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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="1.12.0">
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3 <description>Evaluates alignment results against a ground truth.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>MapAlignmentEvaluation
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11
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12 -in ${param_in}
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13 -gt ${param_gt}
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14 -type ${param_type}
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15 -rt_dev ${param_rt_dev}
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16 -mz_dev ${param_mz_dev}
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17 -int_dev ${param_int_dev}
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18 ${param_use_charge}
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19 -threads \${GALAXY_SLOTS:-24}
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20 </command>
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21 <inputs>
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22 <param name="param_in" type="data" format="consensusXML" optional="False" label="input file: tool" help="(-in)"/>
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23 <param name="param_gt" type="data" format="consensusXML" optional="False" label="input file: ground truth" help="(-gt)"/>
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24 <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type)">
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25 <option value="precision">precision</option>
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26 <option value="recall">recall</option>
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27 <option value="F1">F1</option>
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28 </param>
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29 <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev)"/>
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30 <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev)"/>
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31 <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev)"/>
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32 <param name="param_use_charge" type="boolean" truevalue="-use_charge true" falsevalue="-use_charge false" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical." help="(-use_charge)"/>
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33 </inputs>
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34 <outputs/>
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35 <help>**What it does**
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36
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37 Evaluates alignment results against a ground truth.
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38
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39
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40 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html
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41
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42 @REFERENCES@
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43 </help>
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44 </tool>
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