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annotate CADDSuite-1.5/galaxyconfigs/tools/ScoreAnalyzer.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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1
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2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
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3 <tool id="scoreanalyzer" name="ScoreAnalyzer" version="1.5">
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4 <description>generate ROC or enrichment plots</description>
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5 <command interpreter="bash"><![CDATA[../../ScoreAnalyzer
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6 #if str( $mode ) != '' and str( $mode ) != 'None' :
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7 -mode "$mode"
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8 #end if
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9 #if str( $title ) != '' and str( $title ) != 'None' :
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10 -title "$title"
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11 #end if
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12 #if str( $o ) != '' and str( $o ) != 'None' :
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13 -o "$o"
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14 #end if
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15 #if str( $i ) != '' and str( $i ) != 'None' :
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16 -i "$i"
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17 #end if
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18 #if str( $s ) != '' and str( $s ) != 'None' :
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19 -s "$s"
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20 #end if
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21 #if str( $e ) != '' and str( $e ) != 'None' :
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22 -e "$e"
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23 #end if
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24 #if str( $t ) != '' and str( $t ) != 'None' :
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25 -t "$t"
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26 #end if
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27 #if str( $b ) != '' and str( $b ) != 'None' :
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28 -b
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29 #end if
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30 | tail -n 5
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31 ]]></command>
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32 <inputs>
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33 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
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34 <param name="mode" optional="false" label="'roc', 'top50', 'scatter' or 'enrichment'" type="select">
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35 <option value="roc">roc</option>
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36 <option value="top50">top50</option>
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37 <option value="scatter">scatter</option>
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38 <option value="enrichment">enrichment</option>
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39 </param>
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40 <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
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41 <param name="s" optional="false" label="score label" area="true" type="text" size="1x15" value="score"/>
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42 <param name="e" optional="false" label="binding-free-energy/class label name" area="true" type="text" size="1x15" value="binding_free_energy"/>
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43 <param name="t" optional="true" label="Optional: only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" area="true" type="text" size="1x15"/>
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44 <param name="b" optional="true" label="binary experimental activity data" type="boolean" truevalue="true" falsevalue=""/>
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45 </inputs>
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46 <outputs>
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47 <data name="o" format="png"/>
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48 </outputs>
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49 <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
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50
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51 The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
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52 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
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53
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54 The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
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55 </tool>