view CADDSuite/galaxyconfigs/tools/DockResultMerger.xml @ 3:bb26168c5715

author marcel
date Tue, 12 Jul 2011 10:53:07 -0400
children af446ca2d5c6
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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="dockresultmerger" name="DockResultMerger" version="0.95">
    <description>merge docking output files</description>
    <command interpreter="bash"><![CDATA[../../DockResultMerger 
#for $s in $series_i 
   #if str( "${s.i.file_name}" ) != ''  and str( "${s.i.file_name}" ) != 'None' :
      -i "${s.i.file_name}"
   #end if
#end for 
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $score ) != ''  and str( $score ) != 'None' :
   -score "$score"
#end if
#if str( $min ) != ''  and str( $min ) != 'None' :
   -min "$min"
#end if
#if str( $max ) != ''  and str( $max ) != 'None' :
   -max "$max"
#end if
#if str( $k ) != ''  and str( $k ) != 'None' :
   -k "$k"
#end if
#if str( $rm ) != ''  and str( $rm ) != 'None' :
#end if
 | tail -n 5
        <repeat name="series_i" title="input files" min="1">
            <param name="i" optional="false" label="input files" type="data" format="mol2/sdf/drf"/>
        <param name="score" optional="true" label="Optional: score property name" area="true" type="text" size="1x15" value="score"/>
        <param name="min" optional="true" label="Optional: minimal score value" type="text" area="true" size="1x5" value=""/>
        <param name="max" optional="true" label="Optional: maximal score value" type="text" area="true" size="1x5" value=""/>
        <param name="k" optional="true" label="Optional: number of output molecules" type="text" area="true" size="1x5" value=""/>
        <param name="rm" optional="true" label="remove input files after merging" type="boolean" truevalue="true" falsevalue=""/>
        <data name="o" format="mol2/sdf/drf" format_source="i"/>
    <help>This tool merges and sorts molecule files as generated by docking or rescoring.

You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.

 Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>