Mercurial > repos > lecorguille > ipo
annotate ipo4xcmsSet.r @ 6:03fdfbd914ab draft
planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
author | lecorguille |
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date | Thu, 30 Mar 2017 11:27:09 -0400 |
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children | 80de755766a8 |
rev | line source |
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6
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1 #!/usr/bin/env Rscript |
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2 #Authors Gildas Le Corguille and Yann Guitton |
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3 |
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4 |
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5 # ----- LOG FILE ----- |
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6 log_file=file("log.txt", open = "wt") |
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7 sink(log_file) |
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8 sink(log_file, type = "output") |
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9 |
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10 |
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11 # ----- PACKAGE ----- |
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12 options(bitmapType='cairo') |
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13 cat("\tPACKAGE INFO\n") |
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14 #pkgs=c("xcms","batch") |
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15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch") |
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16 for(pkg in pkgs) { |
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17 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))) |
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18 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") |
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19 } |
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20 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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21 cat("\n\n"); |
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22 |
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23 |
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26 |
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27 # ----- ARGUMENTS ----- |
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28 cat("\tARGUMENTS INFO\n") |
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29 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects |
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30 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') |
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31 |
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32 cat("\n\n"); |
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33 |
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34 |
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35 # ----- ARGUMENTS PROCESSING ----- |
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36 cat("\tINFILE PROCESSING INFO\n") |
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37 |
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38 |
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39 #Import the different functions |
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40 source_local("lib.r") |
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41 |
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42 cat("\n\n") |
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43 |
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44 #Import the different functions |
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45 |
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46 # ----- PROCESSING INFILE ----- |
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47 cat("\tARGUMENTS PROCESSING INFO\n") |
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48 |
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49 xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".") |
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50 if (!is.null(listArguments[["xsetRdataOutput"]])){ |
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51 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL |
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52 } |
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53 |
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54 parametersOutput = "parametersOutput.tsv" |
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55 if (!is.null(listArguments[["parametersOutput"]])){ |
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56 parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL |
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57 } |
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58 |
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59 samplebyclass = 2 |
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60 if (!is.null(listArguments[["samplebyclass"]])){ |
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61 samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL |
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62 } |
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63 |
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64 #necessary to unzip .zip file uploaded to Galaxy |
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65 #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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66 |
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67 |
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68 if (!is.null(listArguments[["zipfile"]])){ |
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69 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL |
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70 } |
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71 |
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72 |
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73 if (!is.null(listArguments[["singlefile_galaxyPath"]])){ |
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74 singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL |
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75 singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL |
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76 } |
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77 |
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78 # single file case |
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79 #@TODO: need to be refactoring |
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80 if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) { |
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81 if(!file.exists(singlefile_galaxyPath)){ |
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82 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
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83 print(error_message); stop(error_message) |
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84 } |
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85 |
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86 cwd=getwd() |
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87 dir.create("raw") |
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88 setwd("raw") |
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89 file.symlink(singlefile_galaxyPath,singlefile_sampleName) |
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90 setwd(cwd) |
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91 |
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92 directory = "raw" |
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93 |
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94 } |
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95 |
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96 # We unzip automatically the chromatograms from the zip files. |
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97 if(exists("zipfile") && (zipfile!="")) { |
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98 if(!file.exists(zipfile)){ |
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99 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
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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 #list all file in the zip file |
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105 #zip_files=unzip(zipfile,list=T)[,"Name"] |
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106 |
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107 # Because IPO only want raw data in its working directory |
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108 dir.create("ipoworkingdir") |
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109 setwd("ipoworkingdir") |
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110 file.symlink(zipfile, ".") |
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111 |
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112 #unzip |
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113 suppressWarnings(unzip(zipfile, unzip="unzip")) |
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114 |
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115 #get the directory name |
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116 filesInZip=unzip(zipfile, list=T); |
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117 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); |
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118 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
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119 directory = "." |
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120 if (length(directories) == 1) directory = directories |
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121 |
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122 cat("files_root_directory\t",directory,"\n") |
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123 |
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124 file.remove(zipfile) |
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125 |
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126 |
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127 } |
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128 |
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129 #addition of the directory to the list of arguments in the first position |
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130 checkXmlStructure(directory) |
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131 checkFilesCompatibilityWithXcms(directory) |
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132 |
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133 cat("\n\n") |
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134 |
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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 # ----- MAIN PROCESSING INFO ----- |
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141 cat("\tMAIN PROCESSING INFO\n") |
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142 |
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143 |
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144 xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass) |
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145 |
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146 |
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147 |
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148 cat("\n\n") |
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149 |
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150 |
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151 # ----- EXPORT ----- |
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152 |
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153 cat("\tXSET OBJECT INFO\n") |
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154 print(xset) |
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155 #delete the parameters to avoid the passage to the next tool in .RData image |
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156 |
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157 |
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158 #saving R data in .Rdata file to save the variables used in the present tool |
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159 objects2save = c("xset","zipfile") |
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160 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) |
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161 |
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162 cat("\n\n") |
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163 |
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164 |
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165 cat("\tDONE\n") |
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166 |