view CADDSuite-1.0.1/galaxyconfigs/tools/ScoreAnalyzer.xml @ 5:e30a41af9d2b

author marcel
date Tue, 15 Nov 2011 10:53:16 -0500
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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="scoreanalyzer" name="ScoreAnalyzer" version="1.0.1">
    <description>generate ROC or enrichment plots</description>
    <command interpreter="bash"><![CDATA[../../ScoreAnalyzer 
#if str( $mode ) != ''  and str( $mode ) != 'None' :
   -mode "$mode"
#end if
#if str( $title ) != ''  and str( $title ) != 'None' :
   -title "$title"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $s ) != ''  and str( $s ) != 'None' :
   -s "$s"
#end if
#if str( $e ) != ''  and str( $e ) != 'None' :
   -e "$e"
#end if
#if str( $t ) != ''  and str( $t ) != 'None' :
   -t "$t"
#end if
#if str( $b ) != ''  and str( $b ) != 'None' :
#end if
 | tail -n 5
        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
        <param name="mode" optional="false" label="'roc', 'top50', 'scatter' or 'enrichment'" type="select">
            <option value="roc">roc</option>
            <option value="top50">top50</option>
            <option value="scatter">scatter</option>
            <option value="enrichment">enrichment</option>
        <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
        <param name="s" optional="false" label="score label" area="true" type="text" size="1x15" value="score"/>
        <param name="e" optional="false" label="binding-free-energy/class label name" area="true" type="text" size="1x15" value="binding_free_energy"/>
        <param name="t" optional="true" label="Optional: only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" area="true" type="text" size="1x15"/>
        <param name="b" optional="true" label="binary experimental activity data" type="boolean" truevalue="true" falsevalue=""/>
        <data name="o" format="png"/>
    <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.

The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.

The output of this tool is a plot in form of an eps or png-file (as chosen).</help>