Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.6/galaxyconfigs/tools/PocketCutter.xml @ 10:eda78e0f5df6 draft default tip
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| author | marcel |
|---|---|
| date | Sun, 30 Nov 2014 03:46:08 -0500 |
| parents | 488032d372e1 |
| children |
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| 9:488032d372e1 | 10:eda78e0f5df6 |
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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="pocketcutter" name="PocketCutter" version="1.6"> | |
| 4 <description>cut binding pocket surface</description> | |
| 5 <command interpreter="bash"><![CDATA[../../PocketCutter | |
| 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( $o ) != '' and str( $o ) != 'None' : | |
| 13 -o "$o" | |
| 14 #end if | |
| 15 #if str( $ini ) != '' and str( $ini ) != 'None' : | |
| 16 -ini "$ini" | |
| 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="true" label="reference ligand" type="data" format="mol2/sdf/drf"/> | |
| 23 <param name="ini" optional="true" label="input ini file" type="data" format="ini"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="o" format="mol2/sdf/drf"/> | |
| 27 </outputs> | |
| 28 <help>This tools selects all atoms from a given protein structure that form part of the binding pocket's SES surface. | |
| 29 | |
| 30 The location and size of the binding pocket can be obtained from either a given reference ligand or an ini file that contains a description as generated by the PocketDetector tool, or both. | |
| 31 | |
| 32 The output of this tool is a molecule file that contain just the selected surface atoms and can be used e.g. with SurfaceMatcher.</help> | |
| 33 </tool> |