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annotate CADDSuite-1.5/galaxyconfigs/tools/SimpleRescorer.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="simplerescorer" name="SimpleRescorer" version="1.5">
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4 <description>rescore docking results</description>
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5 <command interpreter="bash"><![CDATA[../../SimpleRescorer
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6 #if str( $rec ) != '' and str( $rec ) != 'None' :
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7 -rec "$rec"
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8 #end if
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9 #if str( $rl ) != '' and str( $rl ) != 'None' :
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10 -rl "$rl"
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11 #end if
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12 #if str( $ini ) != '' and str( $ini ) != 'None' :
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13 -ini "$ini"
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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( $o ) != '' and str( $o ) != 'None' :
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19 -o "$o"
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20 #end if
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21 #if str( $function ) != '' and str( $function ) != 'None' :
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22 -function "$function"
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23 #end if
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24 #if str( $rm ) != '' and str( $rm ) != 'None' :
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25 -rm
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26 #end if
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27 | tail -n 5
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28 ]]></command>
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29 <inputs>
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30 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
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31 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
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32 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
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33 <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/>
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34 <param name="function" optional="true" label="scoring function: 'MM', 'PLP' or 'PB'" type="select">
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35 <option value="MM">MM</option>
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36 <option value="PLP">PLP</option>
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37 <option value="PB">PB</option>
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38 </param>
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39 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
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40 </inputs>
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41 <outputs>
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42 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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43 </outputs>
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44 <help>This tool rescores docking output poses.
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45 A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).
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46
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47 As input we need:
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48 * a file containing a protonated protein in pdb-format
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49 * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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50 * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
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51
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52 Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
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53 </tool>