annotate lib.r @ 3:f439ed7a8f03 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:09:25 -0400
parents
children 7bb43bf0b546
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f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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3
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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4 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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6 parseCommandArgs <- function(...) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 args <- batch::parseCommandArgs(...)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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8 for (key in names(args)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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9 if (args[key] %in% c("TRUE","FALSE"))
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10 args[key] = as.logical(args[key])
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11 }
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12 return(args)
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13 }
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14
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15 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # This function will
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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17 # - load the packages
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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22 sessioninfo = sessionInfo()
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 cat(sessioninfo$R.version$version.string,"\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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24 cat("Main packages:\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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26 cat("Other loaded packages:\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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28 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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29
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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32 mergeChrom <- function(chrom_merged, chrom) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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33 if (is.null(chrom_merged)) return(NULL)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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35 return(chrom_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 }
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37
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38 #@author G. Le Corguille
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39 # This function merge several xdata into one.
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40 mergeXData <- function(args) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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41 chromTIC <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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42 chromBPI <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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43 chromTIC_adjusted <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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44 chromBPI_adjusted <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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45 for(image in args$images) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46
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47 load(image)
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48 # Handle infiles
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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49 if (!exists("singlefile")) singlefile <- NULL
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50 if (!exists("zipfile")) zipfile <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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52 zipfile <- rawFilePath$zipfile
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53 singlefile <- rawFilePath$singlefile
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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55
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56 if (exists("raw_data")) xdata <- raw_data
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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58
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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61 if (!exists("xdata_merged")) {
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62 xdata_merged <- xdata
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63 singlefile_merged <- singlefile
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64 md5sumList_merged <- md5sumList
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65 sampleNamesList_merged <- sampleNamesList
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66 chromTIC_merged <- chromTIC
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67 chromBPI_merged <- chromBPI
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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83 }
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84 }
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85 rm(image)
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86 xdata <- xdata_merged; rm(xdata_merged)
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$sampleMetadata)) {
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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153 names(group_colors) <- unique(xdata$sample_group)
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154
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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156 for (i in 1:nrow(featureDefinitions(xdata))) {
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax
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159 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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161 }
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162
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163 dev.off()
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164 }
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165
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166 #@author G. Le Corguille
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file
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168 getPlotAdjustedRtime <- function(xdata) {
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169
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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171
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172 # Color by group
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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174 if (length(group_colors) > 1) {
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175 names(group_colors) <- unique(xdata$sample_group)
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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178 }
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179
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180 # Color by sample
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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183
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184 dev.off()
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185 }
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186
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187 #@author G. Le Corguille
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188 # value: intensity values to be used into, maxo or intb
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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193 variableMetadata <- featureDefinitions(xdata)
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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196
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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200
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201 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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202 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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203
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204 }
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205
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lecorguille
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206 #@author G. Le Corguille
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207 # It allow different of field separators
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208 getDataFrameFromFile <- function(filename, header=T) {
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209 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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210 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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211 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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212 if (ncol(myDataFrame) < 2) {
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213 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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214 print(error_message)
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215 stop(error_message)
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216 }
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217 return(myDataFrame)
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218 }
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219
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220 #@author G. Le Corguille
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221 # Draw the BPI and TIC graphics
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222 # colored by sample names or class names
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223 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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224
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225 if (aggregationFun == "sum")
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226 type="Total Ion Chromatograms"
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227 else
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228 type="Base Peak Intensity Chromatograms"
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229
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230 adjusted="Raw"
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231 if (hasAdjustedRtime(xdata))
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232 adjusted="Adjusted"
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233
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234 main <- paste(type,":",adjusted,"data")
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235
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236 pdf(pdfname, width=16, height=10)
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237
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238 # Color by group
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239 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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240 if (length(group_colors) > 1) {
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241 names(group_colors) <- unique(xdata$sample_group)
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242 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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243 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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244 }
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245
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246 # Color by sample
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247 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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248 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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249
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250 dev.off()
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251 }
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252
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253
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254 # Get the polarities from all the samples of a condition
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lecorguille
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255 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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256 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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257 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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258 cat("Creating the sampleMetadata file...\n")
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259
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lecorguille
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260 #Create the sampleMetada dataframe
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261 sampleMetadata <- xdata@phenoData@data
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262 rownames(sampleMetadata) <- NULL
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263 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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diff changeset
264
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265 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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266 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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267
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268 if (any(duplicated(sampleNamesMakeNames))) {
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269 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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270 for (sampleName in sampleNamesOrigin) {
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271 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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272 }
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273 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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274 }
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275
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276 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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277 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
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278 for (sampleName in sampleNamesOrigin) {
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279 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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280 }
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281 }
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282
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283 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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284
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285
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286 #For each sample file, the following actions are done
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287 for (fileIdx in 1:length(fileNames(xdata))) {
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288 #Check if the file is in the CDF format
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289 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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290
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291 # If the column isn't exist, with add one filled with NA
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292 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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293
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294 #Extract the polarity (a list of polarities)
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295 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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296 #Verify if all the scans have the same polarity
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297 uniq_list <- unique(polarity)
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298 if (length(uniq_list)>1){
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299 polarity <- "mixed"
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300 } else {
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301 polarity <- as.character(uniq_list)
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302 }
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303
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304 #Set the polarity attribute
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305 sampleMetadata$polarity[fileIdx] <- polarity
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306 }
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307
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308 }
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309
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310 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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311
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312 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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313
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314 }
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315
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316
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317 # This function check if xcms will found all the files
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318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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319 checkFilesCompatibilityWithXcms <- function(directory) {
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320 cat("Checking files filenames compatibilities with xmcs...\n")
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321 # WHAT XCMS WILL FIND
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322 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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323 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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324 info <- file.info(directory)
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325 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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326 files <- c(directory[!info$isdir], listed)
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327 files_abs <- file.path(getwd(), files)
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328 exists <- file.exists(files_abs)
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329 files[exists] <- files_abs[exists]
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330 files[exists] <- sub("//","/",files[exists])
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331
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332 # WHAT IS ON THE FILESYSTEM
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333 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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334 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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335
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336 # COMPARISON
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337 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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338 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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339 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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340 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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341 }
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342 }
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343
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344
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345 #This function list the compatible files within the directory as xcms did
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346 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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347 getMSFiles <- function (directory) {
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348 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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349 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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350 info <- file.info(directory)
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351 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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352 files <- c(directory[!info$isdir], listed)
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353 exists <- file.exists(files)
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354 files <- files[exists]
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355 return(files)
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356 }
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357
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358 # This function check if XML contains special caracters. It also checks integrity and completness.
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359 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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360 checkXmlStructure <- function (directory) {
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361 cat("Checking XML structure...\n")
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362
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363 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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364 capture <- system(cmd, intern=TRUE)
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365
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366 if (length(capture)>0){
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367 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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368 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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369 write(capture, stderr())
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370 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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371 }
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372
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373 }
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374
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375
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376 # This function check if XML contain special characters
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377 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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diff changeset
378 deleteXmlBadCharacters<- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
379 cat("Checking Non ASCII characters in the XML...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
380
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
381 processed <- F
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
382 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
383 for (i in l){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
384 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
385 capture <- suppressWarnings(system(cmd, intern=TRUE))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
386 if (length(capture)>0){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
387 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
388 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
389 c <- system(cmd, intern=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
390 capture <- ""
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
391 processed <- T
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
392 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
393 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
394 if (processed) cat("\n\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
395 return(processed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
396 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
397
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
398
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
399 # This function will compute MD5 checksum to check the data integrity
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
400 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
401 getMd5sum <- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
402 cat("Compute md5 checksum...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
403 # WHAT XCMS WILL FIND
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
404 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
405 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
406 info <- file.info(directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
407 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
408 files <- c(directory[!info$isdir], listed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
409 exists <- file.exists(files)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
410 files <- files[exists]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
411
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
412 library(tools)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
413
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
414 #cat("\n\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
415
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
416 return(as.matrix(md5sum(files)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
417 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
418
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
419
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
420 # This function get the raw file path from the arguments
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
422 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
423 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
424
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
425 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
426
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
427 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
428 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
429 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
430 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
431 if (exists("singlefile_galaxyPaths")){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
432 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
433 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
434
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
435 singlefile <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
436 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
437 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
438 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
439 # In case, an url is used to import data within Galaxy
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
440 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
441 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
442 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
443 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
444 return(list(zipfile=zipfile, singlefile=singlefile))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
445 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
446
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
447 # This function retrieve the raw file in the working directory
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
448 # - if zipfile: unzip the file with its directory tree
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
449 # - if singlefiles: set symlink with the good filename
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
450 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
451 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
452 if(!is.null(singlefile) && (length("singlefile")>0)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
453 for (singlefile_sampleName in names(singlefile)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
454 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
455 if(!file.exists(singlefile_galaxyPath)){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
456 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
457 print(error_message); stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
458 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
459
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
460 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
461 file.copy(singlefile_galaxyPath, singlefile_sampleName)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
462
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
463 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
464 directory <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
465
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
466 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
467 if(!is.null(zipfile) && (zipfile != "")) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
468 if(!file.exists(zipfile)){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
469 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
470 print(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
471 stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
472 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
473
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
474 #list all file in the zip file
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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475 #zip_files <- unzip(zipfile,list=T)[,"Name"]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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476
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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477 #unzip
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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478 suppressWarnings(unzip(zipfile, unzip="unzip"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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479
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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480 #get the directory name
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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481 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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482 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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483 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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484 directory <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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485 if (length(directories) == 1) directory <- directories
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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486
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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487 cat("files_root_directory\t",directory,"\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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488
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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489 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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490 return (directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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491 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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492
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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493
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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494 # This function retrieve a xset like object
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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495 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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496 getxcmsSetObject <- function(xobject) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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497 # XCMS 1.x
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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498 if (class(xobject) == "xcmsSet")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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499 return (xobject)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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500 # XCMS 3.x
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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501 if (class(xobject) == "XCMSnExp") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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502 # Get the legacy xcmsSet object
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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503 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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504 if (!is.null(xset@phenoData$sample_group))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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505 sampclass(xset) <- xset@phenoData$sample_group
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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506 else
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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507 sampclass(xset) <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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508 return (xset)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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509 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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510 }