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annotate xcms.r @ 15:c04568596f40 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:51:40 -0500
parents fcd93f47dcbf
children 20a75ba4345b
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1 #!/usr/bin/env Rscript
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2 # xcms.r version="2.2.0"
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3 #Authors ABIMS TEAM
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4 #BPC Addition from Y.guitton
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7 # ----- LOG FILE -----
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8 log_file=file("log.txt", open = "wt")
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9 sink(log_file)
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10 sink(log_file, type = "output")
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12
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13 # ----- PACKAGE -----
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14 cat("\tPACKAGE INFO\n")
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15 #pkgs=c("xcms","batch")
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16 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
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17 for(pkg in pkgs) {
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18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
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20 }
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21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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22 cat("\n\n");
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28 # ----- ARGUMENTS -----
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29 cat("\tARGUMENTS INFO\n")
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30 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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31 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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32
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33 cat("\n\n");
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36 # ----- ARGUMENTS PROCESSING -----
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37 cat("\tINFILE PROCESSING INFO\n")
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39 #image is an .RData file necessary to use xset variable given by previous tools
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40 if (!is.null(listArguments[["image"]])){
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41 load(listArguments[["image"]]); listArguments[["image"]]=NULL
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42 }
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43
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44 #Import the different functions
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45 source_local("lib.r")
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46
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47 cat("\n\n")
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48
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49 #Import the different functions
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50
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51 # ----- PROCESSING INFILE -----
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52 cat("\tARGUMENTS PROCESSING INFO\n")
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53
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54 # Save arguments to generate a report
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55 if (!exists("listOFlistArguments")) listOFlistArguments=list()
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56 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
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58
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59 #saving the commun parameters
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60 thefunction = listArguments[["xfunction"]]; listArguments[["xfunction"]]=NULL #delete from the list of arguments
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61
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62 xsetRdataOutput = paste(thefunction,"RData",sep=".")
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63 if (!is.null(listArguments[["xsetRdataOutput"]])){
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64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
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65 }
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66
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67 #saving the specific parameters
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68 rplotspdf = "Rplots.pdf"
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69 if (!is.null(listArguments[["rplotspdf"]])){
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70 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
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71 }
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72 sampleMetadataOutput = "sampleMetadata.tsv"
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73 if (!is.null(listArguments[["sampleMetadataOutput"]])){
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74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
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75 }
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76 variableMetadataOutput = "variableMetadata.tsv"
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77 if (!is.null(listArguments[["variableMetadataOutput"]])){
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78 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
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79 }
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80 dataMatrixOutput = "dataMatrix.tsv"
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81 if (!is.null(listArguments[["dataMatrixOutput"]])){
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82 dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
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83 }
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84 if (!is.null(listArguments[["convertRTMinute"]])){
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85 convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL
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86 }
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87 if (!is.null(listArguments[["numDigitsMZ"]])){
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88 numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL
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89 }
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90 if (!is.null(listArguments[["numDigitsRT"]])){
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91 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL
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92 }
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93 if (!is.null(listArguments[["intval"]])){
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94 intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
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95 }
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96
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97 if (thefunction %in% c("xcmsSet","retcor")) {
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98 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
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99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
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100 }
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101
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102 #necessary to unzip .zip file uploaded to Galaxy
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103 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
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104
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105
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106 if (!is.null(listArguments[["zipfile"]])){
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107 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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108 }
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109
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110 if (!is.null(listArguments[["library"]])){
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111 directory=listArguments[["library"]]; listArguments[["library"]]=NULL
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112 if(!file.exists(directory)){
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113 error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.")
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114 print(error_message)
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115 stop(error_message)
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116 }
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117 }
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118
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119 # We unzip automatically the chromatograms from the zip files.
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120 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
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121 if(exists("zipfile") && (zipfile!="")) {
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122 if(!file.exists(zipfile)){
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123 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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124 print(error_message)
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125 stop(error_message)
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126 }
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127
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128 #list all file in the zip file
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129 #zip_files=unzip(zipfile,list=T)[,"Name"]
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130
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131
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132 #unzip
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133 suppressWarnings(unzip(zipfile, unzip="unzip"))
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134
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135 #get the directory name
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136 filesInZip=unzip(zipfile, list=T);
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137 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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138 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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139 directory = "."
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140 if (length(directories) == 1) directory = directories
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141
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142 cat("files_root_directory\t",directory,"\n")
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143
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144 #
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145 md5sumList=list("origin"=getMd5sum(directory))
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146
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147 # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
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148 # Remove because can create issue with some clean files
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149 #@TODO: fix me
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150 #if (deleteXmlBadCharacters(directory)) {
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151 # md5sumList=list("removalBadCharacters"=getMd5sum(directory))
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152 #}
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153
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154 }
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155 }
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156
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157 #addition of the directory to the list of arguments in the first position
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158 if (thefunction == "xcmsSet") {
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159 checkXmlStructure(directory)
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160 checkFilesCompatibilityWithXcms(directory)
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161 listArguments=append(directory, listArguments)
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162 }
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163
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164
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165 #addition of xset object to the list of arguments in the first position
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166 if (exists("xset")){
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167 listArguments=append(list(xset), listArguments)
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168 }
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169
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170 cat("\n\n")
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171
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172
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173
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174
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175
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176
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177 # ----- MAIN PROCESSING INFO -----
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178 cat("\tMAIN PROCESSING INFO\n")
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179
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180
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181 #Verification of a group step before doing the fillpeaks job.
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182
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183 if (thefunction == "fillPeaks") {
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184 res=try(is.null(groupnames(xset)))
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185 if (class(res) == "try-error"){
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186 error<-geterrmessage()
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187 write(error, stderr())
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188 stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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189 }
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190
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191 }
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192
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193 #change the default display settings
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194 #dev.new(file="Rplots.pdf", width=16, height=12)
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195 pdf(file=rplotspdf, width=16, height=12)
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196 if (thefunction == "group") {
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197 par(mfrow=c(2,2))
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198 }
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199 #else if (thefunction == "retcor") {
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200 #try to change the legend display
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201 # par(xpd=NA)
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202 # par(xpd=T, mar=par()$mar+c(0,0,0,4))
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203 #}
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204
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205
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206 #execution of the function "thefunction" with the parameters given in "listArguments"
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207
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208 cat("\t\tCOMPUTE\n")
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209 xset = do.call(thefunction, listArguments)
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210
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211
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212 cat("\n\n")
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213
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214 dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)
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215
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216 if (thefunction == "xcmsSet") {
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217
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218 #transform the files absolute pathways into relative pathways
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219 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
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220
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221 if(exists("zipfile") && (zipfile!="")) {
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222
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223 #Modify the samples names (erase the path)
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224 for(i in 1:length(sampnames(xset))){
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225
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226 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
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227 sample_name=sample_name[length(sample_name)]
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228 sample_name= unlist(strsplit(sample_name,"[.]"))[1]
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229 sampnames(xset)[i]=sample_name
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230
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231 }
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232
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233 }
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234
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235 }
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236
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237 # -- TIC --
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238 if (thefunction == "xcmsSet") {
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239 cat("\t\tGET TIC GRAPH\n")
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240 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
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241 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
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242 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
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243 } else if (thefunction == "retcor") {
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244 cat("\t\tGET TIC GRAPH\n")
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245 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
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246 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
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247 }
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248
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249 if (thefunction == "fillPeaks") {
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250 cat("\t\tGET THE PEAK LIST\n")
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251 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
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252 }
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253
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254
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255 cat("\n\n")
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256
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257 # ----- EXPORT -----
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258
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259 cat("\tXSET OBJECT INFO\n")
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260 print(xset)
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261 #delete the parameters to avoid the passage to the next tool in .RData image
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262
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263
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264 #saving R data in .Rdata file to save the variables used in the present tool
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265 objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList")
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266 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
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267
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268 cat("\n\n")
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269
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270
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271 cat("\tDONE\n")