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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 16:00:52 +0000
parents 20f8ebc3a391
children
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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1 #!/usr/bin/env Rscript
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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
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13 source_local <- function(fname) {
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14 argv <- commandArgs(trailingOnly = FALSE)
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15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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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", "RColorBrewer")
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21 loadAndDisplayPackages(pkgs)
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22 cat("\n\n")
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24 # ----- ARGUMENTS -----
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25 cat("\tARGUMENTS INFO\n")
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26 # interpretation of arguments given in command line as an R list of objects
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27 args <- parseCommandArgs(evaluate = FALSE)
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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 args_method <- args$method
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37 args_image <- args$image
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38 args_msLevel <- args$msLevel
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39 param_args <- list()
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41 if (args_method == "CleanPeaks") {
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42 param_args$maxPeakwidth <- args$maxPeakwidth
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43 } else if (args_method == "FilterIntensity") {
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44 param_args$threshold <- args$threshold
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45 param_args$value <- args$value
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46 param_args$nValues <- args$nValues
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47 } else if (args_method == "MergeNeighboringPeaks") {
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48 param_args$expandRt <- args$expandRt
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49 param_args$expandMz <- args$expandMz
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50 param_args$ppm <- args$ppm
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51 param_args$minProp <- args$minProp
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52 }
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54 cat("\n\n")
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57 # ----- ARGUMENTS PROCESSING -----
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58 cat("\tINFILE PROCESSING INFO\n")
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60 #image is an .RData file necessary to use xset variable given by previous tools
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61 load(args_image)
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62 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
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64 # Handle infiles
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65 if (!exists("singlefile")) singlefile <- NULL
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66 if (!exists("zipfile")) zipfile <- NULL
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67 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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68 zipfile <- rawFilePath$zipfile
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69 singlefile <- rawFilePath$singlefile
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71 cat("\n\n")
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74 # ----- MAIN PROCESSING INFO -----
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75 cat("\tMAIN PROCESSING INFO\n")
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78 cat("\t\tPREPARE PARAMETERS\n\n")
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80 if (args_method == "CleanPeaks") {
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81 refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
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82 } else if (args_method == "FilterIntensity") {
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83 refineChromPeaksParam <- FilterIntensityParam(
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84 threshold = param_args$threshold,
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85 nValues = param_args$nValues,
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86 value = param_args$value
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87 )
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88 } else if (args_method == "MergeNeighboringPeaks") {
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89 refineChromPeaksParam <- MergeNeighboringPeaksParam(
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90 expandRt = param_args$expandRt,
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91 expandMz = param_args$expandMz,
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92 ppm = param_args$ppm,
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93 minProp = param_args$minProp
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94 )
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95 }
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96
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97 cat(str(refineChromPeaksParam))
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98
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99 cat("\n\n\t\tCOMPUTE\n")
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100
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101 xdata <- updateObject(xdata)
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102
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103 xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
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104
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105 cat("\n\n")
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106
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107 # ----- EXPORT -----
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108
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109 cat("\tXCMSnExp OBJECT INFO\n")
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110 print(xdata)
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111 cat("\n\n")
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112
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113 cat("\txcmsSet OBJECT INFO\n")
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114 # Get the legacy xcmsSet object
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115 xset <- getxcmsSetObject(xdata)
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116 print(xset)
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117 cat("\n\n")
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118
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119 #saving R data in .Rdata file to save the variables used in the present tool
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120 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
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121 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
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122
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123 cat("\n\n")
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124
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125
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126 cat("\tDONE\n")