ipo4retgroup.r

#!/usr/bin/env Rscript
# Authors Gildas Le Corguille and Yann Guitton

# Setup R error handling to go to stderr for better error messages in Galaxy
options(show.error.messages = F, error = function() {
  cat(geterrmessage(), file = stderr())
  q("no", 1, F)
})

# ----- LOG FILE -----
log_file <- file("log.txt", open = "wt")
sink(log_file)
sink(log_file, type = "output")


# ----- PACKAGE -----
options(bitmapType = "cairo")
cat("\tPACKAGE INFO\n")
pkgs <- c("parallel", "BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms", "rsm", "igraph", "CAMERA", "IPO", "snow", "batch")

for (pkg in pkgs) {
  cat(pkg, "\t", as.character(packageVersion(pkg)), "\n", sep = "")
  suppressWarnings(suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE))))
}
source_local <- function(fname) {
  argv <- commandArgs(trailingOnly = FALSE)
  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
  source(paste(base_dir, fname, sep = "/"))
}
cat("\n\n")
# ----- ARGUMENTS -----
cat("\tARGUMENTS INFO\n")
listArguments <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
write.table(as.matrix(listArguments), col.names = F, quote = F, sep = "\t")

cat("\n\n")
# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

# image is an .RData file necessary to use xset variable given by previous tools
if (!is.null(listArguments[["image"]])) {
  load(listArguments[["image"]])
  listArguments[["image"]] <- NULL
}

# Import the different functions
source_local("lib.r")

cat("\n\n")

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

parametersOutput <- "IPO_parameters4retcorGroup.tsv"
if (!is.null(listArguments[["parametersOutput"]])) {
  parametersOutput <- listArguments[["parametersOutput"]]
  listArguments[["parametersOutput"]] <- NULL
}

if (!is.null(listArguments[["sampleMetadataFile"]])) {
  sample.metadata.file <- listArguments[["sampleMetadataFile"]]
  listArguments[["sampleMetadataFile"]] <- NULL
}

# necessary to unzip .zip file uploaded to Galaxy
# thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories


if (!is.null(listArguments[["zipfile"]])) {
  zipfile <- listArguments[["zipfile"]]
  listArguments[["zipfile"]] <- NULL
}


if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
  singlefile_galaxyPath <- listArguments[["singlefile_galaxyPath"]]
  listArguments[["singlefile_galaxyPath"]] <- NULL
  singlefile_sampleName <- listArguments[["singlefile_sampleName"]]
  listArguments[["singlefile_sampleName"]] <- NULL
}

# single file case
# @TODO: need to be refactoring
if (exists("singlefile_galaxyPath") && (singlefile_galaxyPath != "")) {
  cwd <- getwd()
  dir.create("raw")
  setwd("raw")

  for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPath))) {
    if (!file.exists(singlefile_galaxyPath[singlefile_galaxyPath_i])) {
      error_message <- paste("Cannot access the sample:", singlefile_sampleName[singlefile_galaxyPath_i], "located:", singlefile_galaxyPath[singlefile_galaxyPath_i], ". Please, contact your administrator ... if you have one!")
      print(error_message)
      stop(error_message)
    }
    file.symlink(singlefile_galaxyPath[singlefile_galaxyPath_i], singlefile_sampleName[singlefile_galaxyPath_i])
  }

  setwd(cwd)

  directory <- "raw"
}

# We unzip automatically the chromatograms from the zip files.
if (exists("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)
  }

  # list all file in the zip file
  # zip_files=unzip(zipfile,list=T)[,"Name"]

  # Because IPO only want raw data in its working directory
  if (!dir.exists("ipoworkingdir")) {
    dir.create("ipoworkingdir")
  }
  setwd("ipoworkingdir")

  # unzip
  suppressWarnings(unzip(zipfile, unzip = getOption("unzip")))

  # get the directory name
  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")
}

# addition of the directory to the list of arguments in the first position
checkXmlStructure(directory)
checkFilesCompatibilityWithXcms(directory)

cat("\n\n")


# ----- MAIN PROCESSING INFO -----
cat("\tMAIN PROCESSING INFO\n")


ipo4retgroup(xset, sample.metadata.file, directory, parametersOutput, listArguments)

cat("\n\n")

cat("\tDONE\n")