Mercurial > repos > lecorguille > xcms_fillpeaks

annotate xcms_fillpeaks.r @ 31:8fd5b5afa24d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:17:29 -0500
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children d8bac1291473
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31
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #!/usr/bin/env Rscript
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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="/")) }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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14 source_local("lib.r")
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16 pkgs <- c("xcms","batch")
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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 #saving the specific parameters
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32 method <- "FillChromPeaks"
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34 if (!is.null(args$convertRTMinute)){
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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35 convertRTMinute <- args$convertRTMinute; args$convertRTMinute <- NULL
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36 }
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37 if (!is.null(args$numDigitsMZ)){
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38 numDigitsMZ <- args$numDigitsMZ; args$numDigitsMZ <- NULL
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39 }
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40 if (!is.null(args$numDigitsRT)){
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41 numDigitsRT <- args$numDigitsRT; args$numDigitsRT <- NULL
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42 }
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43 if (!is.null(args$intval)){
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44 intval <- args$intval; args$intval <- NULL
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45 }
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47 cat("\n\n")
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50 # ----- ARGUMENTS PROCESSING -----
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51 cat("\tINFILE PROCESSING INFO\n")
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52
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53 #image is an .RData file necessary to use xset variable given by previous tools
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54 load(args$image); args$image=NULL
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55 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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57 #Verification of a group step before doing the fillpeaks job.
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58 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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60 # Handle infiles
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61 if (!exists("singlefile")) singlefile <- NULL
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62 if (!exists("zipfile")) zipfile <- NULL
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63 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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64 zipfile <- rawFilePath$zipfile
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65 singlefile <- rawFilePath$singlefile
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66 args <- rawFilePath$args
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67 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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69 # Check some character issues
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70 md5sumList <- list("origin" = getMd5sum(directory))
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71 checkXmlStructure(directory)
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72 checkFilesCompatibilityWithXcms(directory)
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75 cat("\n\n")
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78 # ----- MAIN PROCESSING INFO -----
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79 cat("\tMAIN PROCESSING INFO\n")
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82 cat("\t\tCOMPUTE\n")
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84 cat("\t\t\tFilling missing peaks using default settings\n")
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85 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
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86 print(fillChromPeaksParam)
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87 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
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89 if (exists("intval")) {
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90 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, "variableMetadata.tsv", "dataMatrix.tsv")
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91 }
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93 cat("\n\n")
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94
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95 # ----- EXPORT -----
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96
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97 cat("\tXCMSnExp OBJECT INFO\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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98 print(xdata)
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99 cat("\n\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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100
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101 cat("\txcmsSet OBJECT INFO\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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102 # Get the legacy xcmsSet object
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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103 xset <- getxcmsSetObject(xdata)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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104 print(xset)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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105 cat("\n\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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106
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107 #saving R data in .Rdata file to save the variables used in the present tool
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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108 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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109 save(list=objects2save[objects2save %in% ls()], file="fillpeaks.RData")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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110
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111 cat("\n\n")
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112
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113
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114 cat("\tDONE\n")