Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.0.1/galaxyconfigs/tools/ScoreAnalyzer.xml @ 5:e30a41af9d2b
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:53:16 -0500 |
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| 4:af446ca2d5c6 | 5:e30a41af9d2b |
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| 1 | |
| 2 <!--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.--> | |
| 3 <tool id="scoreanalyzer" name="ScoreAnalyzer" version="1.0.1"> | |
| 4 <description>generate ROC or enrichment plots</description> | |
| 5 <command interpreter="bash"><![CDATA[../../ScoreAnalyzer | |
| 6 #if str( $mode ) != '' and str( $mode ) != 'None' : | |
| 7 -mode "$mode" | |
| 8 #end if | |
| 9 #if str( $title ) != '' and str( $title ) != 'None' : | |
| 10 -title "$title" | |
| 11 #end if | |
| 12 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 13 -o "$o" | |
| 14 #end if | |
| 15 #if str( $i ) != '' and str( $i ) != 'None' : | |
| 16 -i "$i" | |
| 17 #end if | |
| 18 #if str( $s ) != '' and str( $s ) != 'None' : | |
| 19 -s "$s" | |
| 20 #end if | |
| 21 #if str( $e ) != '' and str( $e ) != 'None' : | |
| 22 -e "$e" | |
| 23 #end if | |
| 24 #if str( $t ) != '' and str( $t ) != 'None' : | |
| 25 -t "$t" | |
| 26 #end if | |
| 27 #if str( $b ) != '' and str( $b ) != 'None' : | |
| 28 -b | |
| 29 #end if | |
| 30 | tail -n 5 | |
| 31 ]]></command> | |
| 32 <inputs> | |
| 33 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> | |
| 34 <param name="mode" optional="false" label="'roc', 'top50', 'scatter' or 'enrichment'" type="select"> | |
| 35 <option value="roc">roc</option> | |
| 36 <option value="top50">top50</option> | |
| 37 <option value="scatter">scatter</option> | |
| 38 <option value="enrichment">enrichment</option> | |
| 39 </param> | |
| 40 <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/> | |
| 41 <param name="s" optional="false" label="score label" area="true" type="text" size="1x15" value="score"/> | |
| 42 <param name="e" optional="false" label="binding-free-energy/class label name" area="true" type="text" size="1x15" value="binding_free_energy"/> | |
| 43 <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"/> | |
| 44 <param name="b" optional="true" label="binary experimental activity data" type="boolean" truevalue="true" falsevalue=""/> | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <data name="o" format="png"/> | |
| 48 </outputs> | |
| 49 <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring. | |
| 50 | |
| 51 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'. | |
| 52 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. | |
| 53 | |
| 54 The output of this tool is a plot in form of an eps or png-file (as chosen).</help> | |
| 55 </tool> |