# HG changeset patch
# User workflow4metabolomics
# Date 1617814034 0
# Node ID b02d1992a43aa397123b3bbc6b77e0268733dd4e
# Parent  eb15a3841da42e85272ca5dbdd45b2fd3ffe6a6e
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"

diff -r eb15a3841da4 -r b02d1992a43a README.rst
--- a/README.rst	Tue Apr 28 09:35:10 2020 -0400
+++ b/README.rst	Wed Apr 07 16:47:14 2021 +0000
@@ -24,6 +24,10 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
+**Version 3.12.0+galaxy* - 03/03/2020**
+
+- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
+
 **Version 3.6.1.0 - 03/09/2019**
 
 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
diff -r eb15a3841da4 -r b02d1992a43a abims_xcms_xcmsSet.xml
--- a/abims_xcms_xcmsSet.xml	Tue Apr 28 09:35:10 2020 -0400
+++ b/abims_xcms_xcmsSet.xml	Wed Apr 07 16:47:14 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy1">
+<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0">
     <description>Chromatographic peak detection</description>
 
     <macros>
@@ -500,11 +500,11 @@
 Changelog/News
 --------------
 
-.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
+@HELP_XCMS_NEWVERSION_31200@
 
 **Version 3.6.1+galaxy1 - 22/04/2020**
 
-- NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods. 
+- NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods.
 
 
 @HELP_XCMS_NEWVERSION_3610@
diff -r eb15a3841da4 -r b02d1992a43a lib.r
--- 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)
     }
 }
diff -r eb15a3841da4 -r b02d1992a43a macros_xcms.xml
--- a/macros_xcms.xml	Tue Apr 28 09:35:10 2020 -0400
+++ b/macros_xcms.xml	Wed Apr 07 16:47:14 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@TOOL_VERSION@">3.6.1</token>
+    <token name="@TOOL_VERSION@">3.12.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
@@ -243,6 +243,7 @@
 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
     </token>
 
@@ -256,6 +257,11 @@
 
 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
     </token>
+    <token name="@HELP_XCMS_NEWVERSION_31200@">
+**Version 3.12.0+galaxy* - 03/03/2020**
+
+- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
+    </token>
 
     <xml name="citation">
         <citations>
diff -r eb15a3841da4 -r b02d1992a43a repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Apr 28 09:35:10 2020 -0400
+++ b/repository_dependencies.xml	Wed Apr 07 16:47:14 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="7800ba9a4c1e"/>
+    <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="544f6d2329ac"/>
 </repositories>
\ No newline at end of file
diff -r eb15a3841da4 -r b02d1992a43a test-data/faahKO.raw.RData
Binary file test-data/faahKO.raw.RData has changed
diff -r eb15a3841da4 -r b02d1992a43a test-data/faahKO_reduce.zip
Binary file test-data/faahKO_reduce.zip has changed
diff -r eb15a3841da4 -r b02d1992a43a xcms_xcmsSet.r
--- a/xcms_xcmsSet.r	Tue Apr 28 09:35:10 2020 -0400
+++ b/xcms_xcmsSet.r	Wed Apr 07 16:47:14 2021 +0000
@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
 # ----- LOG FILE -----
-log_file <- file("log.txt", open="wt")
+log_file <- file("log.txt", open = "wt")
 sink(log_file)
 sink(log_file, type = "output")
 
@@ -10,10 +10,12 @@
 cat("\tSESSION INFO\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 <- 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("xcms","batch")
+pkgs <- c("xcms", "batch")
 loadAndDisplayPackages(pkgs)
 cat("\n\n");
 
@@ -21,7 +23,7 @@
 # ----- ARGUMENTS -----
 cat("\tARGUMENTS INFO\n")
 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')
+write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
 
 cat("\n\n")
 
@@ -31,7 +33,7 @@
 
 #saving the commun parameters
 BPPARAM <- MulticoreParam(1)
-if (!is.null(args$BPPARAM)){
+if (!is.null(args$BPPARAM)) {
     BPPARAM <- MulticoreParam(args$BPPARAM)
 }
 register(BPPARAM)
@@ -44,7 +46,7 @@
 
 method <- args$method
 
-if (!is.null(args$roiList)){
+if (!is.null(args$roiList)) {
     cat("\t\troiList provided\n")
     args$roiList <- list(getDataFrameFromFile(args$roiList))
     print(args$roiList)
@@ -60,7 +62,7 @@
 if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData")
 
 # Handle infiles
-rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
 
@@ -79,34 +81,30 @@
 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
 #Apply this filter only if file contain MS and MSn
-if(length(unique(msLevel(raw_data)))!= 1){
-	raw_data <- filterMsLevel(raw_data,msLevel=1)
+if (length(unique(msLevel(raw_data))) != 1) {
+  raw_data <- filterMsLevel(raw_data, msLevel = 1)
 }
 
 cat("\t\t\tChromatographic peak detection\n")
 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
-args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
+args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
 
-findChromPeaksParam <- do.call(paste0(method,"Param"), args)
+findChromPeaksParam <- do.call(paste0(method, "Param"), args)
 print(findChromPeaksParam)
-xdata <- findChromPeaks(raw_data, param=findChromPeaksParam)
+xdata <- findChromPeaks(raw_data, param = findChromPeaksParam)
 
 # Check if there are no peaks
 if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings")
 
 # Create a sampleMetada file
-sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
-
-#cat("\t\t\tCompute and Store TIC and BPI\n")
-#chromTIC = chromatogram(xdata, aggregationFun = "sum")
-#chromBPI = chromatogram(xdata, aggregationFun = "max")
+sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv")
 
 # Create a chromPeaks table if required
 if (exists("peaklistParam")) {
-    if(peaklistParam){
-      cat("\nCreating the chromatographic peaks' table...\n")
-      write.table(chromPeaks(xdata), file="chromPeak_table.tsv",sep="\t",quote=F,row.names=F)
-	}
+  if (peaklistParam) {
+    cat("\nCreating the chromatographic peaks' table...\n")
+    write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = F, row.names = F)
+  }
 }
 
 cat("\n\n")
@@ -124,8 +122,8 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI")
-save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
+save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
 
 
 cat("\tDONE\n")