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annotate checkFormat_wrapper.R @ 0:0d8099822c49 draft

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
author ethevenot
date Sat, 30 Jul 2016 12:06:35 -0400
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
ethevenot
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1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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3 library(batch) ## parseCommandArgs
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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5 source_local <- function(fname){
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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6 argv <- commandArgs(trailingOnly = FALSE)
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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8 source(paste(base_dir, fname, sep="/"))
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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9 }
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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11 source_local("checkFormat_script.R")
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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13 argVc <- unlist(parseCommandArgs(evaluate = FALSE))
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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16 ##------------------------------
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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17 ## Initializing
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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18 ##------------------------------
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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20 ## options
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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21 ##--------
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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23 strAsFacL <- options()$stringsAsFactors
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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24 options(stringsAsFactors = FALSE)
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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26 ## constants
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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27 ##----------
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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29 modNamC <- "Check Format" ## module name
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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31 ## log file
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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32 ##---------
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34 sink(argVc["information"])
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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36 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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37 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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40 ##------------------------------
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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41 ## Computation
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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42 ##------------------------------
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45 resLs <- readAndCheckF(argVc["dataMatrix_in"],
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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46 argVc["sampleMetadata_in"],
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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47 argVc["variableMetadata_in"])
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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48 chkL <- resLs[["chkL"]]
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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51 ##------------------------------
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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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="")
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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60 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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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()
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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68 stop("Please check the generated 'information' file")
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70 }
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72 ## closing
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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73 ##--------
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75 options(stringsAsFactors = strAsFacL)
0d8099822c49 planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 217d97da5c733c3628997666c73867e81af0a0ee
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77 rm(list = ls())