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annotate macros.xml @ 0:6aea0427511e draft default tip

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planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
author workflow4metabolomics
date Sun, 24 Nov 2024 21:28:57 +0000
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.48.0</token>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="0.4_3">r-snow</requirement>
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8 <requirement type="package" version="1.2.6">bioconductor-genomeinfodbdata</requirement>
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9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-camera</requirement>
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10 <requirement type="package" version="2.48.0">bioconductor-multtest</requirement>
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11 <requirement type="package" version="1.1_5">r-batch</requirement>
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12 <requirement type="package" version="1.3.26">graphicsmagick</requirement>
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13 <requirement type="package" version="3.0">zip</requirement>
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14 </requirements>
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15 </xml>
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16 <xml name="stdio">
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17 <stdio>
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18 <exit_code range="1" level="fatal" />
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19 </stdio>
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20 </xml>
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21
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22 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
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23
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24 <!-- raw file load for planemo test -->
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25 <token name="@COMMAND_FILE_LOAD@">
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26 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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27 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
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28 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
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29 #set singlefile_sampleName = ','.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] )
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30 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
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31 #else
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32 zipfile '$file_load_section.file_load_conditional.input'
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33 #end if
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34 #end if
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35 </token>
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36
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37 <xml name="input_file_load">
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38 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
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39 <conditional name="file_load_conditional">
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40 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server.">
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41 <option value="no">no need</option>
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42 <option value="yes">yes</option>
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43 </param>
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44 <when value="no">
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45 </when>
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46 <when value="yes">
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47 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
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48 </when>
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49 </conditional>
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50 </section>
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51 </xml>
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52
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53 <xml name="test_file_load_zip">
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54 <section name="file_load_section">
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55 <conditional name="file_load_conditional">
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56 <param name="file_load_select" value="yes" />
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57 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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58 </conditional>
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59 </section>
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60 </xml>
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61
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62 <xml name="test_file_load_single">
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63 <section name="file_load_section">
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64 <conditional name="file_load_conditional">
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65 <param name="file_load_select" value="yes" />
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66 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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67 </conditional>
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68 </section>
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69 </xml>
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70
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71 <xml name="test_file_load_faahKO_15">
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72 <section name="file_load_section">
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73 <conditional name="file_load_conditional">
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74 <param name="file_load_select" value="yes" />
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75 <param name="input" value="wt15.CDF,ko15.CDF" ftype="netcdf" />
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76 </conditional>
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77 </section>
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78 </xml>
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79
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80 <!-- peaklist export option management -->
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81 <token name="@COMMAND_PEAKLIST@">
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82 convertRTMinute $export.convertRTMinute
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83 numDigitsMZ $export.numDigitsMZ
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84 numDigitsRT $export.numDigitsRT
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85 intval $export.intval
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86 </token>
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87
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88 <xml name="input_peaklist">
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89 <section name="export" title="Export options">
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90 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
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91 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
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92 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
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93 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
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94 <option value="into" selected="true">into</option>
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95 <option value="maxo">maxo</option>
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96 <option value="intb">intb</option>
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97 </param>
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98 </section>
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99 </xml>
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100
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101 <xml name="test_peaklist">
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102 <section name="export">
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103 <param name="convertRTMinute" value="True"/>
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104 <param name="numDigitsMZ" value="4" />
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105 <param name="numDigitsRT" value="1" />
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106 <param name="intval" value="into"/>
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107 </section>
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108 </xml>
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109
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110 <!-- annotate_diffreport <test> commun part -->
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111 <xml name="test_annotate_diffreport">
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112 <section name="groupfwhm">
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113 <param name="sigma" value="6"/>
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114 <param name="perfwhm" value="0.6"/>
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115 </section>
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116 <section name="findisotopes">
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117 <param name="maxcharge" value="3"/>
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118 <param name="maxiso" value="4"/>
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119 <param name="minfrac" value="0.5"/>
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120 </section>
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121 <section name="findgeneral">
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122 <param name="ppm" value="5"/>
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123 <param name="mzabs" value="0.015"/>
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124 <param name="max_peaks" value="100"/>
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125 </section>
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126 <section name="diffreport">
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127 <conditional name="options">
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128 <param name="option" value="show"/>
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129 <param name="eicmax" value="200"/>
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130 <param name="eicwidth" value="200"/>
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131 <param name="value" value="into"/>
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132 <param name="h" value="480"/>
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133 <param name="w" value="640"/>
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134 <param name="mzdec" value="2"/>
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135 <param name="sortpval" value="False"/>
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136 <param name="tabular2" value="zip"/>
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137 <param name="png2" value="zip"/>
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138 </conditional>
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139 </section>
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140 <expand macro="test_peaklist"/>
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141 </xml>
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142
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143 <xml name="test_annotate_quick_false">
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144 <param name="quick" value="FALSE"/>
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145 <section name="groupcorr">
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146 <param name="cor_eic_th" value="0.75"/>
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147 <param name="graphMethod" value="hcs"/>
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148 <param name="pval" value="0.05"/>
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149 <param name="calcCiS" value="True"/>
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150 <param name="calcIso" value="False"/>
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151 <param name="calcCaS" value="False"/>
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152 </section>
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153 </xml>
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154
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155 <xml name="test_annotate_quick_true">
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156 <conditional name="quick_block">
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157 <param name="quick" value="TRUE"/>
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158 </conditional>
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159 </xml>
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160
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161 <token name="@HELP_AUTHORS@">
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162 .. class:: infomark
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163
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164 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
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165
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166 .. class:: infomark
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167
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168 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
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169
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170 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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171
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172 ---------------------------------------------------
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173
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174 </token>
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175
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176 <token name="@HELP_CAMERA_SUITE@">
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177 **Version 0.1.0+camera1.48.0 - 06/11/2024**
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178
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179 - Initial release with core functionalities for peak annotation, grouping, and visualization using CAMERA (see CAMERA News_).
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180 </token>
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181
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182 <token name="@HELP_CAMERA_NEWVERSION_1480@">
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183 **Version 2.2.6+camera1.48.0 - 11/06/2021**
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184
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185 - UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
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186 </token>
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187
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188 <token name="@HELP_CAMERA_NEWVERSION_1460@">
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189 **Version 2.2.6+camera1.46.0 - 12/04/2021**
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190
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191 - UPGRADE: upgrade the CAMERA version from 1.42.0 to 1.46.0 (see CAMERA News_)
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192 </token>
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193
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194 <token name="@HELP_CAMERA_NEWVERSION_1420@">
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195 **Version 2.2.6+camera1.42.0 - 13/02/2020**
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196
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197 - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 (see CAMERA News_)
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198 </token>
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199
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200 <xml name="citation">
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201 <citations>
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202 <citation type="doi">10.1021/ac202450g</citation>
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203 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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204 </citations>
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205 </xml>
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206
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207 <xml name="creator">
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208 <creator>
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209 <organization name="MELISA" url="https://www.laberca.org/plateforme-melisa/presentation"></organization>
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210 <organization name="Workflow4metabolomics" url="https://workflow4metabolomics.org/"></organization>
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211
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212 <person givenName="Yann" familyName="Guitton" url="https://github.com/yguitton"></person>
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213 <person givenName="Damien" familyName="Rat" url="https://github.com/DamienCode404"></person>
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214 <person givenName="Julien" familyName="Saint-Vanne" url="https://github.com/jsaintvanne"></person>
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215 </creator>
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216 </xml>
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217 </macros>