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<tool id="ctb_multi_obgrep" name="Multi Compound Search" version="0.1">
    <description>an advanced molecular grep program using SMARTS</description>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command interpreter="python">
<![CDATA[

    multi_obgrep.py
        -i $infile
        --iformat ${infile.ext}
        -q $query
        -o "${outfile}"
        $invert_matches
        --n-times $n_times
        $only_name
        $full_match
        $number_of_matches
        --processors "\${GALAXY_SLOTS:-12}"

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
        <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
        <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
        <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" />
        <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern (-f)" truevalue="--full-match" falsevalue="" checked="false" />
        <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
    </inputs>
    <outputs>
        <data name="outfile" format_source="infile" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.

.. _Obgrep: http://openbabel.org/wiki/Obgrep
.. _here: http://openbabel.org/wiki/SMARTS

-----

.. class:: infomark

**Input**

| - `SD-Format`_
| - `SMILES Format`_

.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

**Output**

Same as input format.

-----

.. class:: infomark

**Cite**

N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_

.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page

]]>
    </help>
</tool>