comparison CADDSuite-1.6/galaxyconfigs/tools/WaterFinder.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="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>