<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Analysis]-->
<tool id="SimilarityAnalyzer" name="SimilarityAnalyzer" version="0.9">
  <description>analyze similarity between molecule files</description>
  <macros>
    <token name="@EXECUTABLE@">SimilarityAnalyzer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SimilarityAnalyzer

#if $param_i1:
  -i1 $param_i1
#end if
#if $param_i2:
  -i2 $param_i2
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_title:
  -title     "$param_title"
#end if
#if $param_quiet:
  -quiet $param_quiet
#end if
</command>
  <inputs>
    <param name="param_i1" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file 1" help="(-i1) "/>
    <param name="param_i2" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file 2" help="(-i2) "/>
    <param name="param_title" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="plot title" help="(-title) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not print status" help="(-quiet) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" format="pdf"/>
  </outputs>
  <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.

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.
The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.

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>
</tool>