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annotate runit/checkformat_tests.R @ 3:7f093d78a58c draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 6b7aa0db6cebdb8acfac0a07291647947260a310
author ethevenot
date Thu, 01 Mar 2018 05:09:49 -0500
parents b642f4f87022
children
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059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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1 test_input_default <- function() {
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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3 testDirC <- "input"
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ethevenot
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4 argLs <- list(makeNameL = FALSE)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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ethevenot
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6 argLs <- c(defaultArgF(testDirC), argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
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7 outLs <- wrapperCallF(argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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9 checkEquals(outLs[['infVc']][4], 'The input tables have a correct format and can be used for your analyses.')
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b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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11 }
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b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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13 test_datSamInv <- function() {
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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15 ## first two samples inverted in dataMatrix
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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17 testDirC <- "datSamInv"
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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18 argLs <- list(makeNameL = FALSE)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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20 argLs <- c(defaultArgF(testDirC), argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
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21 outLs <- wrapperCallF(argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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23 checkEquals(outLs[['infVc']][7], 'Warning: The sample and/or variable names or orders from the input tables have been modified')
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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25 }
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27 test_datSamFls <- function() {
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29 ## first sample name in dataMatrix is 17, and in sampleMetadata is X17
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31 ## also used in test-data
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33 testDirC <- "datSamFls"
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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34 argLs <- list(makeNameL = TRUE)
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36 argLs <- c(defaultArgF(testDirC), argLs)
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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37 outLs <- wrapperCallF(argLs)
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38
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39 checkEquals(outLs[['infVc']][5], 'Message: Converting sample and variable names to the standard R format')
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41 checkEquals(outLs[['infVc']][7], 'Warning: The sample and/or variable names or orders from the input tables have been modified')
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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43 checkEquals(rownames(outLs[['datMN']])[1], 'X17')
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45 }
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47 test_datSamFlsInv <- function() {
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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49 ## first sample name in dataMatrix is X17, and in sampleMetadata is 17
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51 testDirC <- "datSamFlsInv"
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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52 argLs <- list(makeNameL = TRUE)
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54 argLs <- c(defaultArgF(testDirC), argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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55 outLs <- wrapperCallF(argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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57 checkEquals(outLs[['infVc']][5], 'Message: Converting sample and variable names to the standard R format')
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59 checkEquals(outLs[['infVc']][7], 'Warning: The sample and/or variable names or orders from the input tables have been modified')
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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61 checkEquals(rownames(outLs[['samDF']])[1], 'X17')
0
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63 }
1
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65 test_datVarInv <- function() {
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67 ## first two variables inverted in variableMetadata
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69 testDirC <- "datVarInv"
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70 argLs <- list(makeNameL = FALSE)
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72 argLs <- c(defaultArgF(testDirC), argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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73 outLs <- wrapperCallF(argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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75 checkEquals(outLs[['infVc']][7], 'Warning: The sample and/or variable names or orders from the input tables have been modified')
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77 }
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79 test_datVarFls <- function() {
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81 ## second variable name in dataMatrix is 3072, and in variableMetadata is X3072
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83 testDirC <- "datVarFls"
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84 argLs <- list(makeNameL = TRUE)
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86 argLs <- c(defaultArgF(testDirC), argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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87 outLs <- wrapperCallF(argLs)
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
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89 checkEquals(outLs[['infVc']][5], 'Message: Converting sample and variable names to the standard R format')
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91 checkEquals(outLs[['infVc']][7], 'Warning: The sample and/or variable names or orders from the input tables have been modified')
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93 checkEquals(colnames(outLs[['datMN']])[2], 'X3072')
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents: 0
diff changeset
94
b642f4f87022 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15
ethevenot
parents: 0
diff changeset
95 }