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annotate FFEval.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="FFEval" name="FFEval" version="2.0.0">
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5 <description>Evaluation tool for feature detection algorithms.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FFEval</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FFEval
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_truth:
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19 -truth $param_truth
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20 #end if
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21 #if $param_rt_tol:
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22 -rt_tol $param_rt_tol
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23 #end if
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24 #if $param_rt_tol_abs:
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25 -rt_tol_abs $param_rt_tol_abs
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26 #end if
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27 #if $param_mz_tol:
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28 -mz_tol $param_mz_tol
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29 #end if
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30 #if $param_out:
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31 -out $param_out
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32 #end if
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33 #if $param_abort_reasons:
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34 -abort_reasons $param_abort_reasons
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35 #end if
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36 #if $param_out_roc:
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37 -out_roc $param_out_roc
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38 #end if
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39 -threads \${GALAXY_SLOTS:-24}
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40 #if $adv_opts.adv_opts_selector=='advanced':
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41 #if $adv_opts.param_force:
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42 -force
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43 #end if
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44 #end if
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45 </command>
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46 <inputs>
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47 <param format="xml" help="(-in) " label="Feature input file, which contains the data to be tested against the truth file" name="param_in" optional="False" type="data"/>
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48 <param format="xml" help="(-truth) " label="Truth feature file that defines what features should be found" name="param_truth" optional="False" type="data"/>
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49 <param help="(-rt_tol) " label="Allowed tolerance of RT relative to average feature RT span" min="0.0" name="param_rt_tol" optional="True" type="float" value="0.3"/>
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50 <param help="(-rt_tol_abs) " label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" min="-1.0" name="param_rt_tol_abs" optional="True" type="float" value="-1.0"/>
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51 <param help="(-mz_tol) " label="Allowed tolerance in m/z (is divided by charge)" min="0.0" name="param_mz_tol" optional="True" type="float" value="0.25"/>
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52 <param format="xml" help="(-abort_reasons) " label="Feature file containing seeds with abort reasons" name="param_abort_reasons" optional="True" type="data"/>
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53 <expand macro="advanced_options">
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54 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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55 </expand>
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56 </inputs>
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57 <outputs>
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58 <data format="xml" name="param_out"/>
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59 <data format="tabular" name="param_out_roc"/>
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60 </outputs>
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61 <help>Evaluation tool for feature detection algorithms.
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63
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64 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html</help>
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65 </tool>