--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib.r	Thu Jun 17 07:42:55 2021 +0000
@@ -0,0 +1,451 @@
+#@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
+    md5sumList <- NULL
+    for (image in args$images) {
+
+        load(image)
+        # Handle infiles
+        if (!exists("singlefile")) singlefile <- NULL
+        if (!exists("zipfile")) zipfile <- NULL
+        rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+        zipfile <- rawFilePath$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")
+
+        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 <- 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$sampleNamesMakeNames)
+            chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
+            chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
+            chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
+            chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
+        }
+    }
+    rm(image)
+    xdata <- xdata_merged; rm(xdata_merged)
+    singlefile <- singlefile_merged; rm(singlefile_merged)
+    md5sumList <- md5sumList_merged; rm(md5sumList_merged)
+    sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
+
+    if (!is.null(args$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, param = NULL, mzdigit = 4) {
+    pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
+
+    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
+
+    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$sample_group)
+    for (i in seq_len(length(group_colors))) {
+      col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
+    }
+
+    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
+    for (i in seq_len(nrow(featureDefinitions(xdata)))) {
+        mzmin <- featureDefinitions(xdata)[i, ]$mzmin
+        mzmax <- featureDefinitions(xdata)[i, ]$mzmax
+        plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
+        legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
+    }
+
+    dev.off()
+}
+
+#@author G. Le Corguille
+# Draw the plotChromPeakDensity 3 per page in a pdf file
+getPlotAdjustedRtime <- function(xdata) {
+
+    pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
+
+    # Color by group
+    if (length(unique(xdata$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)
+    }
+
+    # 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, 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)
+    variableMetadata <- featureDefinitions(xdata)
+    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)
+    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 = ",")
+
+    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
+    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$sample_group)
+        plot(chrom, col = group_colors[chrom$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$sample_name)), cex = 0.8, lty = 1)
+
+    dev.off()
+}
+
+
+# Get the polarities from all the samples of a condition
+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
+getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
+    cat("Creating the sampleMetadata file...\n")
+
+    #Create the sampleMetada dataframe
+    sampleMetadata <- xdata@phenoData@data
+    rownames(sampleMetadata) <- NULL
+    colnames(sampleMetadata) <-  c("sample_name", "class")
+
+    sampleNamesOrigin <- sampleMetadata$sample_name
+    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$sample_name <- sampleNamesMakeNames
+
+
+    #For each sample file, the following actions are done
+    for (fileIdx in seq_len(length(fileNames(xdata)))) {
+        #Check if the file is in the CDF format
+        if (!mzR:::netCDFIsFile(fileNames(xdata))) {
+
+            # If the column isn't exist, with add one filled with NA
+            if (is.null(sampleMetadata$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 will compute MD5 checksum to check the data integrity
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
+getMd5sum <- function(files) {
+    cat("Compute md5 checksum...\n")
+    library(tools)
+    return(as.matrix(md5sum(files)))
+}
+
+# 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 lecorguille@sb-roscoff.fr
+retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
+
+    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)]], "\\|"))
+
+      singlefile <- NULL
+      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[[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)]]
+
+    # single
+    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!")
+                print(error_message); stop(error_message)
+            }
+
+            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!")
+            print(error_message)
+            stop(error_message)
+        }
+        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)$isdir]
+        directory <- "."
+        if (length(directories) == 1) directory <- directories
+
+        cat("files_root_directory\t", directory, "\n")
+
+        filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+        filepattern <- paste(paste("\\.", filepattern, "$", 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(list(zipfile = zipfile, singlefile = singlefile, files = files))
+
+}
+
+
+# This function retrieve a xset like object
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
+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)
+    }
+}