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

author marcel
date Fri, 02 Sep 2011 08:54:17 -0400
parents bb26168c5715
line wrap: on
line source

<!--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="bindingdbcleaner" name="BindingDBCleaner" version="0.9.6">
    <description>fix downloads</description>
    <command interpreter="bash"><![CDATA[../../BindingDBCleaner 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $type ) != ''  and str( $type ) != 'None' :
   -type "$type"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $target ) != ''  and str( $target ) != 'None' :
   -target "$target"
#end if
 | tail -n 5
        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
        <param name="type" optional="false" label="type of contained activity values: 'Ki' or 'IC50'" type="select">
            <option value="IC50">IC50</option>
            <option value="Ki">Ki</option>
        <param name="target" optional="false" label="binding-DB target name" area="true" type="text" size="1x15"/>
        <data name="o" format="mol2/sdf/drf" format_source="i"/>
    <help>This tool cleans up the sd-properties contained in sd-files downloaded from

For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'.

All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.</help>