view ipo4retgroup.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")

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

cat("\n\n")

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

#image is an .RData file necessary to use xset variable given by previous tools
load(args$image); args$image=NULL

# Because so far CAMERA isn't compatible with the new XCMSnExp object
if (exists("xdata")){
    xset <- getxcmsSetObject(xdata)
}

if (!exists("xset")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata' which is provided by the tool: MSnbase readMSData")


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


cat("\n\n")


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

ipo4retgroup(xset, directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)

cat("\n\n")


cat("\tDONE\n")