annotate lib.r @ 9:e3fccadf32a8 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
author lecorguille
date Thu, 07 Mar 2019 07:38:52 -0500
parents a26679f68d4d
children 7dd38bacac3a
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1 #@authors ABiMS TEAM, Y. Guitton
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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3
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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(...) {
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7 args <- batch::parseCommandArgs(...)
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8 for (key in names(args)) {
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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
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16 # This function will
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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)))
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22 sessioninfo = sessionInfo()
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23 cat(sessioninfo$R.version$version.string,"\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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26 cat("Other loaded packages:\n")
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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28 }
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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.
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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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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) {
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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, param = NULL, mzdigit=4) {
3
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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, param = param, 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=groupnames(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=groupnames(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 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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203
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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206
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207 }
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208
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209 #@author G. Le Corguille
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210 # It allow different of field separators
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211 getDataFrameFromFile <- function(filename, header=T) {
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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215 if (ncol(myDataFrame) < 2) {
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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217 print(error_message)
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218 stop(error_message)
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219 }
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220 return(myDataFrame)
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221 }
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222
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223 #@author G. Le Corguille
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224 # Draw the BPI and TIC graphics
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225 # colored by sample names or class names
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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227
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228 if (aggregationFun == "sum")
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229 type="Total Ion Chromatograms"
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230 else
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231 type="Base Peak Intensity Chromatograms"
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232
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233 adjusted="Raw"
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234 if (hasAdjustedRtime(xdata))
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235 adjusted="Adjusted"
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236
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237 main <- paste(type,":",adjusted,"data")
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238
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239 pdf(pdfname, width=16, height=10)
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240
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241 # Color by group
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242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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243 if (length(group_colors) > 1) {
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244 names(group_colors) <- unique(xdata$sample_group)
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245 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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247 }
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248
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249 # Color by sample
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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251 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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252
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253 dev.off()
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254 }
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255
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256
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257 # Get the polarities from all the samples of a condition
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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261 cat("Creating the sampleMetadata file...\n")
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262
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263 #Create the sampleMetada dataframe
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264 sampleMetadata <- xdata@phenoData@data
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265 rownames(sampleMetadata) <- NULL
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266 colnames(sampleMetadata) <- c("sample_name", "class")
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267
7
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268 sampleNamesOrigin <- sampleMetadata$sample_name
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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270
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271 if (any(duplicated(sampleNamesMakeNames))) {
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272 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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273 for (sampleName in sampleNamesOrigin) {
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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275 }
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276 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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277 }
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278
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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280 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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281 for (sampleName in sampleNamesOrigin) {
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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283 }
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284 }
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285
7
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286 sampleMetadata$sample_name <- sampleNamesMakeNames
3
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287
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288
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289 #For each sample file, the following actions are done
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290 for (fileIdx in 1:length(fileNames(xdata))) {
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291 #Check if the file is in the CDF format
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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293
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294 # If the column isn't exist, with add one filled with NA
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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296
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297 #Extract the polarity (a list of polarities)
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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299 #Verify if all the scans have the same polarity
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300 uniq_list <- unique(polarity)
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301 if (length(uniq_list)>1){
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302 polarity <- "mixed"
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303 } else {
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304 polarity <- as.character(uniq_list)
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305 }
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306
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307 #Set the polarity attribute
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308 sampleMetadata$polarity[fileIdx] <- polarity
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309 }
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310
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311 }
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312
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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314
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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316
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317 }
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318
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319
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320 # This function check if xcms will found all the files
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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322 checkFilesCompatibilityWithXcms <- function(directory) {
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323 cat("Checking files filenames compatibilities with xmcs...\n")
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324 # WHAT XCMS WILL FIND
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325 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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326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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327 info <- file.info(directory)
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328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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329 files <- c(directory[!info$isdir], listed)
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330 files_abs <- file.path(getwd(), files)
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331 exists <- file.exists(files_abs)
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332 files[exists] <- files_abs[exists]
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333 files[exists] <- sub("//","/",files[exists])
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334
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335 # WHAT IS ON THE FILESYSTEM
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336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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338
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339 # COMPARISON
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340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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343 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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344 }
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345 }
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346
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347
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348 #This function list the compatible files within the directory as xcms did
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349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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350 getMSFiles <- function (directory) {
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351 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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352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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353 info <- file.info(directory)
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354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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355 files <- c(directory[!info$isdir], listed)
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356 exists <- file.exists(files)
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357 files <- files[exists]
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358 return(files)
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359 }
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360
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361 # This function check if XML contains special caracters. It also checks integrity and completness.
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362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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363 checkXmlStructure <- function (directory) {
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364 cat("Checking XML structure...\n")
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365
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366 cmd <- paste0("IFS=$'\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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367 capture <- system(cmd, intern=TRUE)
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368
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369 if (length(capture)>0){
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370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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372 write(capture, stderr())
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373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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374 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
375
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
376 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
377
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
378
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
379 # This function check if XML contain special characters
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
381 deleteXmlBadCharacters<- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
382 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
383
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
384 processed <- F
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
385 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
386 for (i in l){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
388 capture <- suppressWarnings(system(cmd, intern=TRUE))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
389 if (length(capture)>0){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
390 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
391 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
392 c <- system(cmd, intern=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
393 capture <- ""
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
394 processed <- T
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
395 }
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 if (processed) cat("\n\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
398 return(processed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
399 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
400
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
401
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
402 # 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
403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
404 getMd5sum <- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
405 cat("Compute md5 checksum...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
406 # WHAT XCMS WILL FIND
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
407 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
408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
409 info <- file.info(directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
411 files <- c(directory[!info$isdir], listed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
412 exists <- file.exists(files)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
413 files <- files[exists]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
414
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
415 library(tools)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
416
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
417 #cat("\n\n")
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 return(as.matrix(md5sum(files)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
420 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
421
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
422
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
423 # 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
424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
426 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
427
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
428 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
429
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
433 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
434 if (exists("singlefile_galaxyPaths")){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
437
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
438 singlefile <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
439 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
440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
442 # 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
443 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
444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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 return(list(zipfile=zipfile, singlefile=singlefile))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
448 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
449
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
450 # 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
451 # - 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
452 # - if singlefiles: set symlink with the good filename
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
455 if(!is.null(singlefile) && (length("singlefile")>0)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
456 for (singlefile_sampleName in names(singlefile)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
458 if(!file.exists(singlefile_galaxyPath)){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
459 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
460 print(error_message); stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
461 }
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 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
464 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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 directory <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
468
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
469 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
470 if(!is.null(zipfile) && (zipfile != "")) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
471 if(!file.exists(zipfile)){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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472 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:
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473 print(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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474 stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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475 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
476
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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477 #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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478 #zip_files <- unzip(zipfile,list=T)[,"Name"]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
479
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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480 #unzip
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
481 suppressWarnings(unzip(zipfile, unzip="unzip"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
482
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
483 #get the directory name
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
484 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
487 directory <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
488 if (length(directories) == 1) directory <- directories
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
489
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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490 cat("files_root_directory\t",directory,"\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
491
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
492 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
493 return (directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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494 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
495
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
496
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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497 # 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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498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
parents:
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499 getxcmsSetObject <- function(xobject) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
500 # XCMS 1.x
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
501 if (class(xobject) == "xcmsSet")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
502 return (xobject)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
503 # XCMS 3.x
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
504 if (class(xobject) == "XCMSnExp") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
505 # Get the legacy xcmsSet object
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
506 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
507 if (!is.null(xset@phenoData$sample_group))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
508 sampclass(xset) <- xset@phenoData$sample_group
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
509 else
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
510 sampclass(xset) <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
511 return (xset)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff changeset
512 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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513 }