Mercurial > repos > ethevenot > qualitymetrics

comparison 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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-1:000000000000 0:b4f5b5bc01dd
1 #!/usr/bin/env Rscript
2
3 ## Package
4 ##--------
5
6 library(RUnit)
7
8 ## Constants
9 ##----------
10
11 testOutDirC <- "output"
12 argVc <- commandArgs(trailingOnly = FALSE)
13 scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
14
15
16 ## Functions
17 ##-----------
18
19 ## Reading tables (matrix or data frame)
20 readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
21
22 file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
23
24 switch(typeC,
25 matrix = return(t(as.matrix(read.table(file = fileC,
26 header = TRUE,
27 row.names = 1,
28 sep = "\t",
29 stringsAsFactors = FALSE)))),
30 dataframe = return(read.table(file = fileC,
31 header = TRUE,
32 row.names = 1,
33 sep = "\t",
34 stringsAsFactors = FALSE)))
35
36 }
37
38 ## Call wrapper
39 wrapperCallF <- function(paramLs) {
40
41 ## Set program path
42 wrapperPathC <- file.path(dirname(scriptPathC), "..", "qualitymetrics_wrapper.R")
43
44 ## Set arguments
45 argLs <- NULL
46 for (parC in names(paramLs))
47 argLs <- c(argLs, parC, paramLs[[parC]])
48
49 ## Call
50 wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
51
52 if(.Platform$OS.type == "windows")
53 wrapperCallC <- paste("Rscript", wrapperCallC)
54
55 wrapperCodeN <- system(wrapperCallC)
56
57 if (wrapperCodeN != 0)
58 stop("Error when running qualitymetrics_wrapper.R.")
59
60 ## Get output
61 outLs <- list()
62 if ("dataMatrix_out" %in% names(paramLs))
63 outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
64 if ("sampleMetadata_out" %in% names(paramLs))
65 outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
66 if ("variableMetadata_out" %in% names(paramLs))
67 outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
68 if("information" %in% names(paramLs))
69 outLs[["infVc"]] <- readLines(paramLs[["information"]])
70
71 return(outLs)
72 }
73
74 ## Setting default parameters
75 defaultArgF <- function(testInDirC) {
76
77 defaultArgLs <- list()
78 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
79 defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
80 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
81 defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
82 if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
83 defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
84
85 defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
86 defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
87 defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
88 defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
89
90 defaultArgLs
91
92 }
93
94 ## Main
95 ##-----
96
97 ## Create output folder
98 file.exists(testOutDirC) || dir.create(testOutDirC)
99
100 ## Run tests
101 test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
102 isValidTestSuite(test.suite)
103 test.results <- runTestSuite(test.suite)
104 print(test.results)
105
106