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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_gt:
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16 -gt $param_gt
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17 #end if
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18 #if $param_type:
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19 -type
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20 #if " " in str($param_type):
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21 "$param_type"
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22 #else
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23 $param_type
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24 #end if
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25 #end if
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26 #if $param_rt_dev:
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27 -rt_dev $param_rt_dev
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28 #end if
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29 #if $param_mz_dev:
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30 -mz_dev $param_mz_dev
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31 #end if
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32 #if $param_int_dev:
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33 -int_dev $param_int_dev
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34 #end if
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35 #if $param_use_charge:
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36 -use_charge
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37 #end if
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38 -threads \${GALAXY_SLOTS:-24}
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39 #if $adv_opts.adv_opts_selector=='advanced':
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40 #if $adv_opts.param_force:
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41 -force
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42 #end if
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43 #end if
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44 > $param_stdout
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45 </command>
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46 <inputs>
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47 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file: tool" help="(-in) "/>
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48 <param name="param_gt" type="data" format="consensusxml" optional="False" label="input file: ground truth" help="(-gt) "/>
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49 <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type) ">
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50 <option value="precision">precision</option>
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51 <option value="recall">recall</option>
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52 <option value="F1">F1</option>
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53 </param>
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54 <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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55 <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev) "/>
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56 <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev) "/>
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57 <param name="param_use_charge" type="boolean" truevalue="-use_charge" falsevalue="" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical" help="(-use_charge) "/>
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58 <expand macro="advanced_options">
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59 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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60 </expand>
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61 </inputs>
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62 <outputs>
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63 <data name="param_stdout" format="text" label="Output from stdout"/>
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64 </outputs>
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65 <help>**What it does**
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66
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67 Evaluates alignment results against a ground truth.
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68
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69
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70 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html</help>
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71 <expand macro="references"/>
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72 </tool>
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