Mercurial > repos > lecorguille > xcms_group

annotate xcms_group.r @ 44:6f3567245d0c draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"
author workflow4metabolomics
date Tue, 21 Jul 2020 13:16:30 +0000
parents 9a9d91ddbe75
children 99852755ea5c
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #!/usr/bin/env Rscript
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 # ----- LOG FILE -----
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4 log_file=file("log.txt", open = "wt")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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5 sink(log_file)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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6 sink(log_file, type = "output")
020d065edd9e 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")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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12 #Import the different functions
020d065edd9e 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="/")) }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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14 source_local("lib.r")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 pkgs <- c("xcms","batch","RColorBrewer")
020d065edd9e 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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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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21 # ----- ARGUMENTS -----
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22 cat("\tARGUMENTS INFO\n")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("\n\n")
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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28 # ----- PROCESSING INFILE -----
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29 cat("\tARGUMENTS PROCESSING INFO\n")
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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31 #saving the specific parameters
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32 method <- args$method
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34 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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35 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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36 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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37 if (!is.null(args$intval)) intval <- args$intval
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38 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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40 cat("\n\n")
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43 # ----- ARGUMENTS PROCESSING -----
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44 cat("\tINFILE PROCESSING INFO\n")
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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46 #image is an .RData file necessary to use xset variable given by previous tools
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47 load(args$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 # Handle infiles
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51 if (!exists("singlefile")) singlefile <- NULL
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52 if (!exists("zipfile")) zipfile <- NULL
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53 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
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54 zipfile <- rawFilePath$zipfile
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55 singlefile <- rawFilePath$singlefile
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57 cat("\n\n")
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60 # ----- MAIN PROCESSING INFO -----
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61 cat("\tMAIN PROCESSING INFO\n")
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64 cat("\t\tCOMPUTE\n")
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67 cat("\t\t\tPerform the correspondence\n")
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68 args$sampleGroups = xdata$sample_group
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70 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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71 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list(sampleGroups=c(1,2))))]
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72
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73 groupChromPeaksParam <- do.call(paste0(method,"Param"), args)
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74 print(groupChromPeaksParam)
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75 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam)
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78 cat("\t\tDRAW GRAPHICS\n")
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79 getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
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81 if (exists("intval")) {
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82 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
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83 }
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85 cat("\n\n")
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87 # ----- EXPORT -----
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89 cat("\tXCMSnExp OBJECT INFO\n")
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90 print(xdata)
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91 cat("\n\n")
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93 cat("\txcmsSet OBJECT INFO\n")
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94 # Get the legacy xcmsSet object
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95 xset <- getxcmsSetObject(xdata)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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96 print(xset)
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97 cat("\n\n")
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98
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99 #saving R data in .Rdata file to save the variables used in the present tool
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100 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
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101 save(list=objects2save[objects2save %in% ls()], file="group.RData")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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102
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103 cat("\n\n")
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104
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105
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106 cat("\tDONE\n")