comparison CADDSuite-1.6/galaxyconfigs/tools/AntitargetRescorer.xml @ 8:dbb480e39d95 draft

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author marcel
date Sat, 15 Dec 2012 13:15:46 -0500
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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="antitargetrescorer" name="AntitargetRescorer" version="1.6">
4 <description>rescore w/ anti-target dock-results</description>
5 <command interpreter="bash"><![CDATA[../../AntitargetRescorer
6 #if str( $t ) != '' and str( $t ) != 'None' :
7 -t "$t"
8 #end if
9 #if str( $at ) != '' and str( $at ) != 'None' :
10 -at "$at"
11 #end if
12 #if str( $o ) != '' and str( $o ) != 'None' :
13 -o "$o"
14 #end if
15 | tail -n 5
16 ]]></command>
17 <inputs>
18 <param name="t" optional="false" label="input file w/ target dock-results" type="data" format="mol2/sdf/drf"/>
19 <param name="at" optional="false" label="input file w/ anti-target dock-results" type="data" format="mol2/sdf/drf"/>
20 </inputs>
21 <outputs>
22 <data name="o" format="mol2/sdf/drf" format_source="t"/>
23 </outputs>
24 <help>This tool rescores docking output poses.
25 AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.
26
27 As input we need:
28 * 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 docket into the specified protein (i.e. the target).
29 * a file containing the same compounds docked into the antitarget.
30
31 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 'antitarget_rescore'.</help>
32 </tool>