diff tests/transformation_tests.R @ 0:eacea1349a7c draft

planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/transformation_tests.R	Fri Jul 29 12:11:01 2016 -0400
@@ -0,0 +1,142 @@
+library(RUnit)
+
+wrapperF <- function(argVc) {
+
+        source("../transformation_script.R")
+
+
+#### Start_of_testing_code <- function() {}
+
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()[["stringsAsFactors"]]
+options(stringsAsFactors=FALSE)
+
+## constants
+##----------
+
+modNamC <- "Transformation" ## module name
+metVc <- c("log2", "log10") ## available methods
+
+topEnvC <- environment()
+flagC <- "\n"
+
+## functions
+##----------
+
+flgF <- function(tesC,
+                 envC = topEnvC,
+                 txtC = NA) { ## management of warning and error messages
+
+    tesL <- eval(parse(text = tesC), envir = envC)
+
+    if(!tesL) {
+
+        sink(NULL)
+        stpTxtC <- ifelse(is.na(txtC),
+                          paste0(tesC, " is FALSE"),
+                          txtC)
+
+        stop(stpTxtC,
+             call. = FALSE)
+
+    }
+
+} ## flgF
+
+## 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"]]
+
+## checking
+##---------
+
+flgF("metC %in% metVc", txtC = paste0("Transformation method must be either '", paste(metVc, collapse = "', '"), "'"))
+
+
+##------------------------------
+## 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 = "")
+
+sink()
+
+options(stringsAsFactors = strAsFacL)
+
+
+#### End_of_testing_code <- function() {}
+
+
+    return(list(datDF = datDF))
+
+    rm(list = ls())
+
+}
+
+exaDirOutC <- "output"
+file.exists(exaDirOutC) || dir.create(exaDirOutC)
+
+tesArgLs <- list(input_log10 = c(method = "log10",
+                     .chkC = "checkEqualsNumeric(outLs[['datDF']]['HMDB03072', 'HU_021'], 4.817089, tolerance = 1e-6)"))
+
+for(tesC in names(tesArgLs))
+    tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],
+                          dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),
+                          dataMatrix_out = file.path(exaDirOutC, "dataMatrix.tsv"),
+                          information = file.path(exaDirOutC, "information.txt"))
+
+for(tesC in names(tesArgLs)) {
+    print(tesC)
+    outLs <- wrapperF(tesArgLs[[tesC]])
+    if(".chkC" %in% names(tesArgLs[[tesC]]))
+        stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]])))
+}
+
+message("Checks successfully completed")