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annotate runit/qualitymetrics_runtests.R @ 0:b4f5b5bc01dd draft

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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
author ethevenot
date Sat, 06 Aug 2016 12:01:17 -0400
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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diff changeset
1 #!/usr/bin/env Rscript
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
ethevenot
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3 ## Package
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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4 ##--------
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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5
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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6 library(RUnit)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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8 ## Constants
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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9 ##----------
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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11 testOutDirC <- "output"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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12 argVc <- commandArgs(trailingOnly = FALSE)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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13 scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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16 ## Functions
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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17 ##-----------
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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19 ## Reading tables (matrix or data frame)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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20 readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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22 file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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24 switch(typeC,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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25 matrix = return(t(as.matrix(read.table(file = fileC,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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26 header = TRUE,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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27 row.names = 1,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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28 sep = "\t",
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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29 stringsAsFactors = FALSE)))),
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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30 dataframe = return(read.table(file = fileC,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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31 header = TRUE,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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32 row.names = 1,
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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33 sep = "\t",
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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34 stringsAsFactors = FALSE)))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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36 }
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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37
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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38 ## Call wrapper
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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39 wrapperCallF <- function(paramLs) {
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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40
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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41 ## Set program path
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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42 wrapperPathC <- file.path(dirname(scriptPathC), "..", "qualitymetrics_wrapper.R")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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43
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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44 ## Set arguments
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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45 argLs <- NULL
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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46 for (parC in names(paramLs))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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47 argLs <- c(argLs, parC, paramLs[[parC]])
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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48
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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49 ## Call
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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50 wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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52 if(.Platform$OS.type == "windows")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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53 wrapperCallC <- paste("Rscript", wrapperCallC)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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55 wrapperCodeN <- system(wrapperCallC)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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56
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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57 if (wrapperCodeN != 0)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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58 stop("Error when running qualitymetrics_wrapper.R.")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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59
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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60 ## Get output
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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61 outLs <- list()
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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62 if ("dataMatrix_out" %in% names(paramLs))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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63 outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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64 if ("sampleMetadata_out" %in% names(paramLs))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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65 outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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66 if ("variableMetadata_out" %in% names(paramLs))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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67 outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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68 if("information" %in% names(paramLs))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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69 outLs[["infVc"]] <- readLines(paramLs[["information"]])
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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70
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71 return(outLs)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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72 }
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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73
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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74 ## Setting default parameters
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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75 defaultArgF <- function(testInDirC) {
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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76
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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77 defaultArgLs <- list()
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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78 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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79 defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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80 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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81 defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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82 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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83 defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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84
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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85 defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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86 defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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87 defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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88 defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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89
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90 defaultArgLs
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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92 }
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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93
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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94 ## Main
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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95 ##-----
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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96
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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97 ## Create output folder
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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98 file.exists(testOutDirC) || dir.create(testOutDirC)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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99
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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100 ## Run tests
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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101 test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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102 isValidTestSuite(test.suite)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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103 test.results <- runTestSuite(test.suite)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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104 print(test.results)
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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105
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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106