comparison xcms_merge.r @ 25:7e2770b86a0e draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163

24:bf452dc6e4b0

#!/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)

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")

25:7e2770b86a0e

#!/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)

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")