comparison msnbase_readmsdata.r @ 16:733d32b30aff draft default tip

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

15:b25a582ab6c1

# ----- 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("MSnbase", "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 = FALSE, quote = FALSE, sep = "\t")

cat("\n\n")

print(raw_data)
cat("\t\tphenoData\n")
print(raw_data@phenoData@data)
cat("\n\n")

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


cat("\tDONE\n")

16:733d32b30aff

# ----- 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("MSnbase", "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 = FALSE, quote = FALSE, sep = "\t")

cat("\n\n")

print(raw_data)
cat("\t\tphenoData\n")
print(raw_data@phenoData@data)
cat("\n\n")

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


cat("\tDONE\n")