Mercurial > repos > lecorguille > xcms_fillpeaks

annotate xcms_fillpeaks.r @ 45:1a711c1b8b1f draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 10:28:50 +0000
parents 1b5fb5a27f5e
children 871ffc15a6da
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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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workflow4metabolomics
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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")
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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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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workflow4metabolomics
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13 source_local <- function(fname) {
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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15 }
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16 source_local("lib.r")
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18 pkgs <- c("xcms", "batch")
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19 loadAndDisplayPackages(pkgs)
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20 cat("\n\n");
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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23 # ----- ARGUMENTS -----
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24 cat("\tARGUMENTS INFO\n")
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25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
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28 cat("\n\n")
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30 # ----- PROCESSING INFILE -----
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31 cat("\tARGUMENTS PROCESSING INFO\n")
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33 #saving the specific parameters
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34 method <- "FillChromPeaks"
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36 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
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37 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
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38 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
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39 if (!is.null(args$intval)) intval <- args$intval
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40 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
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42 cat("\n\n")
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45 # ----- ARGUMENTS PROCESSING -----
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46 cat("\tINFILE PROCESSING INFO\n")
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48 #image is an .RData file necessary to use xset variable given by previous tools
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49 load(args$image)
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50 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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52 #Verification of a group step before doing the fillpeaks job.
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53 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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55 # Handle infiles
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56 if (!exists("singlefile")) singlefile <- NULL
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57 if (!exists("zipfile")) zipfile <- NULL
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
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60 singlefile <- rawFilePath$singlefile
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63 cat("\n\n")
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65 # ----- MAIN PROCESSING INFO -----
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66 cat("\tMAIN PROCESSING INFO\n")
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69 cat("\t\tCOMPUTE\n")
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71 cat("\t\t\tFilling missing peaks using default settings\n")
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72 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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73 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
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74
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75 fillChromPeaksParam <- do.call(paste0(method, "Param"), args)
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76 print(fillChromPeaksParam)
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78 # back compatibility between xcms-3.0.0 and xcms-3.5.2
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79 xdata <- updateObject(xdata)
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80 register(SerialParam())
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81 xdata <- fillChromPeaks(xdata, param = fillChromPeaksParam)
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83 if (exists("intval")) {
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84 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
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85 }
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87 cat("\n\n")
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89 # ----- EXPORT -----
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91 cat("\tXCMSnExp OBJECT INFO\n")
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92 print(xdata)
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93 cat("\n\n")
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94
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95 cat("\txcmsSet OBJECT INFO\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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96 # Get the legacy xcmsSet object
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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97 xset <- getxcmsSetObject(xdata)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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98 print(xset)
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99 cat("\n\n")
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100
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101 #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"
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102 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"
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103 save(list = objects2save[objects2save %in% ls()], file = "fillpeaks.RData")
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105 cat("\n\n")
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106
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107
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108 cat("\tDONE\n")