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planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author workflow4metabolomics
date Mon, 11 Sep 2023 22:37:32 +0000
parents ae8de756dfcf
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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28 samplebyclass <- 2
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29 if (!is.null(args$samplebyclass)) {
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30 samplebyclass <- args$samplebyclass
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31 args$samplebyclass <- NULL
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32 }
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34 cat("\n\n")
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36 # ----- INFILE PROCESSING -----
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37 cat("\tINFILE PROCESSING INFO\n")
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38 options(bitmapType = "cairo")
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40 # image is an .RData file necessary to use xset variable given by previous tools
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41 load(args$image)
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42 args$image <- NULL
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44 # Because so far CAMERA isn't compatible with the new XCMSnExp object
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45 if (exists("xdata")) {
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46 xset <- getxcmsSetObject(xdata)
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47 }
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49 if (!exists("xset")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata' which is provided by the tool: MSnbase readMSData")
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52 # Handle infiles
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53 if (!exists("singlefile")) singlefile <- NULL
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54 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
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55 singlefile <- rawFilePath$singlefile
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56 print(singlefile)
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57 directory <- retrieveRawfileInWD(singlefile, NULL)
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60 cat("\n\n")
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63 # ----- MAIN PROCESSING INFO -----
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64 cat("\tMAIN PROCESSING INFO\n")
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66 ipo4retgroup(xset, directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
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68 cat("\n\n")
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71 cat("\tDONE\n")