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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2 # version="0.1.0"
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3 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM
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4
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5
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6
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7 # ----- ARGUMENTS BLACKLIST -----
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8 #xcms.r
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9 argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")
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10 #CAMERA.r
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11 argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")
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12
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13 # ----- PACKAGE -----
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14
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15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch")
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16 for(pkg in pkgs) {
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17 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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18 }
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19
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20
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21 # ----- FUNCTION -----
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22 writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }
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23
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24
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25 # ----- ARGUMENTS -----
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26
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27 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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28
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29
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30 # ----- ARGUMENTS PROCESSING -----
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31
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32 #image is an .RData file necessary to use xset variable given by previous tools
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33 load(listArguments[["image"]]);
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34
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35 htmlOutput = "summary.html"
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36 if (!is.null(listArguments[["htmlOutput"]])) htmlOutput = listArguments[["htmlOutput"]];
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37
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38 user_email = NULL
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39 if (!is.null(listArguments[["user_email"]])) user_email = listArguments[["user_email"]];
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40
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41 # if the RData come from CAMERA
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42 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet
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43
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44 # retrocompatability
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45 if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))
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46
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47 if (!exists("xset")) stop("You need at least a xset or a xa object.")
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48
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49
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50
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51 # ----- MAIN PROCESSING INFO -----
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52 writehtml("<!DOCTYPE html>")
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53 writehtml("<HTML lang='en'>")
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54
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55 writehtml("<HEAD>")
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56 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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57
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58 writehtml("<title>[W4M] XCMS analysis summary</title>")
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59
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60 writehtml("<style>")
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61 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
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62 writehtml("td,th { padding: 5px; padding-right: 12px; }")
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63 writehtml("th { background: #898989; text-align:left;color: white;}")
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64 writehtml("h2 { color: #FFA212; }")
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65 writehtml("ul li { margin-bottom:10px; }")
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66 writehtml("</style>")
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67 writehtml("</HEAD>")
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68
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69 writehtml("<BODY>")
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70 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
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71 # to pass the planemo shed_test
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72 if (user_email != "test@bx.psu.edu") {
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73 if (!is.null(user_email)) writehtml("By: ",user_email," - ")
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74 writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S"))
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75 }
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76 writehtml("</div>")
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77
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78 writehtml("<h2>Samples used:</h2>")
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79 writehtml("<div><table>")
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80 if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) {
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81 sampleNameHeaderHtml = paste("<th>sample</th>")
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82 sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
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83 } else {
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84 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>")
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85 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
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86 }
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87
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88 if (!exists("md5sumList")) {
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89 md5sumHeaderHtml = ""
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90 md5sumHtml = ""
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91 md5sumLegend=""
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92 } else if (is.null(md5sumList$removalBadCharacters)) {
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93 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
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94 md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
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95 md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process."
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96 } else {
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97 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
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98 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>")
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99 md5sumLegend = "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
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100 }
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101
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102 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
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103 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))
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104
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105 writehtml("</table>")
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106 writehtml(md5sumLegend)
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107 writehtml("</div>")
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108
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109 writehtml("<h2>Function launched:</h2>")
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110 writehtml("<div><table>")
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111 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
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112 for(tool in names(listOFlistArguments)) {
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113 listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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114
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115 timestamp = strsplit(tool,"_")[[1]][1]
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116 xcmsFunction = strsplit(tool,"_")[[1]][2]
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117 writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
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118 line_begin=""
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119 for (arg in names(listOFlistArgumentsDisplay)) {
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120 writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
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121 line_begin="<tr>"
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122 }
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123 }
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124 writehtml("</table>")
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125 writehtml("<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss")
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126 writehtml("</div>")
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127
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128 writehtml("<h2>Informations about the xcmsSet object:</h2>")
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129
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130 writehtml("<div><pre>")
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131 log_file=file(htmlOutput, open = "at")
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132 sink(log_file)
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133 sink(log_file, type = "output")
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134 xset
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135 sink()
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136 writehtml("</pre></div>")
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137
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138 if (exists("xa")) {
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139 writehtml("<h2>Informations about the CAMERA object:</h2>")
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140
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141 writehtml("<div>")
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142 writehtml("Number of pcgroup: ",length(xa@pspectra))
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143 writehtml("</div>")
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144 }
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145
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146 writehtml("<h2>Citations:</h2>")
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147 writehtml("<div><ul>")
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148 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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149 writehtml("<ul>")
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150 writehtml("<li>","Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)","</li>")
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151 writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")
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152 writehtml("<li>","H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)","</li>")
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153 writehtml("</ul>")
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154 writehtml("</li>")
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155
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156 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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157 writehtml("<ul>")
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158 writehtml("<li>","Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)","</li>")
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159 writehtml("</ul>")
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160 writehtml("</li>")
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161
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162 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
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163 writehtml("<ul>")
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164 writehtml("<li>","Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813","</li>")
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165 writehtml("</ul>")
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166 writehtml("</li>")
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167 writehtml("</ul></div>")
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168
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169 writehtml("</BODY>")
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170
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171 writehtml("</HTML>")
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172
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