Mercurial > repos > lecorguille > camera_annotate

annotate CAMERA.r @ 12:db270f704d93 draft

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planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
author lecorguille
date Thu, 14 Apr 2016 11:00:27 -0400
parents d33e0ed5f32a
children ba7db5b70639
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1 #!/usr/bin/env Rscript
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2 # CAMERA.r version="2.2.1"
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6 # ----- PACKAGE -----
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7 cat("\tPACKAGE INFO\n")
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8
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9 #pkgs=c("xcms","batch")
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10 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch")
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11 for(p in pkgs) {
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12 suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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13 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
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14 }
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15 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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16
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17 cat("\n\n");
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21 # ----- ARGUMENTS -----
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22 cat("\tARGUMENTS INFO\n")
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23
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24 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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25 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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27 cat("\n\n");
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30 # ----- PROCESSING INFILE -----
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31 cat("\tINFILE PROCESSING INFO\n")
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32
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33 #image is an .RData file necessary to use xset variable given by previous tools
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34 if (!is.null(listArguments[["image"]])){
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35 load(listArguments[["image"]]); listArguments[["image"]]=NULL
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36 }
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37
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38 if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
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39 load(listArguments[["image_pos"]])
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40 xaP=xa
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41 if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
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42
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43 diffrepP=NULL
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44 if (exists("diffrep")) diffrepP=diffrep
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45
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46 load(listArguments[["image_neg"]])
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47 xaN=xa
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48 if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
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49
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50 diffrepN=NULL
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51 if (exists("diffrep")) diffrepN=diffrep
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52 }
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55 cat("\n\n")
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58 # ----- ARGUMENTS PROCESSING -----
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59 cat("\tARGUMENTS PROCESSING INFO\n")
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60
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61 # Save arguments to generate a report
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62 if (!exists("listOFlistArguments")) listOFlistArguments=list()
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63 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
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64
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65
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66 #saving the commun parameters
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67 thefunction = listArguments[["xfunction"]]
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68 listArguments[["xfunction"]]=NULL #delete from the list of arguments
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69
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70 xsetRdataOutput = paste(thefunction,"RData",sep=".")
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71 if (!is.null(listArguments[["xsetRdataOutput"]])){
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72 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
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73 }
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74
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75 rplotspdf = "Rplots.pdf"
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76 if (!is.null(listArguments[["rplotspdf"]])){
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77 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
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78 }
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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
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85 variableMetadataOutput = "variableMetadata.tsv"
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86 if (!is.null(listArguments[["variableMetadataOutput"]])){
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87 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
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88 }
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89
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90 if (!is.null(listArguments[["new_file_path"]])){
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91 new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL
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92 }
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93
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94 #Import the different functions
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95 source_local("lib.r")
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96
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97 #necessary to unzip .zip file uploaded to Galaxy
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98 #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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100
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101 if (!is.null(listArguments[["zipfile"]])){
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102 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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103 }
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104
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105 # We unzip automatically the chromatograms from the zip files.
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106 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
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107 if(exists("zipfile") && (zipfile!="")) {
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108 if(!file.exists(zipfile)){
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109 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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110 print(error_message)
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111 stop(error_message)
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112 }
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113
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114 #unzip
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115 suppressWarnings(unzip(zipfile, unzip="unzip"))
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116
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117 #get the directory name
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118 filesInZip=unzip(zipfile, list=T);
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119 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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120 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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121 directory = "."
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122 if (length(directories) == 1) directory = directories
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123
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124 cat("files_root_directory\t",directory,"\n")
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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
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130 #addition of xset object to the list of arguments in the first position
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131 if (exists("xset") != 0){
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132 listArguments=append(list(xset), listArguments)
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133 }
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134
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135 cat("\n\n")
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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 # ----- PROCESSING INFO -----
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141 cat("\tMAIN PROCESSING INFO\n")
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142
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143 #change the default display settings
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144 pdf(file=rplotspdf, width=16, height=12)
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145
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146
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147 if (thefunction %in% c("annotatediff")) {
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148 results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path)
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149 xa=results_list[["xa"]]
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150 diffrep=results_list[["diffrep"]]
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151 variableMetadata=results_list[["variableMetadata"]]
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152
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153 cat("\n\n")
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154 cat("\tXSET OBJECT INFO\n")
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155 print(xa)
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156 }
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157
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158 if (thefunction %in% c("combinexsAnnos")) {
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159 cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
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160 }
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161
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162 dev.off()
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163
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164
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165 #saving R data in .Rdata file to save the variables used in the present tool
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166 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile")
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167 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
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168
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169 cat("\n\n")
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170
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171 cat("\tDONE\n")