comparison xcms_xcmsSet.r @ 33:f5d51091cf84 draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e

32:b02d1992a43a

# ----- PACKAGE -----
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("lib.r")

pkgs <- c("xcms", "batch")
loadAndDisplayPackages(pkgs)
cat("\n\n");


# ----- 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")

cat("\n\n")


# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")

#saving the commun parameters
BPPARAM <- MulticoreParam(1)
if (!is.null(args$BPPARAM)) {
    BPPARAM <- MulticoreParam(args$BPPARAM)
}
register(BPPARAM)

#saving the specific parameters
if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum

if (!is.null(args$peaklist)) peaklistParam <- args$peaklist

method <- args$method

if (!is.null(args$roiList)) {
    cat("\t\troiList provided\n")
    args$roiList <- list(getDataFrameFromFile(args$roiList))
    print(args$roiList)
}

cat("\n\n")

# ----- INFILE PROCESSING -----

# 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)
  }
}

cat("\n\n")

33:f5d51091cf84

# ----- PACKAGE -----
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("lib.r")

pkgs <- c("xcms", "batch")
loadAndDisplayPackages(pkgs)
cat("\n\n")


# ----- 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 = FALSE, quote = FALSE, sep = "\t")

cat("\n\n")


# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")

#saving the commun parameters
BPPARAM <- MulticoreParam(1)
if (!is.null(args$BPPARAM)) {
  BPPARAM <- MulticoreParam(args$BPPARAM)
}
register(BPPARAM)

#saving the specific parameters
if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum

if (!is.null(args$peaklist)) peaklistParam <- args$peaklist

method <- args$method

if (!is.null(args$roiList)) {
  cat("\t\troiList provided\n")
  args$roiList <- list(getDataFrameFromFile(args$roiList))
  print(args$roiList)
}

cat("\n\n")

# ----- INFILE PROCESSING -----

# 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 = FALSE, row.names = FALSE)
  }
}

cat("\n\n")