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annotate runit/univariate_runtests.R @ 3:140290de7986 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
author ethevenot
date Sun, 30 Oct 2016 14:17:09 -0400
parents 09799fc16bc6
children
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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1 #!/usr/bin/env Rscript
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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3 ## Package
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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4 ##--------
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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6 library(RUnit)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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8 ## Constants
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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9 ##----------
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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11 testOutDirC <- "output"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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12 argVc <- commandArgs(trailingOnly = FALSE)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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13 scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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16 ## Functions
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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17 ##-----------
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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19 ## Reading tables (matrix or data frame)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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20 readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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22 file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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24 switch(typeC,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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25 matrix = return(t(as.matrix(read.table(file = fileC,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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26 header = TRUE,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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27 row.names = 1,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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28 sep = "\t",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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29 stringsAsFactors = FALSE)))),
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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30 dataframe = return(read.table(file = fileC,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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31 header = TRUE,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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32 row.names = 1,
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33 sep = "\t",
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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34 stringsAsFactors = FALSE)))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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36 }
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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38 ## Call wrapper
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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39 wrapperCallF <- function(paramLs) {
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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41 ## Set program path
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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42 wrapperPathC <- file.path(dirname(scriptPathC), "..", "univariate_wrapper.R")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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44 ## Set arguments
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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45 argLs <- NULL
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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46 for (parC in names(paramLs))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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47 argLs <- c(argLs, parC, paramLs[[parC]])
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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49 ## Call
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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50 wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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52 if(.Platform$OS.type == "windows")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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53 wrapperCallC <- paste("Rscript", wrapperCallC)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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55 wrapperCodeN <- system(wrapperCallC)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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57 if (wrapperCodeN != 0)
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58 stop("Error when running univariate_wrapper.R.")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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59
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60 ## Get output
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61 outLs <- list()
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62 if ("dataMatrix_out" %in% names(paramLs))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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63 outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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64 if ("sampleMetadata_out" %in% names(paramLs))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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65 outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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66 if ("variableMetadata_out" %in% names(paramLs))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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67 outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
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68 if("information" %in% names(paramLs))
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69 outLs[["infVc"]] <- readLines(paramLs[["information"]])
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70
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71 return(outLs)
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72 }
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73
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74 ## Setting default parameters
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75 defaultArgF <- function(testInDirC) {
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76
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77 defaultArgLs <- list()
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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78 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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79 defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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80 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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81 defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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82 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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83 defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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84
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85 defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
3
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86 defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
2
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87 defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
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88
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89 defaultArgLs
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90
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91 }
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92
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93 ## Main
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94 ##-----
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95
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96 ## Create output folder
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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97 file.exists(testOutDirC) || dir.create(testOutDirC)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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parents:
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98
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
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99 ## Run tests
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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100 test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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101 isValidTestSuite(test.suite)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents:
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102 test.results <- runTestSuite(test.suite)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
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103 print(test.results)