view transformation_wrapper.R @ 3:cc0e9eff0de2 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2

#!/usr/bin/env Rscript

library(batch) ## parseCommandArgs

# Constants
argv <- commandArgs(trailingOnly = FALSE)
script.path <- sub("--file=","",argv[grep("--file=",argv)])
prog.name <- basename(script.path)

# Print help
if (length(grep('-h', argv)) >0) {
	cat("Usage:", prog.name,
	    "dataMatrix_in myDataMatrixInput.tsv",
	    "method log2|log10|sqrt",
	    "dataMatrix_out myDataMatrixOutput.tsv",
	    "information information.txt",
		"\n")
	quit(status = 0)
}

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("transformation_script.R")

argVc <- unlist(parseCommandArgs(evaluate=FALSE))


##------------------------------
## Initializing
##------------------------------

## options
##--------

strAsFacL <- options()[["stringsAsFactors"]]
options(stringsAsFactors=FALSE)

## constants
##----------

modNamC <- "Transformation" ## module name


## log file
##---------

sink(argVc[["information"]])

cat("\nStart of the '", modNamC, "' module: ",
    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")

## loading
##--------

datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]],
                                check.names = FALSE,
                                header = TRUE,
                                row.names = 1,
                                sep = "\t")))

metC <- argVc[["method"]]


##------------------------------
## Computation
##------------------------------


datMN <- transformF(datMN = datMN, ## dataMatrix
                    metC = metC)  ## transformation method


##------------------------------
## Ending
##------------------------------


## saving
##-------

datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
                          as.data.frame(t(datMN)))
write.table(datDF,
            file = argVc[["dataMatrix_out"]],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

## ending
##-------

cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")

cat("\n\n\n============================================================================")
cat("\nAdditional information about the call:\n")
cat("\n1) Parameters:\n")
print(cbind(value = argVc))

cat("\n2) Session Info:\n")
sessioninfo <- sessionInfo()
cat(sessioninfo$R.version$version.string,"\n")
cat("Main packages:\n")
for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
cat("Other loaded packages:\n")
for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")

cat("============================================================================\n")

sink()

options(stringsAsFactors = strAsFacL)


rm(list = ls())