Mercurial > repos > marcel > caddsuite_linux_x86_64
diff CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml @ 0:bac3c274238f
Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author | marcel |
---|---|
date | Tue, 07 Jun 2011 16:43:30 -0400 |
parents | |
children | 867bf9f815a0 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Tue Jun 07 16:43:30 2011 -0400 @@ -0,0 +1,55 @@ + +<!--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.--> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.93"> + <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' : + -b +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select"> + <option value="roc">roc</option> + <option value="top50">top50</option> + <option value="scatter">scatter</option> + <option value="enrichment">enrichment</option> + </param> + <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/> + <param name="s" label="score label" optional="false" area="true" type="text" size="1x15"/> + <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15"/> + <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/> + <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="png"/> + </outputs> + <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> +</tool> \ No newline at end of file