|
9
|
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> |
