Mercurial > repos > lecorguille > xcms_retcor

annotate xcms_retcor.r @ 39:b0d4fe748c9d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8dfca81480bcbfb5b164ee736b2e2cad324ad8a1-dirty
author lecorguille
date Tue, 02 Oct 2018 09:06:35 -0400
parents 67ee46ce9781
children feb216e6aef7
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1 #!/usr/bin/env Rscript
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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6 sink(log_file, type = "output")
4d6f4cd7c3ef 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
4d6f4cd7c3ef 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="/")) }
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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","RColorBrewer")
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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 <- args$method
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35 cat("\n\n")
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38 # ----- ARGUMENTS PROCESSING -----
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39 cat("\tINFILE PROCESSING INFO\n")
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41 #image is an .RData file necessary to use xset variable given by previous tools
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42 load(args$image); args$image=NULL
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43 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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45 # Handle infiles
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46 if (!exists("singlefile")) singlefile <- NULL
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47 if (!exists("zipfile")) zipfile <- NULL
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48 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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49 zipfile <- rawFilePath$zipfile
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50 singlefile <- rawFilePath$singlefile
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51 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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53 cat("\n\n")
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56 # ----- MAIN PROCESSING INFO -----
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57 cat("\tMAIN PROCESSING INFO\n")
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60 cat("\t\tCOMPUTE\n")
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62 cat("\t\t\tAlignment/Retention Time correction\n")
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63 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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64 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
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65
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66 adjustRtimeParam <- do.call(paste0(method,"Param"), args)
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67 print(adjustRtimeParam)
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68 xdata <- adjustRtime(xdata, param=adjustRtimeParam)
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69
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70 cat("\t\t\tCompute and Store TIC and BPI\n")
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71 chromTIC_adjusted = chromatogram(xdata, aggregationFun = "sum")
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72 chromBPI_adjusted = chromatogram(xdata, aggregationFun = "max")
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73
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74 cat("\n\n")
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77 # -- TIC --
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78 cat("\t\tDRAW GRAPHICS\n")
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79 getPlotAdjustedRtime(xdata)
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81 cat("\n\n")
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83 # ----- EXPORT -----
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85 cat("\tXCMSnExp OBJECT INFO\n")
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86 print(xdata)
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87 cat("\n\n")
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89 cat("\txcmsSet OBJECT INFO\n")
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90 # Get the legacy xcmsSet object
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91 xset <- getxcmsSetObject(xdata)
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92 print(xset)
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93 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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94
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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95 #saving R data in .Rdata file to save the variables used in the present tool
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96 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList", "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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97 save(list=objects2save[objects2save %in% ls()], file="retcor.RData")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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98
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99 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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100
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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102 cat("\tDONE\n")