Mercurial > repos > lecorguille > camera_annotate
annotate CAMERA.r @ 33:3b2b642542f6 draft
planemo upload commit 896ef116e72008394779322f65137c632af5f4d2
author | lecorguille |
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date | Wed, 05 Apr 2017 11:27:56 -0400 |
parents | fce12d692a41 |
children | b02797fbead1 |
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1 #!/usr/bin/env Rscript |
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2 # CAMERA.r version="2.2.1" |
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3 |
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4 |
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5 |
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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 setRepositories(graphics=F, ind=31) |
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10 |
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11 #pkgs=c("xcms","batch") |
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12 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch") |
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13 for(p in pkgs) { |
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14 suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
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15 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") |
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16 } |
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17 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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18 |
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19 cat("\n\n"); |
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20 |
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22 |
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23 # ----- ARGUMENTS ----- |
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24 cat("\tARGUMENTS INFO\n") |
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25 |
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26 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects |
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27 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') |
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28 |
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29 cat("\n\n"); |
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30 |
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31 |
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32 # ----- PROCESSING INFILE ----- |
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33 cat("\tINFILE PROCESSING INFO\n") |
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34 |
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35 #image is an .RData file necessary to use xset variable given by previous tools |
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36 if (!is.null(listArguments[["image"]])){ |
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37 load(listArguments[["image"]]); listArguments[["image"]]=NULL |
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38 } |
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39 |
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40 if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) { |
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41 load(listArguments[["image_pos"]]) |
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42 xaP=xa |
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43 listOFlistArgumentsP=listOFlistArguments |
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44 if (exists("xsAnnotate_object")) xaP=xsAnnotate_object |
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45 |
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46 diffrepP=NULL |
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47 if (exists("diffrep")) diffrepP=diffrep |
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48 |
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49 load(listArguments[["image_neg"]]) |
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50 xaN=xa |
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51 listOFlistArgumentsN=listOFlistArguments |
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52 if (exists("xsAnnotate_object")) xaN=xsAnnotate_object |
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53 |
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54 diffrepN=NULL |
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55 if (exists("diffrep")) diffrepN=diffrep |
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56 } |
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57 |
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58 |
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59 cat("\n\n") |
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60 |
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61 |
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62 # ----- ARGUMENTS PROCESSING ----- |
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63 cat("\tARGUMENTS PROCESSING INFO\n") |
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64 |
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65 # Save arguments to generate a report |
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66 if (!exists("listOFlistArguments")) listOFlistArguments=list() |
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67 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments |
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68 |
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69 |
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70 #saving the commun parameters |
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71 thefunction = listArguments[["xfunction"]] |
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72 listArguments[["xfunction"]]=NULL #delete from the list of arguments |
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73 |
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74 xsetRdataOutput = paste(thefunction,"RData",sep=".") |
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75 if (!is.null(listArguments[["xsetRdataOutput"]])){ |
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76 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL |
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77 } |
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78 |
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79 rplotspdf = "Rplots.pdf" |
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80 if (!is.null(listArguments[["rplotspdf"]])){ |
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81 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL |
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82 } |
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83 |
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84 dataMatrixOutput = "dataMatrix.tsv" |
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85 if (!is.null(listArguments[["dataMatrixOutput"]])){ |
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86 dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL |
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87 } |
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88 |
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89 variableMetadataOutput = "variableMetadata.tsv" |
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90 if (!is.null(listArguments[["variableMetadataOutput"]])){ |
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91 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=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 # We unzip automatically the chromatograms from the zip files. |
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98 if (thefunction %in% c("annotatediff")) { |
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99 if (!exists("zipfile")) zipfile=NULL |
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100 if (!exists("singlefile")) singlefile=NULL |
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101 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) |
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102 zipfile = rawFilePath$zipfile |
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103 singlefile = rawFilePath$singlefile |
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104 listArguments = rawFilePath$listArguments |
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105 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) |
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106 } |
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107 |
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108 |
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109 #addition of xset object to the list of arguments in the first position |
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110 if (exists("xset") != 0){ |
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111 listArguments=append(list(xset), listArguments) |
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112 } |
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113 |
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114 cat("\n\n") |
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115 |
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116 |
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117 |
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118 |
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119 # ----- PROCESSING INFO ----- |
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120 cat("\tMAIN PROCESSING INFO\n") |
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121 |
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122 #change the default display settings |
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123 pdf(file=rplotspdf, width=16, height=12) |
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124 |
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125 |
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126 if (thefunction %in% c("annotatediff")) { |
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127 results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput) |
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128 xa=results_list[["xa"]] |
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129 diffrep=results_list[["diffrep"]] |
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130 variableMetadata=results_list[["variableMetadata"]] |
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131 |
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132 cat("\n\n") |
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133 cat("\tXSET OBJECT INFO\n") |
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134 print(xa) |
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135 } |
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136 |
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137 if (thefunction %in% c("combinexsAnnos")) { |
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138 cAnnot=combinexsAnnos_function( |
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139 xaP=xaP,xaN=xaN, |
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140 listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN, |
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141 diffrepP=diffrepP,diffrepN=diffrepN, |
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142 pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]], |
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143 convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]], |
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144 variableMetadataOutput=variableMetadataOutput |
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145 ) |
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146 } |
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147 |
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148 dev.off() |
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149 |
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150 |
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151 #saving R data in .Rdata file to save the variables used in the present tool |
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152 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile","singlefile") |
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153 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) |
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154 |
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155 cat("\n\n") |
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156 |
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157 cat("\tDONE\n") |