<tool id="openbabel_subsearch" name="Substructure Search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>of fingerprint data sets</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[

    python '$__tool_directory__/subsearch.py'
        -i '${query}'
        --iformat '${query.ext}'
        --fastsearch-index '${os.path.join($fastsearch.extra_files_path, 'molecule.fs')}'
        -o '${outfile}'
        --oformat $oformat
        --max-candidates $max_candidates
        --processors "\${GALAXY_SLOTS:-12}"

]]>
    </command>
    <inputs>
        <param name="query" type='data' format="tabular,smi,sdf,inchi,txt" label="Query"/>
        <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index" help="The OpenBabel fastsearch index can be created with the compound conversion tool."/>
        <param name="max_candidates" type="integer" value="4000" label="Maximum number of candidates"/>
        <param name='oformat' type='select' format='text' label="Output format">
            <option value='smi'>SMILES</option>
            <option value='inchi'>InChI</option>
            <option value='sdf'>SD-Files</option>
            <option value='mol2'>mol2</option>
            <option value='names'>Return the molecule names only</option>
        </param>
    </inputs>
    <outputs>
       <data format="smi" name="outfile">
         <change_format>
           <when input="oformat" value="inchi" format="inchi"/>
           <when input="oformat" value="sdf" format="sdf"/>
           <when input="oformat" value="mol2" format="mol2"/>
           <when input="oformat" value="names" format="tabular"/>
         </change_format>
       </data>
    </outputs>
    <tests>
        <test>
            <param name="query" ftype="sdf" value="CID_2244.sdf"/>
            <param name="fastsearch" value="ob_convert_on_CID2244_obfs.txt" ftype="obfs" >
                <composite_data value='molecule.sdf' />
                <composite_data value='molecule.fs'/>
            </param>
            <param name="oformat" value="names" />
            <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile.

.. _FastSearch: http://openbabel.org/wiki/FastSearch

-----

.. class:: infomark

**Input**

SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES.


]]>
    </help>
    <expand macro="citations"/>
</tool>