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annotate runit/profia_runtests.R @ 0:39ccace77270 draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
author ethevenot
date Sun, 26 Mar 2017 17:37:12 -0400
parents
children 3f8ae071bdda
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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1 #!/usr/bin/env Rscript
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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3 ## Package
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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4 ##--------
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6 library(RUnit)
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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8 ## Constants
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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9 ##----------
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11 testOutDirC <- "output"
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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12 argVc <- commandArgs(trailingOnly = FALSE)
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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13 scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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16 ## Functions
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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17 ##-----------
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19 ## Reading tables (matrix or data frame)
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20 readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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22 file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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24 switch(typeC,
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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25 matrix = return(t(as.matrix(read.table(file = fileC,
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26 header = TRUE,
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27 row.names = 1,
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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28 sep = "\t",
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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29 stringsAsFactors = FALSE)))),
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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30 dataframe = return(read.table(file = fileC,
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31 header = TRUE,
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32 row.names = 1,
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33 sep = "\t",
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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34 stringsAsFactors = FALSE)))
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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36 }
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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38 ## Call wrapper
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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39 wrapperCallF <- function(paramLs) {
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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41 ## Set program path
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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42 wrapperPathC <- file.path(dirname(scriptPathC), "..", "profia_wrapper.R")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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44 ## Set arguments
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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45 argLs <- NULL
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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46 for (parC in names(paramLs))
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47 argLs <- c(argLs, parC, paramLs[[parC]])
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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49 ## Call
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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50 wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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52 print(wrapperCallC)
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54 if(.Platform$OS.type == "windows")
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55 wrapperCallC <- paste("Rscript", wrapperCallC)
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57 wrapperCodeN <- system(wrapperCallC)
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59 if (wrapperCodeN != 0)
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60 stop("Error when running profia_wrapper.R.")
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62 ## Get output
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63 outLs <- list()
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64 if ("dataMatrix_out" %in% names(paramLs))
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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65 outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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66 if ("sampleMetadata_out" %in% names(paramLs))
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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67 outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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68 if ("variableMetadata_out" %in% names(paramLs))
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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69 outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
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70 if("information" %in% names(paramLs))
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71 outLs[["infVc"]] <- readLines(paramLs[["information"]])
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73 return(outLs)
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74 }
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76 ## Setting default parameters
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77 defaultArgF <- function(testInDirC) {
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79 defaultArgLs <- list()
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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80 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
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81 defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
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82 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
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83 defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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84 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
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85 defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
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86
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87 defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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88 defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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89 defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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90 defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
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91 defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
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93 defaultArgLs
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95 }
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96
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97 ## Main
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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98 ##-----
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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99
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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100 ## Create output folder
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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101 file.exists(testOutDirC) || dir.create(testOutDirC)
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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102
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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103 ## Run tests
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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104 test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
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105 isValidTestSuite(test.suite)
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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106 test.results <- runTestSuite(test.suite)
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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107 print(test.results)