Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite/galaxyconfigs/tools/TaGRes-train.xml @ 0:8ce0411aaeb3
Uploaded CADDSuite version 0.94
author | marcel |
---|---|
date | Sun, 26 Jun 2011 14:01:09 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:8ce0411aaeb3 |
---|---|
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-train" name="TaGRes-train" version="0.94"> | |
4 <description>Target-specific Grid-Rescoring, training</description> | |
5 <command interpreter="bash"><![CDATA[../../TaGRes-train | |
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( $o ) != '' and str( $o ) != 'None' : | |
19 -o "$o" | |
20 #end if | |
21 #if str( $method ) != '' and str( $method ) != 'None' : | |
22 -method "$method" | |
23 #end if | |
24 #if str( $function ) != '' and str( $function ) != 'None' : | |
25 -function "$function" | |
26 #end if | |
27 #if str( $exp ) != '' and str( $exp ) != 'None' : | |
28 -exp "$exp" | |
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="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/> | |
37 <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> | |
38 <option value="Rescoring3D">Rescoring3D</option> | |
39 <option value="Rescoring4D">Rescoring4D</option> | |
40 <option value="Rescoring1D">Rescoring1D</option> | |
41 </param> | |
42 <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> | |
43 <option value="MM">MM</option> | |
44 <option value="PLP">PLP</option> | |
45 </param> | |
46 <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> | |
47 </inputs> | |
48 <outputs> | |
49 <data name="o" format="mod"/> | |
50 </outputs> | |
51 <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes). | |
52 As input we need: | |
53 | |
54 * a file containing a protonated protein in pdb-format | |
55 * 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). | |
56 * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein. | |
57 | |
58 A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it. | |
59 | |
60 The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help> | |
61 </tool> |