Mercurial > repos > lecorguille > xcms_fillpeaks

annotate xcms_fillpeaks.r @ 43:eeade1310758 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:14:27 -0400
parents a98dbb09fed1
children 1b5fb5a27f5e
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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1 #!/usr/bin/env Rscript
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 # ----- LOG FILE -----
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 pkgs <- c("xcms","batch")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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"
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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34 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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35 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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36 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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37 if (!is.null(args$intval)) intval <- args$intval
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38 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
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40 cat("\n\n")
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43 # ----- ARGUMENTS PROCESSING -----
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44 cat("\tINFILE PROCESSING INFO\n")
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46 #image is an .RData file necessary to use xset variable given by previous tools
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47 load(args$image)
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48 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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50 #Verification of a group step before doing the fillpeaks job.
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51 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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53 # Handle infiles
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54 if (!exists("singlefile")) singlefile <- NULL
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55 if (!exists("zipfile")) zipfile <- NULL
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56 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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57 zipfile <- rawFilePath$zipfile
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58 singlefile <- rawFilePath$singlefile
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59 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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61 # Check some character issues
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62 md5sumList <- list("origin" = getMd5sum(directory))
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63 checkXmlStructure(directory)
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64 checkFilesCompatibilityWithXcms(directory)
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67 cat("\n\n")
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69 # ----- MAIN PROCESSING INFO -----
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70 cat("\tMAIN PROCESSING INFO\n")
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73 cat("\t\tCOMPUTE\n")
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75 cat("\t\t\tFilling missing peaks using default settings\n")
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76 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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77 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
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78
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79 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
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80 print(fillChromPeaksParam)
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82 # back compatibility between xcms-3.0.0 and xcms-3.5.2
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83 xdata <- updateObject(xdata)
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84
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85 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
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87 if (exists("intval")) {
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88 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
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89 }
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91 cat("\n\n")
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93 # ----- EXPORT -----
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94
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95 cat("\tXCMSnExp OBJECT INFO\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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96 print(xdata)
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97 cat("\n\n")
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98
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99 cat("\txcmsSet OBJECT INFO\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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100 # Get the legacy xcmsSet object
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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101 xset <- getxcmsSetObject(xdata)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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102 print(xset)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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103 cat("\n\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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104
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105 #saving R data in .Rdata file to save the variables used in the present tool
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106 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
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107 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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108
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109 cat("\n\n")
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110
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111
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112 cat("\tDONE\n")