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comparison galaxy_stubs/AntitargetRescorer.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Rescoring]-->
4 <tool id="AntitargetRescorer" name="AntitargetRescorer" version="1.1.0">
5 <description>rescore w/ anti-target dock-results</description>
6 <macros>
7 <token name="@EXECUTABLE@">AntitargetRescorer</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>AntitargetRescorer
13
14 #if $param_t:
15 -t $param_t
16 #end if
17 #if $param_at:
18 -at $param_at
19 #end if
20 #if $param_o:
21 -o $param_o
22 #end if
23 </command>
24 <inputs>
25 <param name="param_t" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file w/ target dock-results" help="(-t) "/>
26 <param name="param_at" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file w/ anti-target dock-results" help="(-at) "/>
27 </inputs>
28 <expand macro="advanced_options"/>
29 <outputs>
30 <data name="param_o" metadata_source="param_t" format="input"/>
31 </outputs>
32 <help>This tool rescores docking output poses.
33 AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.
34
35 As input we need:
36 * 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 docket into the specified protein (i.e. the target).
37 * a file containing the same compounds docked into the antitarget.
38
39 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 'antitarget_rescore'.
40
41 </help>
42 </tool>