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annotate CADDSuite-1.5/galaxyconfigs/tools/SimilarityAnalyzer.xml @ 15:ac342506cd4e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -0400
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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.-->
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3 <tool id="similarityanalyzer" name="SimilarityAnalyzer" version="1.5">
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4 <description>analyze similarity between molecule files</description>
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5 <command interpreter="bash"><![CDATA[../../SimilarityAnalyzer
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6 #if str( $i1 ) != '' and str( $i1 ) != 'None' :
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7 -i1 "$i1"
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8 #end if
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9 #if str( $i2 ) != '' and str( $i2 ) != 'None' :
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10 -i2 "$i2"
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11 #end if
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12 #if str( $o ) != '' and str( $o ) != 'None' :
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13 -o "$o"
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14 #end if
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15 #if str( $title ) != '' and str( $title ) != 'None' :
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16 -title "$title"
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17 #end if
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18 -quiet
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19 | tail -n 5
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20 ]]></command>
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21 <inputs>
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22 <param name="i1" optional="false" label="input molecule file 1" type="data" format="mol2/sdf/drf"/>
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23 <param name="i2" optional="false" label="input molecule file 2" type="data" format="mol2/sdf/drf"/>
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24 <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
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25 </inputs>
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26 <outputs>
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27 <data name="o" format="png"/>
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28 </outputs>
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29 <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.
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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.
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32 The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
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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>
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35 </tool>