Mercurial > repos > lecorguille > xcms_fillpeaks

annotate xcms.r @ 7:6472d3486309 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
author lecorguille
date Mon, 04 Jul 2016 11:55:32 -0400
parents 2edfa5e1f719
children ee29f0a6e361
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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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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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67 rplotspdf = "Rplots.pdf"
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68 if (!is.null(listArguments[["rplotspdf"]])){
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69 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
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70 }
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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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80 if (thefunction %in% c("xcmsSet","retcor")) {
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81 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
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82 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
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83 }
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85 #necessary to unzip .zip file uploaded to Galaxy
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86 #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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89 if (!is.null(listArguments[["zipfile"]])){
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90 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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91 }
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93 if (!is.null(listArguments[["library"]])){
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94 directory=listArguments[["library"]]; listArguments[["library"]]=NULL
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95 if(!file.exists(directory)){
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96 error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.")
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97 print(error_message)
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98 stop(error_message)
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99 }
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100 }
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101
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102 # We unzip automatically the chromatograms from the zip files.
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103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
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104 if(exists("zipfile") && (zipfile!="")) {
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105 if(!file.exists(zipfile)){
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106 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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107 print(error_message)
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108 stop(error_message)
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109 }
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110
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111 #list all file in the zip file
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112 #zip_files=unzip(zipfile,list=T)[,"Name"]
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113
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114
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115 #unzip
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116 suppressWarnings(unzip(zipfile, unzip="unzip"))
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117
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118 #get the directory name
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119 filesInZip=unzip(zipfile, list=T);
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120 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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121 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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122 directory = "."
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123 if (length(directories) == 1) directory = directories
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124
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125 cat("files_root_directory\t",directory,"\n")
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126
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127 #
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128 md5sumList=list("origin"=getMd5sum(directory))
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129
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130 # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
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131 # Remove because can create issue with some clean files
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132 #@TODO: fix me
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133 #if (deleteXmlBadCharacters(directory)) {
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134 # md5sumList=list("removalBadCharacters"=getMd5sum(directory))
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135 #}
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136
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137 }
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138 }
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139
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140 #addition of the directory to the list of arguments in the first position
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141 if (thefunction == "xcmsSet") {
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142 checkXmlStructure(directory)
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143 checkFilesCompatibilityWithXcms(directory)
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144 listArguments=append(directory, listArguments)
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145 }
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146
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147
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148 #addition of xset object to the list of arguments in the first position
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149 if (exists("xset")){
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150 listArguments=append(list(xset), listArguments)
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151 }
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152
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153 cat("\n\n")
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154
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155
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156
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157
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158
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159
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160 # ----- MAIN PROCESSING INFO -----
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161 cat("\tMAIN PROCESSING INFO\n")
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162
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163
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164 #Verification of a group step before doing the fillpeaks job.
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165
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166 if (thefunction == "fillPeaks") {
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167 res=try(is.null(groupnames(xset)))
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168 if (class(res) == "try-error"){
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169 error<-geterrmessage()
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170 write(error, stderr())
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171 stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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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 #change the default display settings
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177 #dev.new(file="Rplots.pdf", width=16, height=12)
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178 pdf(file=rplotspdf, width=16, height=12)
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179 if (thefunction == "group") {
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180 par(mfrow=c(2,2))
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181 }
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182 #else if (thefunction == "retcor") {
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183 #try to change the legend display
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184 # par(xpd=NA)
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185 # par(xpd=T, mar=par()$mar+c(0,0,0,4))
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186 #}
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187
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188
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189 #execution of the function "thefunction" with the parameters given in "listArguments"
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190 xset = do.call(thefunction, listArguments)
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191
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192
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193 cat("\n\n")
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194
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195 dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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197 if (thefunction == "xcmsSet") {
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199 #transform the files absolute pathways into relative pathways
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200 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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201
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202 if(exists("zipfile") && (zipfile!="")) {
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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204 #Modify the samples names (erase the path)
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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205 for(i in 1:length(sampnames(xset))){
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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207 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
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208 sample_name=sample_name[length(sample_name)]
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209 sample_name= unlist(strsplit(sample_name,"[.]"))[1]
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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210 sampnames(xset)[i]=sample_name
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212 }
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214 }
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216 }
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218 # -- TIC --
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219 if (thefunction == "xcmsSet") {
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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220 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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221 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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222 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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223 } else if (thefunction == "retcor") {
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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224 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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225 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
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226 }
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227
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228 cat("\n\n")
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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231 # ----- EXPORT -----
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233 cat("\tXSET OBJECT INFO\n")
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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234 print(xset)
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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235 #delete the parameters to avoid the passage to the next tool in .RData image
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236
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237
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238 #saving R data in .Rdata file to save the variables used in the present tool
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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239 objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList")
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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240 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
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241
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242 cat("\n\n")
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243
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245 cat("\tDONE\n")
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246