annotate checkformat_wrapper.R @ 1:e194eec8e70c draft

planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
author ethevenot
date Sat, 06 Aug 2016 11:54:28 -0400
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children b6a6b4cc932a
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e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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1 #!/usr/bin/env Rscript
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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3 library(batch) ## parseCommandArgs
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5 source_local <- function(fname){
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6 argv <- commandArgs(trailingOnly = FALSE)
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7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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8 source(paste(base_dir, fname, sep="/"))
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9 }
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11 source_local("checkformat_script.R")
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13 argVc <- unlist(parseCommandArgs(evaluate = FALSE))
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16 ##------------------------------
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17 ## Initializing
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18 ##------------------------------
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20 ## options
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21 ##--------
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23 strAsFacL <- options()$stringsAsFactors
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24 options(stringsAsFactors = FALSE)
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26 ## constants
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27 ##----------
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29 modNamC <- "Check Format" ## module name
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31 ## log file
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32 ##---------
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34 sink(argVc["information"])
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36 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
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37 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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40 ##------------------------------
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41 ## Computation
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42 ##------------------------------
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45 resLs <- readAndCheckF(argVc["dataMatrix_in"],
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46 argVc["sampleMetadata_in"],
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47 argVc["variableMetadata_in"])
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48 chkL <- resLs[["chkL"]]
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51 ##------------------------------
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52 ## Ending
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53 ##------------------------------
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56 if(chkL) {
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58 cat("\nTable formats are OK; enjoy your analyses!\n", sep="")
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60 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
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61 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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63 sink()
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65 } else {
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67 sink()
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68 stop("Please check the generated 'information' file")
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70 }
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72 ## closing
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73 ##--------
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75 options(stringsAsFactors = strAsFacL)
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77 rm(list = ls())