Mercurial > repos > ethevenot > multivariate
view runit/multivariate_runtests.R @ 2:fa173e12e185 draft
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty
author | ethevenot |
---|---|
date | Sat, 06 Aug 2016 12:07:13 -0400 |
parents | |
children |
line wrap: on
line source
#!/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), "..", "multivariate_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$OS.type == "windows") wrapperCallC <- paste("Rscript", wrapperCallC) wrapperCodeN <- system(wrapperCallC) if (wrapperCodeN != 0) stop("Error when running multivariate_wrapper.R.") ## Get output outLs <- list() if ("dataMatrix_out" %in% names(paramLs)) outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix") if ("sampleMetadata_out" %in% names(paramLs)) outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe") if ("variableMetadata_out" %in% names(paramLs)) outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe") if("information" %in% names(paramLs)) outLs[["infVc"]] <- readLines(paramLs[["information"]]) return(outLs) } ## Setting default parameters defaultArgF <- function(testInDirC) { defaultArgLs <- list() if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv"))) defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv") if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv"))) defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv") if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv"))) defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv") defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv") defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv") defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf") defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt") defaultArgLs } ## Main ##----- ## Create output folder file.exists(testOutDirC) || dir.create(testOutDirC) ## Run tests test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$') isValidTestSuite(test.suite) test.results <- runTestSuite(test.suite) print(test.results)