Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.0/galaxyconfigs/tools/SimilarityAnalyzer.xml @ 14:55c32b55c2c2
Uploaded Version 1.1
| author | marcel |
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| date | Thu, 12 Jan 2012 11:00:43 -0500 |
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| 13:cce3667779c2 | 14:55c32b55c2c2 |
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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="similarityanalyzer" name="SimilarityAnalyzer" version="0.9"> | |
| 4 <description>analyze similarity between molecule files</description> | |
| 5 <command interpreter="bash"><![CDATA[../../SimilarityAnalyzer | |
| 6 #if str( $i1 ) != '' and str( $i1 ) != 'None' : | |
| 7 -i1 "$i1" | |
| 8 #end if | |
| 9 #if str( $i2 ) != '' and str( $i2 ) != 'None' : | |
| 10 -i2 "$i2" | |
| 11 #end if | |
| 12 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 13 -o "$o" | |
| 14 #end if | |
| 15 #if str( $title ) != '' and str( $title ) != 'None' : | |
| 16 -title "$title" | |
| 17 #end if | |
| 18 -quiet | |
| 19 | tail -n 5 | |
| 20 ]]></command> | |
| 21 <inputs> | |
| 22 <param name="i1" optional="false" label="input molecule file 1" type="data" format="mol2/sdf/drf"/> | |
| 23 <param name="i2" optional="false" label="input molecule file 2" type="data" format="mol2/sdf/drf"/> | |
| 24 <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data name="o" format="png"/> | |
| 28 </outputs> | |
| 29 <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result. | |
| 30 | |
| 31 Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure. | |
| 32 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. | |
| 33 | |
| 34 The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.</help> | |
| 35 </tool> |