Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.6/galaxyconfigs/tools/GridBuilder.xml @ 17:25a03362403c draft
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| author | marcel |
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| date | Sat, 15 Dec 2012 13:10:41 -0500 |
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| 16:1a24aef40d01 | 17:25a03362403c |
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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="1.6"> | |
| 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.gz"/> | |
| 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> |