#!/usr/bin/env Rscript

library(batch) ## parseCommandArgs

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("transformation_script.R")

argVc <- unlist(parseCommandArgs(evaluate=FALSE))


##------------------------------
## Initializing
##------------------------------

## options
##--------

strAsFacL <- options()[["stringsAsFactors"]]
options(stringsAsFactors=FALSE)

## constants
##----------

modNamC <- "Transformation" ## module name


## log file
##---------

sink(argVc[["information"]])

cat("\nStart of the '", modNamC, "' module: ",
    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")

## loading
##--------

datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]],
                                check.names = FALSE,
                                header = TRUE,
                                row.names = 1,
                                sep = "\t")))

metC <- argVc[["method"]]


##------------------------------
## Computation
##------------------------------


datMN <- transformF(datMN = datMN, ## dataMatrix
                    metC = metC)  ## transformation method


##------------------------------
## Ending
##------------------------------


## saving
##-------

datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
                          as.data.frame(t(datMN)))
write.table(datDF,
            file = argVc[["dataMatrix_out"]],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

## ending
##-------

cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")

sink()

options(stringsAsFactors = strAsFacL)


rm(list = ls())