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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136

#!/usr/bin/env Rscript

## 070115_NmrBucketing2galaxy_v1.R
## Marie Tremblay-Franco
## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
## www.metabohub.fr/en
## [e-mail]

runExampleL <- FALSE


##------------------------------
## Options
##------------------------------
strAsFacL <- options()$stringsAsFactors
options(stringsAsFactors = FALSE)
options(scipen=999)


##------------------------------
## Libraries laoding
##------------------------------
# For parseCommandArgs function
library(batch) 

# Constants
argv <- commandArgs(trailingOnly = FALSE)
script.path <- sub("--file=","",argv[grep("--file=",argv)])
prog.name <- basename(script.path)

# Print help
if (length(grep('-h', argv)) >0) {
	cat("Usage:", prog.name,
	    "dataMatrix myDataMatrix.tsv",
	    "scalingMethod PQN|QuantitativeVariable",
	    "graphType None|Overlay|One_per_individual",
	    "logOut myLog.txt",
	    "dataMatrixOut myDataMatrixOutput.tsv",
	    "graphOut myGraph.pdf",
		"\n")
	quit(status = 0)
}

# R script call
source_local <- function(fname)
{
	argv <- commandArgs(trailingOnly = FALSE)
	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
	source(paste(base_dir, fname, sep="/"))
}
#Import the different functions
source_local("NmrNormalization_script.R")
source_local("DrawSpec.R")


##------------------------------
## Errors ?????????????????????
##------------------------------


##------------------------------
## Constants
##------------------------------
topEnvC <- environment()
flagC <- "\n"


##------------------------------
## Script
##------------------------------
if(!runExampleL)
    argLs <- parseCommandArgs(evaluate=FALSE)


## Parameters Loading
##-------------------
  # Inputs
data <- read.table(argLs[["dataMatrix"]], check.names=FALSE, header=TRUE, sep="\t", row.names=1)
names <- rownames(data)
	## Add a test to check if all values are numercical
if (!all(vapply(data, is.numeric, FUN.VALUE = FALSE)))
  stop("Data are not numeric")
	## Integer conversion to avoid stack overflow when computin the sum
data <- as.data.frame(lapply(data, as.numeric))
rownames(data) <- names

scaling <- argLs[["scalingMethod"]]
graphique <- argLs[["graphType"]]

if (scaling=='PQN')
{
 metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
 factor<- argLs[["factor"]]
 ControlGroup <- argLs[["controlGroup"]]
}
if (scaling=='QuantitativeVariable')
{
  metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
  factor <- argLs[["factor"]]
}

  # Outputs
nomGraphe <- argLs[["graphOut"]]
dataMatrixOut <- argLs[["dataMatrixOut"]]
log <- argLs[["logOut"]]


## Checking R packages
##--------------------
sink(log)
cat("\tPACKAGE INFO\n")
pkgs=c("batch")
for(pkg in pkgs) {
    suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
    cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
}
cat("\n")


## Checking arguments
##-------------------
error.stock <- "\n"
if(length(error.stock) > 1)
  stop(error.stock)
  
  
## Computation
##------------
NormalizationResults <- NmrNormalization(dataMatrix=data,scalingMethod=scaling,sampleMetadata=metadataSample,
                                    bioFactor=factor,ControlGroup=ControlGroup,
                                    graph=graphique,nomFichier=nomGraphe,savLog.txtC=log)

data_normalized <- NormalizationResults[[1]]


## Graphical outputs
##------------------
if (graphique != "None")
{
  # Graphic Device opening
  pdf(nomGraphe,onefile=TRUE)
  
  if (graphique == "Overlay")
  {
    # Global spectral window
    spectra <- data.frame(t(data_normalized))
    drawSpec(spectra,xlab="", ylab="Intensity", main="")
  }
  else
  {
    for (i in 1:ncol(data_normalized))
    {
      spectra <- t(data_normalized[,i])
      drawSpec(spectra,xlab="", ylab="Intensity", main=colnames(data_normalized)[i])
    }
  }
  dev.off()
}


## Saving
##-------
  # Data
data_normalized <- cbind(rownames(data_normalized),data_normalized)
colnames(data_normalized) <- c("Variable",colnames(data_normalized)[-1])
write.table(data_normalized,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")


## Ending
##---------------------
cat("\nEnd of 'Normalization' Galaxy module call: ", as.character(Sys.time()), sep = "")
sink()
options(stringsAsFactors = strAsFacL)
rm(list = ls())