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annotate runit/multivariate_runtests.R @ 1:60c360e466a8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3
author ethevenot
date Wed, 28 Feb 2018 10:04:14 -0500
parents 4b9488602d57
children
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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1 #!/usr/bin/env Rscript
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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3 ## Package
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4 ##--------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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6 library(RUnit)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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8 ## Constants
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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9 ##----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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11 testOutDirC <- "output"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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12 argVc <- commandArgs(trailingOnly = FALSE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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13 scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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16 ## Functions
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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17 ##-----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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19 ## Reading tables (matrix or data frame)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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20 readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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22 file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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24 switch(typeC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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25 matrix = return(t(as.matrix(read.table(file = fileC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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26 header = TRUE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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27 row.names = 1,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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28 sep = "\t",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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29 stringsAsFactors = FALSE)))),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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30 dataframe = return(read.table(file = fileC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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31 header = TRUE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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32 row.names = 1,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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33 sep = "\t",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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34 stringsAsFactors = FALSE)))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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36 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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37
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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38 ## Call wrapper
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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39 wrapperCallF <- function(paramLs) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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41 ## Set program path
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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42 wrapperPathC <- file.path(dirname(scriptPathC), "..", "multivariate_wrapper.R")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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43
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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44 ## Set arguments
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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45 argLs <- NULL
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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46 for (parC in names(paramLs))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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47 argLs <- c(argLs, parC, paramLs[[parC]])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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49 ## Call
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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50 wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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52 if(.Platform$OS.type == "windows")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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53 wrapperCallC <- paste("Rscript", wrapperCallC)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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54
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55 wrapperCodeN <- system(wrapperCallC)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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56
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57 if (wrapperCodeN != 0)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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58 stop("Error when running multivariate_wrapper.R.")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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59
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60 ## Get output
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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61 outLs <- list()
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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62 if ("dataMatrix_out" %in% names(paramLs))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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63 outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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64 if ("sampleMetadata_out" %in% names(paramLs))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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65 outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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66 if ("variableMetadata_out" %in% names(paramLs))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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67 outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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68 if("information" %in% names(paramLs))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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69 outLs[["infVc"]] <- readLines(paramLs[["information"]])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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70
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71 return(outLs)
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72 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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73
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74 ## Setting default parameters
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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75 defaultArgF <- function(testInDirC) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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76
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77 defaultArgLs <- list()
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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78 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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79 defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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80 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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81 defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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82 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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83 defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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84
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85 defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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86 defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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87 defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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88 defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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89
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90 defaultArgLs
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91
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92 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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93
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94 ## Main
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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95 ##-----
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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96
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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97 ## Create output folder
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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98 file.exists(testOutDirC) || dir.create(testOutDirC)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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99
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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100 ## Run tests
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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101 test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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102 isValidTestSuite(test.suite)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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103 test.results <- runTestSuite(test.suite)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
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104 print(test.results)