Mercurial > repos > lecorguille > xcms_fillpeaks

annotate xcms_fillpeaks.r @ 38:a3e80894efd3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
author lecorguille
date Mon, 17 Sep 2018 08:46:47 -0400
parents e67cbb96d9e9
children a98dbb09fed1
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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)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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")
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15 source_local("lib-xcms3.x.x.r")
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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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29 # ----- PROCESSING INFILE -----
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30 cat("\tARGUMENTS PROCESSING INFO\n")
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32 #saving the specific parameters
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33 method <- "FillChromPeaks"
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35 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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36 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
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37 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
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38 if (!is.null(args$intval)) intval <- args$intval
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39 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
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41 cat("\n\n")
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44 # ----- ARGUMENTS PROCESSING -----
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45 cat("\tINFILE PROCESSING INFO\n")
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47 #image is an .RData file necessary to use xset variable given by previous tools
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48 load(args$image)
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49 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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51 #Verification of a group step before doing the fillpeaks job.
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52 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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54 # Handle infiles
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55 if (!exists("singlefile")) singlefile <- NULL
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56 if (!exists("zipfile")) zipfile <- NULL
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57 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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58 zipfile <- rawFilePath$zipfile
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59 singlefile <- rawFilePath$singlefile
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60 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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62 # Check some character issues
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63 md5sumList <- list("origin" = getMd5sum(directory))
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64 checkXmlStructure(directory)
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65 checkFilesCompatibilityWithXcms(directory)
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68 cat("\n\n")
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71 # ----- MAIN PROCESSING INFO -----
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72 cat("\tMAIN PROCESSING INFO\n")
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75 cat("\t\tCOMPUTE\n")
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77 cat("\t\t\tFilling missing peaks using default settings\n")
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78 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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79 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
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80
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81 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
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82 print(fillChromPeaksParam)
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83 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)
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85 if (exists("intval")) {
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86 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
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87 }
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89 cat("\n\n")
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91 # ----- EXPORT -----
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93 cat("\tXCMSnExp OBJECT INFO\n")
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94 print(xdata)
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95 cat("\n\n")
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96
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97 cat("\txcmsSet OBJECT INFO\n")
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98 # Get the legacy xcmsSet object
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99 xset <- getxcmsSetObject(xdata)
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100 print(xset)
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101 cat("\n\n")
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102
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103 #saving R data in .Rdata file to save the variables used in the present tool
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104 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList", "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
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105 save(list=objects2save[objects2save %in% ls()], file="fillpeaks.RData")
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106
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107 cat("\n\n")
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108
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109
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110 cat("\tDONE\n")