Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.r @ 2:e6fdadaf039e draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:37:40 -0400
parents fe1f0f16d9e6
children 60b156e58529
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1 #!/usr/bin/env Rscript
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3 # ----- LOG FILE -----
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4 log_file=file("log.txt", open = "wt")
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5 sink(log_file)
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6 sink(log_file, type = "output")
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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12 #Import the different functions
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13 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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14 source_local("lib.r")
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16 pkgs <- c("xcms","batch","RColorBrewer")
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17 loadAndDisplayPackages(pkgs)
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18 cat("\n\n");
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21 # ----- ARGUMENTS -----
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22 cat("\tARGUMENTS INFO\n")
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23 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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26 cat("\n\n")
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28 # ----- PROCESSING INFILE -----
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29 cat("\tARGUMENTS PROCESSING INFO\n")
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31 cat("\n\n")
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34 # ----- ARGUMENTS PROCESSING -----
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35 cat("\tINFILE PROCESSING INFO\n")
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36
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37 mergeXDataReturn <- mergeXData(args)
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38 xdata <- mergeXDataReturn$xdata
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39 singlefile <- mergeXDataReturn$singlefile
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40 md5sumList <- mergeXDataReturn$md5sumList
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41 sampleNamesList <- mergeXDataReturn$sampleNamesList
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43 cat("\n\n")
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46 # ----- MAIN PROCESSING INFO -----
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47 cat("\tMAIN PROCESSING INFO\n")
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50 cat("\t\tDRAW GRAPHICS\n")
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52 getPlotTICs(xdata, pdfname="TICs.pdf")
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53 getPlotBPIs(xdata, pdfname="BPIs.pdf")
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55 cat("\n\n")
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57 # ----- EXPORT -----
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59 cat("\tXCMSnExp OBJECT INFO\n")
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60 print(xdata)
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61 cat("\n\n")
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63 cat("\txcmsSet OBJECT INFO\n")
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64 # Get the legacy xcmsSet object
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65 xset <- getxcmsSetObject(xdata)
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66 print(xset)
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67 cat("\n\n")
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70 cat("\tDONE\n")