#!/usr/bin/Rscript --vanilla --slave --no-site-file

####################################################################
# WRAPPER for INTENSITY CHECK
#Script: Script_intensity_check_v1.R
#Xml: xml_intensity_check_v1.xml
#
# V1: Fold and NA
#
# Input: Data Matrix, VariableMetadata, SampleMetadata
# Output: VariableMetadata, Graphics (barplots and boxplots) 
#
#
####################################################################


library(batch) #necessary for parseCommandArgs function
args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects

source_local <- function(...){
  argv <- commandArgs(trailingOnly = FALSE)
  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
  for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
}
#Import the different functions
source_local("Script_intensity_check.R", "RcheckLibrary.R")


if(length(args) < 7){ stop("NOT enough argument !!!") }

class1 <- NULL
if(args$type == "One_class"){
  class1 <- args$class1
}

#print args
cat("\n-------------------------------\nIntensity Check parameters:\n\n")
print(args)
cat("--------------------------------\n")


intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$type,
          args$class_col, class1, args$variableMetadata_out, args$graphs_out)

sessionInfo()
cat("--------------------------------\n")

#delete the parameters to avoid the passage to the next tool in .RData image
rm(args)