annotate runit/biosigner_runtests.R @ 2:b2414be87d4b draft

planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79

#!/usr/bin/env Rscript

## Package
##--------

library(RUnit)

## Constants
##----------

testOutDirC <- "output"
argVc <- commandArgs(trailingOnly = FALSE)
scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])


## Functions
##-----------

## Reading tables (matrix or data frame)
readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {

    	file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))

        switch(typeC,
               matrix = return(t(as.matrix(read.table(file = fileC,
                   header = TRUE,
                   row.names = 1,
                   sep = "\t",
                   stringsAsFactors = FALSE)))),
               dataframe = return(read.table(file = fileC,
                   header = TRUE,
                   row.names = 1,
                   sep = "\t",
                   stringsAsFactors = FALSE)))

}

## Call wrapper
wrapperCallF <- function(paramLs) {

	## Set program path
    	wrapperPathC <- file.path(dirname(scriptPathC), "..", "biosigner_wrapper.R")

	## Set arguments
	argLs <- NULL
	for (parC in names(paramLs))
		argLs <- c(argLs, parC, paramLs[[parC]])

	## Call
	wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")

        if(.Platform$OS.type == "windows")
            wrapperCallC <- paste("Rscript", wrapperCallC)

	wrapperCodeN <- system(wrapperCallC)

	if (wrapperCodeN != 0)
		stop("Error when running biosigner_wrapper.R.")

	## Get output
	outLs <- list()
	if ("dataMatrix_out" %in% names(paramLs))
            outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
	if ("sampleMetadata_out" %in% names(paramLs))
            outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
	if ("variableMetadata_out" %in% names(paramLs))
            outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
        if("information" %in% names(paramLs))
            outLs[["infVc"]] <- readLines(paramLs[["information"]])

	return(outLs)
}

## Setting default parameters
defaultArgF <- function(testInDirC) {

    defaultArgLs <- list()
    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
        defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
        defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
        defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")

    defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
    defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")

    defaultArgLs

}

## Main
##-----

## Create output folder
file.exists(testOutDirC) || dir.create(testOutDirC)

## Run tests
test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
isValidTestSuite(test.suite)
test.results <- runTestSuite(test.suite)
print(test.results)