Mercurial > repos > ethevenot > univariate
annotate tests/univariate_tests.R @ 1:fdefbc780d2e draft
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 59a3d6b0634a8bbe682d7b755bbb3735c07548dc
author | ethevenot |
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date | Sat, 30 Jul 2016 12:38:02 -0400 |
parents | ef64d3752050 |
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rev | line source |
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ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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changeset
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1 library(RUnit) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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2 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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3 wrapperF <- function(argVc) { |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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4 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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5 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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6 source("../univariate_script.R") |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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7 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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8 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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9 #### Start_of_testing_code <- function() {} |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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10 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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11 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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12 ##------------------------------ |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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13 ## Initializing |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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14 ##------------------------------ |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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15 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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16 ## options |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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17 ##-------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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18 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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19 strAsFacL <- options()$stringsAsFactors |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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20 options(stringsAsFactors = FALSE) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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21 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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22 ## packages |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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23 ##--------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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24 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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changeset
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25 library(PMCMR) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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26 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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27 ## constants |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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28 ##---------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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29 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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30 modNamC <- "Univariate" ## module name |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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31 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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32 topEnvC <- environment() |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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33 flagC <- "\n" |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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34 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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35 ## functions |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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36 ##---------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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37 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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38 flgF <- function(tesC, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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39 envC = topEnvC, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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40 txtC = NA) { ## management of warning and error messages |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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41 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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42 tesL <- eval(parse(text = tesC), envir = envC) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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43 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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44 if(!tesL) { |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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45 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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46 sink(NULL) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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47 stpTxtC <- ifelse(is.na(txtC), |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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48 paste0(tesC, " is FALSE"), |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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49 txtC) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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50 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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51 stop(stpTxtC, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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52 call. = FALSE) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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53 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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54 } |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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55 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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56 } ## flgF |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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57 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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58 ## log file |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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59 ##--------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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60 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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61 sink(argVc["information"]) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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62 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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63 cat("\nStart of the '", modNamC, "' Galaxy module call: ", |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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64 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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65 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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66 ## loading |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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67 ##-------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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68 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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69 datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"], |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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70 check.names = FALSE, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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71 header = TRUE, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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72 row.names = 1, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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73 sep = "\t"))) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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74 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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75 samDF <- read.table(argVc["sampleMetadata_in"], |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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76 check.names = FALSE, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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77 header = TRUE, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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78 row.names = 1, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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79 sep = "\t") |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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80 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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81 varDF <- read.table(argVc["variableMetadata_in"], |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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82 check.names = FALSE, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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83 header = TRUE, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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84 row.names = 1, |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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85 sep = "\t") |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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86 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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87 tesC <- argVc["tesC"] |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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88 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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89 ## checking |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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90 ##--------- |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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91 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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92 flgF("identical(rownames(datMN), rownames(samDF))", txtC = "Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section") |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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93 flgF("identical(colnames(datMN), rownames(varDF))", txtC = "Row names of the dataMatrix are not identical to the row names of the variableMetadata; check your data with the 'Check Format' module in the 'Quality Control' section") |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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94 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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95 flgF("argVc['facC'] %in% colnames(samDF)", txtC = paste0("Required factor of interest '", argVc['facC'], "' could not be found in the column names of the sampleMetadata")) |
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96 flgF("mode(samDF[, argVc['facC']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc['facC'], "' column of the sampleMetadata should contain either number only, or character only")) |
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97 |
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98 flgF("!(tesC %in% c('ttest', 'wilcoxon')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) == 2)", txtC = paste0("For 'ttest' and 'wilcoxon', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with only two different classes")) |
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99 flgF("!(tesC %in% c('anova', 'kruskal')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) > 2)", txtC = paste0("For 'anova' and 'kruskal', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with at least three different classes")) |
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100 flgF("!(tesC %in% c('pearson', 'spearman')) || mode(samDF[, argVc['facC']]) == 'numeric'", txtC = paste0("For 'pearson' and 'spearman', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain numbers only")) |
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101 |
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102 flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')") |
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103 |
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104 flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1", |
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105 txtC = "(corrected) p-value threshold must be between 0 and 1") |
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106 |
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107 |
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108 ##------------------------------ |
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109 ## Computation |
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110 ##------------------------------ |
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111 |
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112 |
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113 varDF <- univariateF(datMN = datMN, |
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114 samDF = samDF, |
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115 varDF = varDF, |
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116 facC = argVc["facC"], |
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117 tesC = tesC, |
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118 adjC = argVc["adjC"], |
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119 thrN = as.numeric(argVc["thrN"])) |
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120 |
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121 |
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122 ##------------------------------ |
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123 ## Ending |
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124 ##------------------------------ |
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125 |
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126 |
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127 ## saving |
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128 ##-------- |
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129 |
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130 varDF <- cbind.data.frame(variableMetadata = rownames(varDF), |
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131 varDF) |
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132 write.table(varDF, |
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133 file = argVc["variableMetadata_out"], |
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134 quote = FALSE, |
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135 row.names = FALSE, |
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136 sep = "\t") |
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137 |
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138 ## closing |
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139 ##-------- |
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140 |
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141 cat("\nEnd of '", modNamC, "' Galaxy module call: ", |
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142 as.character(Sys.time()), "\n", sep = "") |
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143 |
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144 sink() |
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145 |
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146 options(stringsAsFactors = strAsFacL) |
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147 |
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148 |
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149 |
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150 #### End_of_testing_code <- function() {} |
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151 |
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152 |
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153 return(list(varDF = varDF)) |
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154 |
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155 rm(list = ls()) |
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156 |
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157 } |
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158 |
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159 exaDirOutC <- "output" |
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160 if(!file.exists(exaDirOutC)) |
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161 stop("Please create an 'output' subfolder into the (current) 'tests' folder") |
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162 |
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163 tesArgLs <- list(input_kruskal = c(facC = "ageGroup", |
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164 tesC = "kruskal", |
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165 adjC = "fdr", |
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166 thrN = "0.05", |
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167 .chkC = "checkEqualsNumeric(outLs[['varDF']]['HMDB01032', 'ageGroup_kruskal_senior-experienced_pva'], 0.1231246, tolerance = 1e-6)"), |
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168 example1_wilcoxDif = c(facC = "jour", |
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169 tesC = "wilcoxon", |
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170 adjC = "fdr", |
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171 thrN = "0.05", |
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172 .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_wilcoxon_J3-J10_dif'], 0.216480042, tolerance = 1e-8)"), |
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173 example1_ttestFdr = c(facC = "jour", |
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174 tesC = "ttest", |
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175 adjC = "fdr", |
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176 thrN = "0.05", |
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177 .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_ttest_J3-J10_fdr'], 0.7605966, tolerance = 1e-6)")) |
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178 |
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179 for(tesC in names(tesArgLs)) |
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180 tesArgLs[[tesC]] <- c(tesArgLs[[tesC]], |
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181 dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"), |
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182 sampleMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "sampleMetadata.tsv"), |
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183 variableMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "variableMetadata.tsv"), |
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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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184 variableMetadata_out = file.path(exaDirOutC, "variableMetadata.tsv"), |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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185 information = file.path(exaDirOutC, "information.txt")) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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186 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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187 for(tesC in names(tesArgLs)) { |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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188 print(tesC) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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189 outLs <- wrapperF(tesArgLs[[tesC]]) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
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190 if(".chkC" %in% names(tesArgLs[[tesC]])) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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191 stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]]))) |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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192 } |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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193 |
ef64d3752050
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
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194 message("Checks successfully completed") |