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planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author workflow4metabolomics
date Mon, 11 Sep 2023 22:36:51 +0000
parents 364756ea5f42
children
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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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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) {
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10 argv <- commandArgs(trailingOnly = FALSE)
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11 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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12 source(paste(base_dir, fname, sep = "/"))
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13 }
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14 source_local("lib.r")
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16 pkgs <- c("IPO", "batch")
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17 loadAndDisplayPackages(pkgs)
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18 cat("\n\n")
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19 # ----- ARGUMENTS -----
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20 cat("\tARGUMENTS INFO\n")
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21 args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
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22 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
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24 cat("\n\n")
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25 # ----- PROCESSING INFILE -----
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26 cat("\tARGUMENTS PROCESSING INFO\n")
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27 options(bitmapType = "cairo")
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29 samplebyclass <- 2
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30 if (!is.null(args$samplebyclass)) {
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31 samplebyclass <- args$samplebyclass
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32 args$samplebyclass <- NULL
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33 }
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35 # ----- INFILE PROCESSING -----
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36 cat("\tINFILE PROCESSING INFO\n")
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38 # Handle infiles
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39 if (!exists("singlefile")) singlefile <- NULL
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40 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
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41 singlefile <- rawFilePath$singlefile
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42 directory <- retrieveRawfileInWD(singlefile, NULL)
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44 # Check some character issues
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45 checkXmlStructure(directory)
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47 cat("\n\n")
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52 # ----- MAIN PROCESSING INFO -----
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53 cat("\tMAIN PROCESSING INFO\n")
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56 xset <- ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
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60 cat("\n\n")
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63 # ----- EXPORT -----
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65 cat("\tXSET OBJECT INFO\n")
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66 print(xset)
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67 # delete the parameters to avoid the passage to the next tool in .RData image
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70 # saving R data in .Rdata file to save the variables used in the present tool
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71 objects2save <- c("xset", "singlefile")
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72 save(list = objects2save[objects2save %in% ls()], file = "ipo4xcmsSet.RData")
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74 cat("\n\n")
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77 cat("\tDONE\n")