--- a/lib.r	Tue Apr 28 09:35:10 2020 -0400
+++ b/lib.r	Wed Apr 07 16:47:14 2021 +0000
@@ -6,8 +6,8 @@
 parseCommandArgs <- function(...) {
     args <- batch::parseCommandArgs(...)
     for (key in names(args)) {
-        if (args[key] %in% c("TRUE","FALSE"))
-            args[key] = as.logical(args[key])
+        if (args[key] %in% c("TRUE", "FALSE"))
+            args[key] <- as.logical(args[key])
     }
     return(args)
 }
@@ -17,14 +17,20 @@
 # - 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)))
+    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")
+    sessioninfo <- sessionInfo()
+    cat(sessioninfo$R.version$version.string, "\n")
     cat("Main packages:\n")
-    for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+    for (pkg in names(sessioninfo$otherPkgs)) {
+      cat(paste(pkg, packageVersion(pkg)), "\t")
+    }
+    cat("\n")
     cat("Other loaded packages:\n")
-    for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+    for (pkg in names(sessioninfo$loadedOnly)) {
+      cat(paste(pkg, packageVersion(pkg)), "\t")
+    }
+    cat("\n")
 }
 
 #@author G. Le Corguille
@@ -43,20 +49,20 @@
     chromTIC_adjusted <- NULL
     chromBPI_adjusted <- NULL
     md5sumList <- NULL
-    for(image in args$images) {
+    for (image in args$images) {
 
         load(image)
         # Handle infiles
         if (!exists("singlefile")) singlefile <- NULL
         if (!exists("zipfile")) zipfile <- NULL
-        rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
+        rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
         zipfile <- rawFilePath$zipfile
         singlefile <- rawFilePath$singlefile
 
         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$sampleNamesOrigin,"\n")
+        cat(sampleNamesList$sampleNamesOrigin, "\n")
 
         if (!exists("xdata_merged")) {
             xdata_merged <- xdata
@@ -68,14 +74,14 @@
             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 <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
+            if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
+            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.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$sampleNamesMakeNames)
+            singlefile_merged <- c(singlefile_merged, singlefile)
+            md5sumList_merged$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)
@@ -91,75 +97,93 @@
     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)]
+        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=" "))
+            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 }
+    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))
+    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){
+    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
+        variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
+        variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
+        variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
     }
-    return (variableMetadata)
+    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"))])
+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){
+    if (naTOzero) {
         dataMatrix[is.na(dataMatrix)] <- 0
     }
-    return (dataMatrix)
+    return(dataMatrix)
 }
 
 #@author G. Le Corguille
 # Draw the plotChromPeakDensity 3 per page in a pdf file
-getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
-    pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
+getPlotChromPeakDensity <- function(xdata, param = NULL, 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(length(unique(xdata$sample_group)), "Set1")
+    if (length(unique(xdata$sample_group)) < 10) {
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
+    }
     names(group_colors) <- unique(xdata$sample_group)
     col_per_samp <- as.character(xdata$sample_group)
-    for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
+    for (i in seq_len(length(group_colors))) {
+      col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
+    }
 
     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, param = param, mz=c(mzmin,mzmax), col=col_per_samp, 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)
+    for (i in seq_len(nrow(featureDefinitions(xdata)))) {
+        mzmin <- featureDefinitions(xdata)[i, ]$mzmin
+        mzmax <- featureDefinitions(xdata)[i, ]$mzmax
+        plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, 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()
@@ -169,53 +193,57 @@
 # Draw the plotChromPeakDensity 3 per page in a pdf file
 getPlotAdjustedRtime <- function(xdata) {
 
-    pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
+    pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
 
     # Color by group
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if (length(unique(xdata$sample_group)) < 10) {
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    } else {
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
+    }
     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)
+        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$sample_name)), cex=0.8, lty=1)
+    legend("topright", legend = xdata@phenoData@data$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, sampleNamesList) {
-    dataMatrix <- featureValues(xdata, method="medret", value=intval)
+getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = F, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
+    dataMatrix <- featureValues(xdata, method = "medret", value = intval)
     colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
-    dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
+    dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
     variableMetadata <- featureDefinitions(xdata)
-    colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
-    variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
+    colnames(variableMetadata)[1] <- "mz"; colnames(variableMetadata)[4] <- "rt"
+    variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
 
     variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
-    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
+    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
     dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
 
     # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
-    variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
+    variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
 
-    write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
-    write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
+    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)
+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"
+        error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
         print(error_message)
         stop(error_message)
     }
@@ -225,32 +253,36 @@
 #@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") {
+getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
 
     if (aggregationFun == "sum")
-        type="Total Ion Chromatograms"
+        type <- "Total Ion Chromatograms"
     else
-        type="Base Peak Intensity Chromatograms"
+        type <- "Base Peak Intensity Chromatograms"
 
-    adjusted="Raw"
+    adjusted <- "Raw"
     if (hasAdjustedRtime(xdata))
-        adjusted="Adjusted"
+        adjusted <- "Adjusted"
 
-    main <- paste(type,":",adjusted,"data")
+    main <- paste(type, ":", adjusted, "data")
 
-    pdf(pdfname, width=16, height=10)
+    pdf(pdfname, width = 16, height = 10)
 
     # Color by group
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if (length(unique(xdata$sample_group)) < 10) {
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
+    }
     if (length(group_colors) > 1) {
         names(group_colors) <- unique(xdata$sample_group)
-        plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")
-        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+        plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
+        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$sample_name)), main=main, peakType = "none")
-    legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
+    plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
+    legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
 
     dev.off()
 }
@@ -259,7 +291,7 @@
 # Get the polarities from all the samples of a condition
 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
-getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
+getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
     cat("Creating the sampleMetadata file...\n")
 
     #Create the sampleMetada dataframe
@@ -273,7 +305,7 @@
     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())
+            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.")
     }
@@ -281,7 +313,7 @@
     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"))
+            cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
         }
     }
 
@@ -289,7 +321,7 @@
 
 
     #For each sample file, the following actions are done
-    for (fileIdx in 1:length(fileNames(xdata))) {
+    for (fileIdx in seq_len(length(fileNames(xdata)))) {
         #Check if the file is in the CDF format
         if (!mzR:::netCDFIsFile(fileNames(xdata))) {
 
@@ -297,10 +329,10 @@
             if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
 
             #Extract the polarity (a list of polarities)
-            polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
+            polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
             #Verify if all the scans have the same polarity
             uniq_list <- unique(polarity)
-            if (length(uniq_list)>1){
+            if (length(uniq_list) > 1) {
                 polarity <- "mixed"
             } else {
                 polarity <- as.character(uniq_list)
@@ -312,16 +344,16 @@
 
     }
 
-    write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
+    write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
 
-    return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
+    return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
 
 }
 
 
 # This function will compute MD5 checksum to check the data integrity
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
-getMd5sum <- function (files) {
+getMd5sum <- function(files) {
     cat("Compute md5 checksum...\n")
     library(tools)
     return(as.matrix(md5sum(files)))
@@ -331,71 +363,71 @@
 #   - if zipfile: unzip the file with its directory tree
 #   - if singlefiles: set symlink with the good filename
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
-retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") {
+retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
 
-    if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
+    if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
 
     # single - if the file are passed in the command arguments -> refresh singlefile
-    if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
-      singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|"))
-      singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|"))
+    if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
+      singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
+      singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
 
       singlefile <- NULL
-      for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
+      for (singlefile_galaxyPath_i in seq_len(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_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
         singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
       }
     }
     # zipfile - if the file are passed in the command arguments -> refresh zipfile
-    if (!is.null(args[[paste0("zipfile",prefix)]]))
-      zipfile <- args[[paste0("zipfile",prefix)]]
+    if (!is.null(args[[paste0("zipfile", prefix)]]))
+      zipfile <- args[[paste0("zipfile", prefix)]]
 
     # single
-    if(!is.null(singlefile) && (length("singlefile")>0)) {
+    if (!is.null(singlefile) && (length("singlefile") > 0)) {
         files <- vector()
         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!")
+            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)))
+            if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))
                 file.copy(singlefile_galaxyPath, singlefile_sampleName)
             files <- c(files, singlefile_sampleName)
         }
     }
     # zipfile
-    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!")
+    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)
         }
-        suppressWarnings(unzip(zipfile, unzip="unzip"))
+        suppressWarnings(unzip(zipfile, unzip = "unzip"))
 
         #get the directory name
-        suppressWarnings(filesInZip <- unzip(zipfile, list=T))
-        directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
+        suppressWarnings(filesInZip <- unzip(zipfile, list = T))
+        directories <- unique(unlist(lapply(strsplit(filesInZip$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")
+        cat("files_root_directory\t", directory, "\n")
 
-        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, "$", sep=""),collapse="|")
+        filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+        filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
         info <- file.info(directory)
-        listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
+        listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
         files <- c(directory[!info$isdir], listed)
         exists <- file.exists(files)
         files <- files[exists]
 
     }
-    return(list(zipfile=zipfile, singlefile=singlefile, files=files))
+    return(list(zipfile = zipfile, singlefile = singlefile, files = files))
 
 }
 
@@ -405,15 +437,15 @@
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
     if (class(xobject) == "xcmsSet")
-        return (xobject)
+        return(xobject)
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
         if (!is.null(xset@phenoData$sample_group))
             sampclass(xset) <- xset@phenoData$sample_group
         else
             sampclass(xset) <- "."
-        return (xset)
+        return(xset)
     }
 }