Mercurial > repos > lecorguille > xcms_group

annotate xcms_group.r @ 28:2b676d5eb848 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:16:31 +0000
parents d45a786cbc40
children
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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1 #!/usr/bin/env Rscript
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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16 source(paste(base_dir, fname, sep = "/"))
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d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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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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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 <- args$method
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38 if (!is.null(args$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 # 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 <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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58 zipfile <- rawFilePath$zipfile
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59 singlefile <- rawFilePath$singlefile
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61 cat("\n\n")
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64 # ----- MAIN PROCESSING INFO -----
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65 cat("\tMAIN PROCESSING INFO\n")
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68 cat("\t\tCOMPUTE\n")
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71 cat("\t\t\tPerform the correspondence\n")
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72 args$sampleGroups <- xdata$sample_group
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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(sampleGroups = c(1, 2))))]
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76
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77 groupChromPeaksParam <- do.call(paste0(method, "Param"), args)
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78 print(groupChromPeaksParam)
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79 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam)
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82 cat("\t\tDRAW GRAPHICS\n")
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83 getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
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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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d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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104 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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105 save(list = objects2save[objects2save %in% ls()], file = "group.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")