view CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml @ 4:af446ca2d5c6

author marcel
date Fri, 02 Sep 2011 08:54:17 -0400
parents bb26168c5715
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<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy ( This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.9.6">
    <description>define interaction constraint</description>
    <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner 
#if str( $res ) != ''  and str( $res ) != 'None' :
   -res "$res"
#end if
#if str( $ini ) != ''  and str( $ini ) != 'None' :
   -ini "$ini"
#end if
#if str( $s ) != ''  and str( $s ) != 'None' :
   -s "$s"
#end if
#if str( $p ) != ''  and str( $p ) != 'None' :
   -p "$p"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
 | tail -n 5
        <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
        <param name="res" optional="false" label="residue ID" area="true" type="text" size="1x15"/>
        <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"/>
        <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="10"/>
        <data name="o" format="ini"/>
    <help>This tool allows to define interaction constraints for docking or scoring.

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.

Output of this tool is a ini-file that contains the desired interaction constraint.</help>