Mercurial > repos > lecorguille > xcms_xcmsset

annotate xcms_xcmsSet.r @ 41:bca66ffdf02a draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 09:46:51 -0400
parents e8d7395a70b2
children a8f0dd2aff5a
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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 -----
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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
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")
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e8d7395a70b2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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15 source_local("lib-xcms3.x.x.r")
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 pkgs <- c("xcms","batch")
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18 loadAndDisplayPackages(pkgs)
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19 cat("\n\n");
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22 # ----- ARGUMENTS -----
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23 cat("\tARGUMENTS INFO\n")
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24 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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25 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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27 cat("\n\n")
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30 # ----- PROCESSING INFILE -----
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31 cat("\tARGUMENTS PROCESSING INFO\n")
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33 #saving the commun parameters
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34 BPPARAM <- MulticoreParam(1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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35 if (!is.null(args$BPPARAM)){
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36 BPPARAM <- MulticoreParam(args$BPPARAM)
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37 }
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38 register(BPPARAM)
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40 #saving the specific parameters
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41 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum
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42 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt
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43 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
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45 method <- args$method
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47 if (!is.null(args$roiList)){
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48 cat("\t\troiList provided\n")
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49 args$roiList <- list(getDataFrameFromFile(args$roiList))
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50 print(args$roiList)
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51 }
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53 cat("\n\n")
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55 # ----- INFILE PROCESSING -----
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56 cat("\tINFILE PROCESSING INFO\n")
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57
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58 #image is an .RData file necessary to use xset variable given by previous tools
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59 load(args$image)
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60 if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData")
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61
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62 # Handle infiles
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63 if (!exists("singlefile")) singlefile <- NULL
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64 if (!exists("zipfile")) zipfile <- NULL
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65 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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66 zipfile <- rawFilePath$zipfile
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67 singlefile <- rawFilePath$singlefile
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68 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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71 cat("\n\n")
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74 # ----- MAIN PROCESSING INFO -----
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75 cat("\tMAIN PROCESSING INFO\n")
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78 cat("\t\tCOMPUTE\n")
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80 ## Get the full path to the files
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81 files <- getMSFiles(directory)
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82
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83 cat("\t\t\tApply filter[s] (if asked)\n")
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84 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
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85 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
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86 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
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87 #Apply this filter only if file contain MS and MSn
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88 if(length(unique(msLevel(raw_data)))!= 1){
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89 raw_data <- filterMsLevel(raw_data,msLevel=1)
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90 }
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92 cat("\t\t\tChromatographic peak detection\n")
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93 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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94 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
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96 findChromPeaksParam <- do.call(paste0(method,"Param"), args)
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97 print(findChromPeaksParam)
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98 xdata <- findChromPeaks(raw_data, param=findChromPeaksParam)
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99
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100 # Check if there are no peaks
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101 if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings")
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102
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103 # Transform the files absolute pathways into relative pathways
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104 xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)
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105
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106 # Create a sampleMetada file
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107 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
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108
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109 cat("\t\t\tCompute and Store TIC and BPI\n")
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110 chromTIC = chromatogram(xdata, aggregationFun = "sum")
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111 chromBPI = chromatogram(xdata, aggregationFun = "max")
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112
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113 cat("\n\n")
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114
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115 # ----- EXPORT -----
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116
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117 cat("\tXCMSnExp OBJECT INFO\n")
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118 print(xdata)
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119 cat("\n\n")
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120
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121 cat("\txcmsSet OBJECT INFO\n")
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122 # Get the legacy xcmsSet object
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123 xset <- getxcmsSetObject(xdata)
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124 print(xset)
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125 cat("\n\n")
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126
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127 #saving R data in .Rdata file to save the variables used in the present tool
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128 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
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129 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
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130
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131
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132 cat("\tDONE\n")