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annotate xcms.r @ 19:7b74ec867ad2 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8
author lecorguille
date Wed, 08 Feb 2017 05:27:41 -0500
parents 65dc5e8b53f7
children 02bb34af0921
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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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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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44 #Import the different functions
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45 source_local("lib.r")
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47 cat("\n\n")
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49 #Import the different functions
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51 # ----- PROCESSING INFILE -----
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52 cat("\tARGUMENTS PROCESSING INFO\n")
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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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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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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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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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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[["singlefile_galaxyPath"]])){
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111 singlefile_galaxyPaths = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
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112 singlefile_sampleNames = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
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113
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114 singlefile=NULL
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115 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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116 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
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117 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
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118 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
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119 }
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120 }
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121
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122 # We unzip automatically the chromatograms from the zip files.
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123 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
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124 if(exists("singlefile") && (length("singlefile")>0)) {
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125 for (singlefile_sampleName in names(singlefile)) {
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126 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
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127 if(!file.exists(singlefile_galaxyPath)){
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128 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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129 print(error_message); stop(error_message)
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130 }
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131
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132 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
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133 }
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134 directory = "."
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135
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136 md5sumList=list("origin"=getMd5sum(directory))
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137
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138 }
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139 if(exists("zipfile") && (zipfile!="")) {
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140 if(!file.exists(zipfile)){
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141 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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142 print(error_message)
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143 stop(error_message)
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144 }
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145
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146 #list all file in the zip file
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147 #zip_files=unzip(zipfile,list=T)[,"Name"]
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148
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149 #unzip
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150 suppressWarnings(unzip(zipfile, unzip="unzip"))
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151
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152 #get the directory name
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153 filesInZip=unzip(zipfile, list=T);
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154 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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155 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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156 directory = "."
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157 if (length(directories) == 1) directory = directories
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158
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159 cat("files_root_directory\t",directory,"\n")
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160
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161 md5sumList=list("origin"=getMd5sum(directory))
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162 }
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163 }
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164
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165 #addition of the directory to the list of arguments in the first position
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166 if (thefunction == "xcmsSet") {
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167 checkXmlStructure(directory)
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168 checkFilesCompatibilityWithXcms(directory)
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169 listArguments=append(directory, listArguments)
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170 }
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171
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172
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173 #addition of xset object to the list of arguments in the first position
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174 if (exists("xset")){
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175 listArguments=append(list(xset), listArguments)
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176 }
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177
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178 cat("\n\n")
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179
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180
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181
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182
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183 # ----- MAIN PROCESSING INFO -----
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184 cat("\tMAIN PROCESSING INFO\n")
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185
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186
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187 #Verification of a group step before doing the fillpeaks job.
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188
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189 if (thefunction == "fillPeaks") {
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190 res=try(is.null(groupnames(xset)))
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191 if (class(res) == "try-error"){
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192 error<-geterrmessage()
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193 write(error, stderr())
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194 stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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195 }
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196
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197 }
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198
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199 #change the default display settings
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200 #dev.new(file="Rplots.pdf", width=16, height=12)
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201 pdf(file=rplotspdf, width=16, height=12)
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202 if (thefunction == "group") {
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203 par(mfrow=c(2,2))
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204 }
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205 #else if (thefunction == "retcor") {
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206 #try to change the legend display
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207 # par(xpd=NA)
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208 # par(xpd=T, mar=par()$mar+c(0,0,0,4))
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209 #}
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210
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211
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212 #execution of the function "thefunction" with the parameters given in "listArguments"
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213
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214 cat("\t\tCOMPUTE\n")
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215 xset = do.call(thefunction, listArguments)
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216
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218 cat("\n\n")
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219
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220 dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)
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221
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222 if (thefunction == "xcmsSet") {
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223
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224 #transform the files absolute pathways into relative pathways
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225 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
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226
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227 if(exists("zipfile") && (zipfile!="")) {
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228
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229 #Modify the samples names (erase the path)
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230 for(i in 1:length(sampnames(xset))){
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231
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232 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
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233 sample_name=sample_name[length(sample_name)]
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234 sample_name= unlist(strsplit(sample_name,"[.]"))[1]
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235 sampnames(xset)[i]=sample_name
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236
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237 }
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238
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239 }
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240
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241 }
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242
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243 # -- TIC --
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244 if (thefunction == "xcmsSet") {
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245 cat("\t\tGET TIC GRAPH\n")
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246 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
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247 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
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248 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
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249 } else if (thefunction == "retcor") {
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250 cat("\t\tGET TIC GRAPH\n")
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251 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
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252 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
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253 }
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254
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255 if (thefunction == "fillPeaks" && exists("intval")) {
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256 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
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257 }
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259
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260 cat("\n\n")
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261
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262 # ----- EXPORT -----
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263
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264 cat("\tXSET OBJECT INFO\n")
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265 print(xset)
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266 #delete the parameters to avoid the passage to the next tool in .RData image
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267
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268
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269 #saving R data in .Rdata file to save the variables used in the present tool
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270 objects2save = c("xset","zipfile","singlefile","listOFlistArguments","md5sumList","sampleNamesList")
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271 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
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272
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273 cat("\n\n")
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274
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276 cat("\tDONE\n")