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comparison CADDSuite/galaxyconfigs/tools/TaGRes.xml @ 0:8ce0411aaeb3

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Uploaded CADDSuite version 0.94
author marcel
date Sun, 26 Jun 2011 14:01:09 -0400
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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="tagres" name="TaGRes" version="0.94">
4 <description>Target-specific Grid-Rescoring</description>
5 <command interpreter="bash"><![CDATA[../../TaGRes
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( $i ) != '' and str( $i ) != 'None' :
16 -i "$i"
17 #end if
18 #if str( $mod ) != '' and str( $mod ) != 'None' :
19 -mod "$mod"
20 #end if
21 #if str( $o ) != '' and str( $o ) != 'None' :
22 -o "$o"
23 #end if
24 #if str( $method ) != '' and str( $method ) != 'None' :
25 -method "$method"
26 #end if
27 #if str( $function ) != '' and str( $function ) != 'None' :
28 -function "$function"
29 #end if
30 | tail -n 5
31 ]]></command>
32 <inputs>
33 <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
34 <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
35 <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
36 <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
37 <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/>
38 <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
39 <option value="Rescoring3D">Rescoring3D</option>
40 <option value="Rescoring4D">Rescoring4D</option>
41 <option value="Rescoring1D">Rescoring1D</option>
42 </param>
43 <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
44 <option value="MM">MM</option>
45 <option value="PLP">PLP</option>
46 </param>
47 </inputs>
48 <outputs>
49 <data name="o" format="mol2/sdf/drf" format_source="i"/>
50 </outputs>
51 <help>This tool rescores docking output poses using Target-specific Grid-Rescoring.
52 Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool.
53 As input TaGRes needs:
54
55 * a file containing a protonated protein in pdb-format
56 * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
57 * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
58 * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
59
60 TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy.
61
62 Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
63 </tool>