Mercurial > repos > lecorguille > xcms_xcmsset

annotate xcms_xcmsSet.r @ 32:2bf1cb023c94 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:14:39 -0500
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children c363b9f1caef
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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1 #!/usr/bin/env Rscript
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 # ----- LOG FILE -----
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4 log_file <- file("log.txt", open="wt")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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5 sink(log_file)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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6 sink(log_file, type = "output")
2bf1cb023c94 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
2bf1cb023c94 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="/")) }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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14 source_local("lib.r")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 pkgs <- c("xcms","batch")
2bf1cb023c94 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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29 # ----- PROCESSING INFILE -----
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30 cat("\tARGUMENTS PROCESSING INFO\n")
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32 #saving the commun parameters
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33 BPPARAM <- MulticoreParam(1)
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34 if (!is.null(args$BPPARAM)){
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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35 BPPARAM <- MulticoreParam(args$BPPARAM); args$BPPARAM <- NULL
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36 }
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37 register(BPPARAM)
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39 #saving the specific parameters
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40 method <- args$method; args$method <- NULL
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42 cat("\n\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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44 # ----- INFILE PROCESSING -----
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45 cat("\tINFILE PROCESSING INFO\n")
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47 # Handle infiles
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48 if (!exists("singlefile")) singlefile <- NULL
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49 if (!exists("zipfile")) zipfile <- NULL
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50 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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51 zipfile <- rawFilePath$zipfile
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52 singlefile <- rawFilePath$singlefile
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53 args <- rawFilePath$args
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54 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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56 # Check some character issues
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57 md5sumList <- list("origin" = getMd5sum(directory))
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58 checkXmlStructure(directory)
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59 checkFilesCompatibilityWithXcms(directory)
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62 cat("\n\n")
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65 # ----- MAIN PROCESSING INFO -----
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66 cat("\tMAIN PROCESSING INFO\n")
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69 cat("\t\tCOMPUTE\n")
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71 ## Get the full path to the files
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72 files <- getMSFiles(directory)
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74 cat("\t\t\tCreate a phenodata data.frame\n")
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75 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1))
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76 s_name <- tools::file_path_sans_ext(basename(files))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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77 pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE)
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78 print(pd)
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80 cat("\t\t\tLoad Raw Data\n")
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81 raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk")
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83 cat("\t\t\tChromatographic peak detection\n")
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84 findChromPeaksParam <- do.call(paste0(method,"Param"), args)
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85 print(findChromPeaksParam)
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86 xdata <- findChromPeaks(raw_data, param=findChromPeaksParam)
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87
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88 # Check if there are no peaks
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89 if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings")
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90
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91 # Transform the files absolute pathways into relative pathways
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92 xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)
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93 save.image()
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94 # Create a sampleMetada file
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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95 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
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96
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97 # Get the legacy xcmsSet object
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98 xset <- getxcmsSetObject(xdata)
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99
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100 cat("\n\n")
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101
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102
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103 # -- TIC --
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104 cat("\t\tGET TIC GRAPH\n")
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105 #@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
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106 getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
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107 getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")
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108
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109 cat("\n\n")
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110
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111 # ----- EXPORT -----
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112
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113 cat("\tXCMSnExp OBJECT INFO\n")
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114 print(xdata)
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115 cat("\n\n")
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116
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117 cat("\txcmsSet OBJECT INFO\n")
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118 print(xset)
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119 cat("\n\n")
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120
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121 #saving R data in .Rdata file to save the variables used in the present tool
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122 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
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123 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
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124
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125
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126 cat("\tDONE\n")