annotate checkformat_wrapper.R @ 5:e7c5811ec12f draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 6b7aa0db6cebdb8acfac0a07291647947260a310

#!/usr/bin/env Rscript

library(batch) ## parseCommandArgs

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("checkformat_script.R")

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


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

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

strAsFacL <- options()$stringsAsFactors
options(stringsAsFactors = FALSE)

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

modNamC <- "Check Format" ## module name

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

sink(argVc["information"])

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


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


resLs <- readAndCheckF(argVc["dataMatrix_in"],
                       argVc["sampleMetadata_in"],
                       argVc["variableMetadata_in"],
                       as.logical(argVc["makeNameL"]))


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


## dataMatrix

datMN <- resLs[["datMN"]]
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")

## sampleMetadata

samDF <- resLs[["samDF"]]
samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
                          samDF)
write.table(samDF,
            file = argVc["sampleMetadata_out"],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

## variableMetadata

varDF <- resLs[["varDF"]]
varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
                          varDF)
write.table(varDF,
            file = argVc["variableMetadata_out"],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

if(resLs[["chkL"]]) {

    if(resLs[["newL"]]) {
        
        cat("\nWarning: The sample and/or variable names or orders from the input tables have been modified\n(see the information file for details); please use the new output tables for your analyses.\n")
        
    } else {

        cat("\nThe input tables have a correct format and can be used for your analyses.\n")
        
    }

}
    
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()

if(!resLs[["chkL"]]) {
    stop("Please check the generated 'information' file")
}


## closing
##--------

options(stringsAsFactors = strAsFacL)

rm(list = ls())