasAdjustedRtime(xdata))
+        adjusted="Adjusted"
+
+    main <- paste(type,":",adjusted,"data")
+
+    pdf(pdfname, width=16, height=10)
+
+    # Color by group
+    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
+    if (length(group_colors) > 1) {
+        names(group_colors) <- unique(xdata$sample_group)
+        plot(chrom, col = group_colors[chrom$sample_group], main=main)
+        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    }
+
+    # Color by sample
+    plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
+    legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
+
+    dev.off()
+}
+
+
+# Get the polarities from all the samples of a condition
+#@author Misharl Monsoor [e-mail] ABiMS TEAM
+#@author Gildas Le Corguille [e-mail] ABiMS TEAM
+getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
+    cat("Creating the sampleMetadata file...\n")
+
+    #Create the sampleMetada dataframe
+    sampleMetadata <- xdata@phenoData@data
+    rownames(sampleMetadata) <- NULL
+    colnames(sampleMetadata) <-  c("sampleMetadata", "class")
+
+    sampleNamesOrigin <- sampleMetadata$sampleMetadata
+    sampleNamesMakeNames <- make.names(sampleNamesOrigin)
+
+    if (any(duplicated(sampleNamesMakeNames))) {
+        write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
+        for (sampleName in sampleNamesOrigin) {
+            write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
+        }
+        stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
+    }
+
+    if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
+        cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
+        for (sampleName in sampleNamesOrigin) {
+            cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
+        }
+    }
+
+    sampleMetadata$sampleMetadata <- sampleNamesMakeNames
+
+
+    #For each sample file, the following actions are done
+    for (fileIdx in 1:length(fileNames(xdata))) {
+        #Check if the file is in the CDF format
+        if (!mzR:::netCDFIsFile(fileNames(xdata))) {
+
+            # If the column isn't exist, with add one filled with NA
+            if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
+
+            #Extract the polarity (a list of polarities)
+            polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
+            #Verify if all the scans have the same polarity
+            uniq_list <- unique(polarity)
+            if (length(uniq_list)>1){
+                polarity <- "mixed"
+            } else {
+                polarity <- as.character(uniq_list)
+            }
+
+            #Set the polarity attribute
+            sampleMetadata$polarity[fileIdx] <- polarity
+        }
+
+    }
+
+    write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
+
+    return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
+
+}
+
+
+# This function check if xcms will found all the files
+#@author Gildas Le Corguille [e-mail] ABiMS TEAM
+checkFilesCompatibilityWithXcms <- function(directory) {
+    cat("Checking files filenames compatibilities with xmcs...\n")
+    # WHAT XCMS WILL FIND
+    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+    filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
+    info <- file.info(directory)
+    listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
+    files <- c(directory[!info$isdir], listed)
+    files_abs <- file.path(getwd(), files)
+    exists <- file.exists(files_abs)
+    files[exists] <- files_abs[exists]
+    files[exists] <- sub("//","/",files[exists])
+
+    # WHAT IS ON THE FILESYSTEM
+    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
+    filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
+
+    # COMPARISON
+    if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
+        write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
+        write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
+        stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
+    }
+}
+
+
+#This function list the compatible files within the directory as xcms did
+#@author Gildas Le Corguille [e-mail] ABiMS TEAM
+getMSFiles <- function (directory) {
+    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+    filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
+    info <- file.info(directory)
+    listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
+    files <- c(directory[!info$isdir], listed)
+    exists <- file.exists(files)
+    files <- files[exists]
+    return(files)
+}
+
+# This function check if XML contains special caracters. It also checks integrity and completness.
+#@author Misharl Monsoor [e-mail] ABiMS TEAM
+checkXmlStructure <- function (directory) {
+    cat("Checking XML structure...\n")
+
+    cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
+    capture <- system(cmd, intern=TRUE)
+
+    if (length(capture)>0){
+        #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
+        write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
+        write(capture, stderr())
+        stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
+    }
+
+}
+
+
+# This function check if XML contain special characters
+#@author Misharl Monsoor [e-mail] ABiMS TEAM
+deleteXmlBadCharacters<- function (directory) {
+    cat("Checking Non ASCII characters in the XML...\n")
+
+    processed <- F
+    l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
+    for (i in l){
+        cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
+        capture <- suppressWarnings(system(cmd, intern=TRUE))
+        if (length(capture)>0){
+            cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
+            print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
+            c <- system(cmd, intern=TRUE)
+            capture <- ""
+            processed <- T
+        }
+    }
+    if (processed) cat("\n\n")
+    return(processed)
+}
+
+
+# This function will compute MD5 checksum to check the data integrity
+#@author Gildas Le Corguille [e-mail]
+getMd5sum <- function (directory) {
+    cat("Compute md5 checksum...\n")
+    # WHAT XCMS WILL FIND
+    filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+    filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
+    info <- file.info(directory)
+    listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
+    files <- c(directory[!info$isdir], listed)
+    exists <- file.exists(files)
+    files <- files[exists]
+
+    library(tools)
+
+    #cat("\n\n")
+
+    return(as.matrix(md5sum(files)))
+}
+
+
+# This function get the raw file path from the arguments
+#@author Gildas Le Corguille [e-mail]
+getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
+  if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
+
+  if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
+
+  if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
+    singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
+    singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
+  }
+  if (exists("singlefile_galaxyPaths")){
+    singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
+    singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
+
+    singlefile <- NULL
+    for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
+      singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
+      singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
+      # In case, an url is used to import data within Galaxy
+      singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
+      singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
+    }
+  }
+  return(list(zipfile=zipfile, singlefile=singlefile))
+}
+
+# This function retrieve the raw file in the working directory
+#   - if zipfile: unzip the file with its directory tree
+#   - if singlefiles: set symlink with the good filename
+#@author Gildas Le Corguille [e-mail]
+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
+    if(!is.null(singlefile) && (length("singlefile")>0)) {
+        for (singlefile_sampleName in names(singlefile)) {
+            singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
+            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)
+            }
+
+            if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
+                file.copy(singlefile_galaxyPath, singlefile_sampleName)
+
+        }
+        directory <- "."
+
+    }
+    if(!is.null(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)
+        }
+
+        #list all file in the zip file
+        #zip_files <- unzip(zipfile,list=T)[,"Name"]
+
+        #unzip
+        suppressWarnings(unzip(zipfile, unzip="unzip"))
+
+        #get the directory name
+        suppressWarnings(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")
+
+    }
+    return (directory)
+}
+
+
+# This function retrieve a xset like object
+#@author Gildas Le Corguille [e-mail]
+getxcmsSetObject <- function(xobject) {
+    # XCMS 1.x
+    if (class(xobject) == "xcmsSet")
+        return (xobject)
+    # XCMS 3.x
+    if (class(xobject) == "XCMSnExp") {
+        # Get the legacy xcmsSet object
+        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
+        if (!is.null(xset@phenoData$sample_group))
+            sampclass(xset) <- xset@phenoData$sample_group
+        else
+            sampclass(xset) <- "."
+        return (xset)
+    }
+}