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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FFEval" name="FFEval" version="2.0.0">
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3 <description>Evaluation tool for feature detection algorithms.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FFEval</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>FFEval
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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_truth:
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16 -truth $param_truth
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17 #end if
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18 #if $param_rt_tol:
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19 -rt_tol $param_rt_tol
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20 #end if
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21 #if $param_rt_tol_abs:
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22 -rt_tol_abs $param_rt_tol_abs
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23 #end if
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24 #if $param_mz_tol:
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25 -mz_tol $param_mz_tol
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26 #end if
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27 #if $param_out:
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28 -out $param_out
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29 #end if
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30 #if $param_abort_reasons:
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31 -abort_reasons $param_abort_reasons
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32 #end if
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33 #if $param_out_roc:
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34 -out_roc $param_out_roc
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35 #end if
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36 -threads \${GALAXY_SLOTS:-24}
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37 #if $adv_opts.adv_opts_selector=='advanced':
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38 #if $adv_opts.param_force:
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39 -force
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40 #end if
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41 #end if
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42 </command>
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43 <inputs>
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44 <param name="param_in" type="data" format="featurexml" optional="False" label="Feature input file, which contains the data to be tested against the truth file" help="(-in) "/>
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45 <param name="param_truth" type="data" format="featurexml" optional="False" label="Truth feature file that defines what features should be found" help="(-truth) "/>
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46 <param name="param_rt_tol" type="float" min="0.0" optional="True" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help="(-rt_tol) "/>
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47 <param name="param_rt_tol_abs" type="float" min="-1.0" optional="True" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help="(-rt_tol_abs) "/>
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48 <param name="param_mz_tol" type="float" min="0.0" optional="True" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help="(-mz_tol) "/>
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49 <param name="param_abort_reasons" type="data" format="featurexml" optional="True" label="Feature file containing seeds with abort reasons" help="(-abort_reasons) "/>
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50 <expand macro="advanced_options">
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51 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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52 </expand>
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53 </inputs>
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54 <outputs>
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55 <data name="param_out" format="featurexml"/>
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56 <data name="param_out_roc" format="tabular"/>
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57 </outputs>
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58 <help>**What it does**
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59
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60 Evaluation tool for feature detection algorithms.
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61
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62
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63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html</help>
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64 <expand macro="references"/>
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65 </tool>
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