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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253

#@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 = FALSE)
    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 = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, 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 = FALSE, row.names = FALSE)
  write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)

}

#@author G. Le Corguille
# It allow different of field separators
getDataFrameFromFile <- function(filename, header = TRUE) {
  myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
  if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
  if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
  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 [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("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 [e-mail]
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 [e-mail]
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 = TRUE)))
        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 = TRUE))
    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 [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)
  }
}