Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.6/galaxyconfigs/tools/WaterFinder.xml @ 8:dbb480e39d95 draft
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| author | marcel |
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| date | Sat, 15 Dec 2012 13:15:46 -0500 |
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| 7:bfab27640f5e | 8:dbb480e39d95 |
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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="waterfinder" name="WaterFinder" version="1.6"> | |
| 4 <description>find strongly bound waters</description> | |
| 5 <command interpreter="bash"><![CDATA[../../WaterFinder | |
| 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( $wat ) != '' and str( $wat ) != 'None' : | |
| 16 -wat "$wat" | |
| 17 #end if | |
| 18 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 19 -o "$o" | |
| 20 #end if | |
| 21 #if str( $ai ) != '' and str( $ai ) != 'None' : | |
| 22 -ai | |
| 23 #end if | |
| 24 | tail -n 5 | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> | |
| 28 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> | |
| 29 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> | |
| 30 <param name="wat" optional="true" label="input pdb-file containing water molecules (if not part of rec.-file)" type="data" format="pdb"/> | |
| 31 <param name="ai" optional="true" label="use ab-initio water search (ignore water in pdb-file), experimental!" type="boolean" truevalue="true" falsevalue=""/> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="o" format="pdb"/> | |
| 35 </outputs> | |
| 36 <help>This tool searches for crystal waters that | |
| 37 * either interact very strongly with the receptor | |
| 38 * or that interact strongly with receptor and reference ligand, | |
| 39 thus functioning as a water bridge. | |
| 40 | |
| 41 Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done. | |
| 42 | |
| 43 As input we need: | |
| 44 * a file containing a protonated protein in pdb-format. | |
| 45 This file should contain water molecules that are to be evaluated by this tool. | |
| 46 However, you can also use a separate pdb-file as input for the water molecules (see below). | |
| 47 * a file containing a reference ligand. | |
| 48 This reference ligand should be located in the binding pocket. | |
| 49 Supported formats are mol2, sdf or drf (DockResultFile, xml-based). | |
| 50 * optionally a file in pdb-format containing water molecules. | |
| 51 If you specify such a file , all water molecules appearing in the | |
| 52 protein input-file (if any) will be ignored. | |
| 53 | |
| 54 Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help> | |
| 55 </tool> |