annotate xcms_merge.r @ 16:6d475a389abc draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253

#!/usr/bin/env Rscript

#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("xcms", "batch")
loadAndDisplayPackages(pkgs)
cat("\n\n")

args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects


cat("\tXSET MERGING...\n")

mergeXDataReturn <- mergeXData(args)
xdata <- mergeXDataReturn$xdata
singlefile <- mergeXDataReturn$singlefile
md5sumList <- mergeXDataReturn$md5sumList
sampleNamesList <- mergeXDataReturn$sampleNamesList
chromTIC <- mergeXDataReturn$chromTIC
chromBPI <- mergeXDataReturn$chromBPI

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv")

cat("\n\n")

cat("\tXCMSnExp OBJECT INFO\n")
print(pData(xdata))
print(xdata)
cat("\n\n")

cat("\txcmsSet OBJECT INFO\n")
# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)
print(xset@phenoData)
print(xset)
cat("\n\n")

cat("\tSAVE RData\n")
#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI")
save(list = objects2save[objects2save %in% ls()], file = "merged.RData")