Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.5/galaxyconfigs/tools/SimpleRescorer.xml @ 7:bfab27640f5e draft
CADDSuite version 1.5
| author | Marcel Schumann <schumann.marcel@gmail.com> |
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| date | Tue, 24 Jul 2012 11:13:59 -0400 |
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| 6:decca54699e3 | 7:bfab27640f5e |
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| 1 | |
| 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.--> | |
| 3 <tool id="simplerescorer" name="SimpleRescorer" version="1.5"> | |
| 4 <description>rescore docking results</description> | |
| 5 <command interpreter="bash"><![CDATA[../../SimpleRescorer | |
| 6 #if str( $rec ) != '' and str( $rec ) != 'None' : | |
| 7 -rec "$rec" | |
| 8 #end if | |
| 9 #if str( $rl ) != '' and str( $rl ) != 'None' : | |
| 10 -rl "$rl" | |
| 11 #end if | |
| 12 #if str( $ini ) != '' and str( $ini ) != 'None' : | |
| 13 -ini "$ini" | |
| 14 #end if | |
| 15 #if str( $i ) != '' and str( $i ) != 'None' : | |
| 16 -i "$i" | |
| 17 #end if | |
| 18 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 19 -o "$o" | |
| 20 #end if | |
| 21 #if str( $function ) != '' and str( $function ) != 'None' : | |
| 22 -function "$function" | |
| 23 #end if | |
| 24 #if str( $rm ) != '' and str( $rm ) != 'None' : | |
| 25 -rm | |
| 26 #end if | |
| 27 | tail -n 5 | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 30 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> | |
| 31 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> | |
| 32 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> | |
| 33 <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> | |
| 34 <param name="function" optional="true" label="scoring function: 'MM', 'PLP' or 'PB'" type="select"> | |
| 35 <option value="MM">MM</option> | |
| 36 <option value="PLP">PLP</option> | |
| 37 <option value="PB">PB</option> | |
| 38 </param> | |
| 39 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data name="o" format="mol2/sdf/drf" format_source="i"/> | |
| 43 </outputs> | |
| 44 <help>This tool rescores docking output poses. | |
| 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). | |
| 46 | |
| 47 As input we need: | |
| 48 * a file containing a protonated protein in pdb-format | |
| 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). | |
| 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. | |
| 51 | |
| 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> | |
| 53 </tool> |