#!/usr/bin/env Rscript

#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")

args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects


sampleMetadata <- NULL
for (image in args$images) {
  load(image)
  if (exists("raw_data")) xdata <- raw_data
  if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
  if (is.null(sampleMetadata))
    sampleMetadata <- xdata@phenoData@data
  else
    sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data)
}
colnames(sampleMetadata) <- c("sample_name", "class")
sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name)

# Create a sampleMetada file
write.table(sampleMetadata, file = "sampleMetadata.tsv", sep = "\t", row.names = FALSE, quote = FALSE)