diff runit/batchcorrection_runtests.R @ 0:b74d1d533dea draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/batchcorrection_runtests.R	Thu Aug 04 11:40:35 2016 -0400
@@ -0,0 +1,131 @@
+#!/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, allLoessL) {
+
+    ## Set program path
+    wrapperPathC <- file.path(dirname(scriptPathC), "..",
+                              ifelse(allLoessL,
+                                     "batch_correction_all_loess_wrapper.R",
+                                     "batch_correction_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)
+
+
+    print(wrapperCallC)
+    
+
+    wrapperCodeN <- system(wrapperCallC)
+
+    if (wrapperCodeN != 0)
+        stop(paste0("Error when running 'batch_correction_",
+                    ifelse(allLoessL, "all_loess_", ""),
+                    "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"]])
+
+    if("out_preNormSummary" %in% names(paramLs))
+        outLs[["sumDF"]] <- readTableF(paramLs[["out_preNormSummary"]], "dataframe")
+
+    return(outLs)
+    
+}
+
+## Setting default parameters
+defaultArgF <- function(testInDirC, determineL) {
+
+    defaultArgLs <- list()
+
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
+        defaultArgLs[["dataMatrix"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
+        defaultArgLs[["sampleMetadata"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
+
+    if(!determineL)
+        if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
+            defaultArgLs[["variableMetadata"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
+
+    if(determineL) { ## determinebc
+
+        defaultArgLs[["out_graph_pdf"]] <- file.path(dirname(scriptPathC), testOutDirC, "out_graph.pdf")
+        defaultArgLs[["out_preNormSummary"]] <- file.path(dirname(scriptPathC), testOutDirC, "preNormSummary.txt")
+
+    } else { ## batchcorrection
+        
+        defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
+        defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
+        defaultArgLs[["variable_for_simca"]] <- file.path(dirname(scriptPathC), testOutDirC, "variable_for_simca.tsv")
+        defaultArgLs[["graph_output"]] <- file.path(dirname(scriptPathC), testOutDirC, "graph_output.pdf")
+        defaultArgLs[["rdata_output"]] <- file.path(dirname(scriptPathC), testOutDirC, "rdata_output.rdata")
+        
+       }
+
+    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)
+