diff runit/checkformat_runtests.R @ 0:059eb452931e draft

planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/checkformat_runtests.R	Tue Oct 24 08:44:02 2017 -0400
@@ -0,0 +1,101 @@
+#!/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), "..", "checkformat_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$OS.type == "windows")
+            wrapperCallC <- paste("Rscript", wrapperCallC)
+
+	wrapperCodeN <- system(wrapperCallC)
+
+	if (wrapperCodeN != 0)
+		stop("Error when running checkformat_wrapper.R.")
+
+	## Get output
+	outLs <- list()
+	if ("dataMatrix_out" %in% names(paramLs))
+            outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
+	if ("sampleMetadata_out" %in% names(paramLs))
+            outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
+	if ("variableMetadata_out" %in% names(paramLs))
+            outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
+        if("information" %in% names(paramLs))
+            outLs[["infVc"]] <- readLines(paramLs[["information"]])
+
+	return(outLs)
+}
+
+## Setting default parameters
+defaultArgF <- function(testInDirC) {
+
+    defaultArgLs <- list()
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
+        defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
+        defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
+        defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
+
+    defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
+
+    defaultArgLs
+
+}
+
+## Main
+##-----
+
+## Create output folder
+file.exists(testOutDirC) || dir.create(testOutDirC)
+
+## Run tests
+test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
+isValidTestSuite(test.suite)
+test.results <- runTestSuite(test.suite)
+print(test.results)