Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.6/galaxyconfigs/tools/TaGRes.xml @ 10:eda78e0f5df6 draft default tip
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author | marcel |
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date | Sun, 30 Nov 2014 03:46:08 -0500 |
parents | 488032d372e1 |
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9:488032d372e1 | 10:eda78e0f5df6 |
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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="1.6"> | |
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( $tf ) != '' and str( $tf ) != 'None' : | |
22 -tf "$tf" | |
23 #end if | |
24 #if str( $o ) != '' and str( $o ) != 'None' : | |
25 -o "$o" | |
26 #end if | |
27 #if str( $method ) != '' and str( $method ) != 'None' : | |
28 -method "$method" | |
29 #end if | |
30 #if str( $function ) != '' and str( $function ) != 'None' : | |
31 -function "$function" | |
32 #end if | |
33 #if str( $rm ) != '' and str( $rm ) != 'None' : | |
34 -rm | |
35 #end if | |
36 | tail -n 5 | |
37 ]]></command> | |
38 <inputs> | |
39 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> | |
40 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> | |
41 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> | |
42 <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> | |
43 <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="mod"/> | |
44 <param name="tf" optional="true" label="Optional: top-scored fraction of compounds not to be rescored" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> | |
45 <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select"> | |
46 <option value="Rescoring3D">Rescoring3D</option> | |
47 <option value="Rescoring4D">Rescoring4D</option> | |
48 <option value="Rescoring1D">Rescoring1D</option> | |
49 </param> | |
50 <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select"> | |
51 <option value="MM">MM</option> | |
52 <option value="PLP">PLP</option> | |
53 </param> | |
54 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> | |
55 </inputs> | |
56 <outputs> | |
57 <data name="o" format="mol2/sdf/drf" format_source="i"/> | |
58 </outputs> | |
59 <help>This tool rescores docking output poses using Target-specific Grid-Rescoring. | |
60 Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool. | |
61 As input TaGRes needs: | |
62 | |
63 * a file containing a protonated protein in pdb-format | |
64 * 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). | |
65 * 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. | |
66 * a regression model file as generated by TaGRes-train for same protein target than the one specified here. | |
67 | |
68 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. | |
69 | |
70 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> | |
71 </tool> |