comparison CADDSuite-1.0.1/galaxyconfigs/tools/GridBuilder.xml @ 9:2cff9609f2c7

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author marcel
date Tue, 15 Nov 2011 10:40:26 -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="gridbuilder" name="GridBuilder" version="1.0.1">
4 <description>create score-grids for docking</description>
5 <command interpreter="bash"><![CDATA[../../GridBuilder
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( $grd ) != '' and str( $grd ) != 'None' :
16 -grd "$grd"
17 #end if
18 | tail -n 5
19 ]]></command>
20 <inputs>
21 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
22 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
23 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
24 </inputs>
25 <outputs>
26 <data name="grd" format="grd.tgz"/>
27 </outputs>
28 <help>This tool precalculates a score-grid for a binding pocket of a given receptor.
29
30 As input we need:
31 * a file containing a protonated protein in pdb-format
32 * a file containing a reference ligand.
33 This reference ligand should be located in the binding pocket,
34 so that a grid can be precalculated around it.
35 Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
36
37 Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).</help>
38 </tool>