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annotate ipo4xcmsSet.r @ 1:ae8de756dfcf draft

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"planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
author workflow4metabolomics
date Mon, 16 Dec 2019 05:26:42 -0500
parents ac5f2936575b
children 8e5f667359cb
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1 #!/usr/bin/env Rscript
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2 #Authors Gildas Le Corguille and Yann Guitton
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ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
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5 # ----- PACKAGE -----
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6 cat("\tSESSION INFO\n")
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8 #Import the different functions
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9 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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10 source_local("lib.r")
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12 pkgs <- c("IPO","batch")
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13 loadAndDisplayPackages(pkgs)
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14 cat("\n\n");
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17 # ----- ARGUMENTS -----
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18 cat("\tARGUMENTS INFO\n")
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19 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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20 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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22 cat("\n\n");
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24 # ----- PROCESSING INFILE -----
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25 cat("\tARGUMENTS PROCESSING INFO\n")
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26 options(bitmapType='cairo')
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28 samplebyclass = 2
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29 if (!is.null(args$samplebyclass)){
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30 samplebyclass = args$samplebyclass; args$samplebyclass=NULL
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31 }
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33 # ----- INFILE PROCESSING -----
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34 cat("\tINFILE PROCESSING INFO\n")
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36 # Handle infiles
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37 if (!exists("singlefile")) singlefile <- NULL
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38 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
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39 singlefile <- rawFilePath$singlefile
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40 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL)
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42 # Check some character issues
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43 checkXmlStructure(directory)
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45 cat("\n\n")
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50 # ----- MAIN PROCESSING INFO -----
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51 cat("\tMAIN PROCESSING INFO\n")
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54 xset = ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
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58 cat("\n\n")
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61 # ----- EXPORT -----
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63 cat("\tXSET OBJECT INFO\n")
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64 print(xset)
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65 #delete the parameters to avoid the passage to the next tool in .RData image
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68 #saving R data in .Rdata file to save the variables used in the present tool
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69 objects2save = c("xset", "singlefile")
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70 save(list=objects2save[objects2save %in% ls()], file="ipo4xcmsSet.RData")
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72 cat("\n\n")
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75 cat("\tDONE\n")
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