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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
author ethevenot
date Thu, 04 Aug 2016 11:40:35 -0400
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b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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1 #!/usr/bin/env Rscript
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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3 ## Package
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4 ##--------
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6 library(RUnit)
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8 ## Constants
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9 ##----------
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11 testOutDirC <- "output"
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12 argVc <- commandArgs(trailingOnly = FALSE)
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13 scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
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16 ## Functions
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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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]) {
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22 file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
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24 switch(typeC,
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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,
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28 sep = "\t",
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29 stringsAsFactors = FALSE)))),
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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",
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34 stringsAsFactors = FALSE)))
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36 }
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38 ## Call wrapper
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39 wrapperCallF <- function(paramLs, allLoessL) {
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41 ## Set program path
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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42 wrapperPathC <- file.path(dirname(scriptPathC), "..",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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43 ifelse(allLoessL,
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44 "batch_correction_all_loess_wrapper.R",
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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45 "batch_correction_wrapper.R"))
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47 ## Set arguments
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48 argLs <- NULL
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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49 for (parC in names(paramLs))
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50 argLs <- c(argLs, parC, paramLs[[parC]])
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52 ## Call
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53 wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
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55 if(.Platform$OS.type == "windows")
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56 wrapperCallC <- paste("Rscript", wrapperCallC)
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59 print(wrapperCallC)
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62 wrapperCodeN <- system(wrapperCallC)
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64 if (wrapperCodeN != 0)
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65 stop(paste0("Error when running 'batch_correction_",
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66 ifelse(allLoessL, "all_loess_", ""),
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67 "wrapper.R'"))
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68
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69 ## Get output
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70 outLs <- list()
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71 if ("dataMatrix_out" %in% names(paramLs))
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72 outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
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73 if ("sampleMetadata_out" %in% names(paramLs))
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74 outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
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75 if ("variableMetadata_out" %in% names(paramLs))
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76 outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
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77 if("information" %in% names(paramLs))
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78 outLs[["infVc"]] <- readLines(paramLs[["information"]])
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79
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80 if("out_preNormSummary" %in% names(paramLs))
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81 outLs[["sumDF"]] <- readTableF(paramLs[["out_preNormSummary"]], "dataframe")
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83 return(outLs)
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84
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85 }
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86
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87 ## Setting default parameters
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88 defaultArgF <- function(testInDirC, determineL) {
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89
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90 defaultArgLs <- list()
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91
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92 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
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93 defaultArgLs[["dataMatrix"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
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94 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
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95 defaultArgLs[["sampleMetadata"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
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96
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97 if(!determineL)
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98 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
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99 defaultArgLs[["variableMetadata"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
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101 if(determineL) { ## determinebc
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103 defaultArgLs[["out_graph_pdf"]] <- file.path(dirname(scriptPathC), testOutDirC, "out_graph.pdf")
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104 defaultArgLs[["out_preNormSummary"]] <- file.path(dirname(scriptPathC), testOutDirC, "preNormSummary.txt")
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105
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106 } else { ## batchcorrection
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107
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108 defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
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109 defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
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110 defaultArgLs[["variable_for_simca"]] <- file.path(dirname(scriptPathC), testOutDirC, "variable_for_simca.tsv")
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111 defaultArgLs[["graph_output"]] <- file.path(dirname(scriptPathC), testOutDirC, "graph_output.pdf")
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112 defaultArgLs[["rdata_output"]] <- file.path(dirname(scriptPathC), testOutDirC, "rdata_output.rdata")
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113
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114 }
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115
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116 defaultArgLs
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117
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118 }
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119
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120 ## Main
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121 ##-----
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122
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123 ## Create output folder
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124 file.exists(testOutDirC) || dir.create(testOutDirC)
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125
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126 ## Run tests
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127 test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
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128 isValidTestSuite(test.suite)
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129 test.results <- runTestSuite(test.suite)
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130 print(test.results)
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131