Mercurial > repos > lecorguille > xcms_fillpeaks

annotate xcms_fillpeaks.r @ 46:871ffc15a6da draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:52:02 +0000
parents 1a711c1b8b1f
children 1241183c8ae0
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 # ----- LOG FILE -----
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1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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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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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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12 #Import the different functions
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13 source_local <- function(fname) {
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14 argv <- commandArgs(trailingOnly = FALSE)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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16 source(paste(base_dir, fname, sep = "/"))
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17 }
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18 source_local("lib.r")
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20 pkgs <- c("xcms", "batch")
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21 loadAndDisplayPackages(pkgs)
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22 cat("\n\n")
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25 # ----- ARGUMENTS -----
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26 cat("\tARGUMENTS INFO\n")
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27 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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28 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
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30 cat("\n\n")
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32 # ----- PROCESSING INFILE -----
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33 cat("\tARGUMENTS PROCESSING INFO\n")
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35 #saving the specific parameters
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36 method <- "FillChromPeaks"
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37
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38 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
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39 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
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40 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
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41 if (!is.null(args$intval)) intval <- args$intval
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42 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
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44 cat("\n\n")
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47 # ----- ARGUMENTS PROCESSING -----
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48 cat("\tINFILE PROCESSING INFO\n")
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50 #image is an .RData file necessary to use xset variable given by previous tools
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51 load(args$image)
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52 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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54 #Verification of a group step before doing the fillpeaks job.
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55 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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57 # Handle infiles
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58 if (!exists("singlefile")) singlefile <- NULL
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59 if (!exists("zipfile")) zipfile <- NULL
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60 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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61 zipfile <- rawFilePath$zipfile
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62 singlefile <- rawFilePath$singlefile
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65 cat("\n\n")
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67 # ----- MAIN PROCESSING INFO -----
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68 cat("\tMAIN PROCESSING INFO\n")
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71 cat("\t\tCOMPUTE\n")
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73 cat("\t\t\tFilling missing peaks using default settings\n")
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74 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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75 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
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76
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77 fillChromPeaksParam <- do.call(paste0(method, "Param"), args)
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78 print(fillChromPeaksParam)
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80 # back compatibility between xcms-3.0.0 and xcms-3.5.2
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81 xdata <- updateObject(xdata)
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82 register(SerialParam())
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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")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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94 print(xdata)
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95 cat("\n\n")
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97 cat("\txcmsSet OBJECT INFO\n")
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98 # Get the legacy xcmsSet object
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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99 xset <- getxcmsSetObject(xdata)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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100 print(xset)
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101 cat("\n\n")
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103 #saving R data in .Rdata file to save the variables used in the present tool
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1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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104 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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105 save(list = objects2save[objects2save %in% ls()], file = "fillpeaks.RData")
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107 cat("\n\n")
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110 cat("\tDONE\n")