comparison CADDSuite-1.0.1/galaxyconfigs/tools/InteractionConstraintDefiner.xml @ 9:2cff9609f2c7

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author marcel
date Tue, 15 Nov 2011 10:40:26 -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="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="1.0.1">
4 <description>define interaction constraint</description>
5 <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner
6 #if str( $res ) != '' and str( $res ) != 'None' :
7 -res "$res"
8 #end if
9 #if str( $ini ) != '' and str( $ini ) != 'None' :
10 -ini "$ini"
11 #end if
12 #if str( $s ) != '' and str( $s ) != 'None' :
13 -s "$s"
14 #end if
15 #if str( $p ) != '' and str( $p ) != 'None' :
16 -p "$p"
17 #end if
18 #if str( $o ) != '' and str( $o ) != 'None' :
19 -o "$o"
20 #end if
21 | tail -n 5
22 ]]></command>
23 <inputs>
24 <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
25 <param name="res" optional="false" label="residue ID" area="true" type="text" size="1x15"/>
26 <param name="s" optional="false" label="desired minimal interation (score) between ligand and specified residue(s)" type="text" area="true" size="1x5" value="-2.0"/>
27 <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="10"/>
28 </inputs>
29 <outputs>
30 <data name="o" format="ini"/>
31 </outputs>
32 <help>This tool allows to define interaction constraints for docking or scoring.
33
34 The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: &lt;chain-ID&gt;:&lt;residue-ID&gt;, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
35
36 Output of this tool is a ini-file that contains the desired interaction constraint.</help>
37 </tool>