view ipo4xcmsSet.r @ 1:ae8de756dfcf draft

"planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"

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


# ----- PACKAGE -----
cat("\tSESSION INFO\n")

#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("IPO","batch")
loadAndDisplayPackages(pkgs)
cat("\n\n");


# ----- ARGUMENTS -----
cat("\tARGUMENTS INFO\n")
args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
write.table(as.matrix(args), col.names=F, quote=F, sep='\t')

cat("\n\n");

# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")
options(bitmapType='cairo')

samplebyclass = 2
if (!is.null(args$samplebyclass)){
  samplebyclass = args$samplebyclass; args$samplebyclass=NULL
}

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

# Handle infiles
if (!exists("singlefile")) singlefile <- NULL
rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
singlefile <- rawFilePath$singlefile
directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL)

# Check some character issues
checkXmlStructure(directory)

cat("\n\n")




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


xset = ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)



cat("\n\n")


# ----- EXPORT -----

cat("\tXSET OBJECT INFO\n")
print(xset)
#delete the parameters to avoid the passage to the next tool in .RData image


#saving R data in .Rdata file to save the variables used in the present tool
objects2save = c("xset", "singlefile")
save(list=objects2save[objects2save %in% ls()], file="ipo4xcmsSet.RData")

cat("\n\n")


cat("\tDONE\n")