Mercurial > repos > lecorguille > xcms_merge

annotate lib.r @ 18:9128f47ffd12 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 09:48:26 -0400
parents 40791ab6c06b
children 7b77a7238777
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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3
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4 #@author G. Le Corguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
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6 parseCommandArgs <- function(...) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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7 args <- batch::parseCommandArgs(...)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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8 for (key in names(args)) {
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9 if (args[key] %in% c("TRUE","FALSE"))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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10 args[key] = as.logical(args[key])
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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11 }
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12 return(args)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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13 }
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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15 #@author G. Le Corguille
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 # This function will
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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22 sessioninfo = sessionInfo()
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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23 cat(sessioninfo$R.version$version.string,"\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("Other loaded packages:\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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28 }
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
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32 mergeChrom <- function(chrom_merged, chrom) {
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33 if (is.null(chrom_merged)) return(NULL)
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
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35 return(chrom_merged)
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36 }
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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) {
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41 chromTIC <- NULL
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42 chromBPI <- NULL
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43 chromTIC_adjusted <- NULL
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44 chromBPI_adjusted <- NULL
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45 for(image in args$images) {
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46
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47 load(image)
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48 # Handle infiles
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49 if (!exists("singlefile")) singlefile <- NULL
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50 if (!exists("zipfile")) zipfile <- NULL
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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52 zipfile <- rawFilePath$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
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
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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$sampleNamesMakeNames)
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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83 }
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84 }
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85 rm(image)
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86 xdata <- xdata_merged; rm(xdata_merged)
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$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, sampleNamesList) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- make.names(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
10
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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
15
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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$sample_group], main=main)
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243 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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244 }
10
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245
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246 # Color by sample
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247 plot(chrom, col = rainbow(length(xdata@phenoData@data$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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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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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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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))) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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]")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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326 files <- c(directory[!info$isdir], listed)
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327 files_abs <- file.path(getwd(), files)
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328 exists <- file.exists(files_abs)
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329 files[exists] <- files_abs[exists]
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330 files[exists] <- sub("//","/",files[exists])
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331
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332 # WHAT IS ON THE FILESYSTEM
8
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333 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
7
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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]")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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$isdir], listed)
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353 exists <- file.exists(files)
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354 files <- files[exists]
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355 return(files)
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356 }
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357
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358 # This function check if XML contains special caracters. It also checks integrity and completness.
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359 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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360 checkXmlStructure <- function (directory) {
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361 cat("Checking XML structure...\n")
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362
8
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363 cmd <- paste0("IFS=$'\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;")
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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371 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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372
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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373 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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374
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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375
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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376 # This function check if XML contain special characters
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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377 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
378 deleteXmlBadCharacters<- function (directory) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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379 cat("Checking Non ASCII characters in the XML...\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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380
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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381 processed <- F
8
6b5504f877ff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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382 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
383 for (i in l){
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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384 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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385 capture <- suppressWarnings(system(cmd, intern=TRUE))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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386 if (length(capture)>0){
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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387 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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388 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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389 c <- system(cmd, intern=TRUE)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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390 capture <- ""
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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391 processed <- T
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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392 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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393 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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394 if (processed) cat("\n\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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395 return(processed)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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396 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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397
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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398
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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399 # This function will compute MD5 checksum to check the data integrity
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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400 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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401 getMd5sum <- function (directory) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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402 cat("Compute md5 checksum...\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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403 # WHAT XCMS WILL FIND
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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404 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
405 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
406 info <- file.info(directory)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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407 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
408 files <- c(directory[!info$isdir], listed)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
409 exists <- file.exists(files)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
410 files <- files[exists]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
411
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
412 library(tools)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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413
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
414 #cat("\n\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
415
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
416 return(as.matrix(md5sum(files)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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417 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
418
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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419
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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420 # This function get the raw file path from the arguments
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
14
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
422 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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diff changeset
423 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
424
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lecorguille
parents: 12
diff changeset
425 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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426
14
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lecorguille
parents: 12
diff changeset
427 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
428 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
429 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
430 }
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
431 if (exists("singlefile_galaxyPaths")){
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
432 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
433 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
434
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
435 singlefile <- NULL
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
436 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
437 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
438 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
15
2c7d3db37974 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 14
diff changeset
439 # In case, an url is used to import data within Galaxy
14
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
440 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
441 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
442 }
14
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
443 }
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
diff changeset
444 return(list(zipfile=zipfile, singlefile=singlefile))
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
445 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
446
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
447 # This function retrieve the raw file in the working directory
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
448 # - if zipfile: unzip the file with its directory tree
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
449 # - if singlefiles: set symlink with the good filename
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
450 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
451 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
452 if(!is.null(singlefile) && (length("singlefile")>0)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
453 for (singlefile_sampleName in names(singlefile)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
454 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
455 if(!file.exists(singlefile_galaxyPath)){
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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!")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
457 print(error_message); stop(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
458 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
459
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
460 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
461 file.copy(singlefile_galaxyPath, singlefile_sampleName)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
462
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
463 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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464 directory <- "."
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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465
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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466 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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467 if(!is.null(zipfile) && (zipfile != "")) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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468 if(!file.exists(zipfile)){
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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469 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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470 print(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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471 stop(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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472 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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473
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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474 #list all file in the zip file
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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475 #zip_files <- unzip(zipfile,list=T)[,"Name"]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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476
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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477 #unzip
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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478 suppressWarnings(unzip(zipfile, unzip="unzip"))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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479
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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480 #get the directory name
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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481 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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482 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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483 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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484 directory <- "."
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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485 if (length(directories) == 1) directory <- directories
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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486
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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487 cat("files_root_directory\t",directory,"\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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488
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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489 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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490 return (directory)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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491 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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492
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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493
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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494 # This function retrieve a xset like object
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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495 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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496 getxcmsSetObject <- function(xobject) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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497 # XCMS 1.x
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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498 if (class(xobject) == "xcmsSet")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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499 return (xobject)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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500 # XCMS 3.x
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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501 if (class(xobject) == "XCMSnExp") {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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502 # Get the legacy xcmsSet object
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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503 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
14
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lecorguille
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504 if (!is.null(xset@phenoData$sample_group))
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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505 sampclass(xset) <- xset@phenoData$sample_group
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 12
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506 else
40ae497bdc57 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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507 sampclass(xset) <- "."
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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508 return (xset)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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509 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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510 }