<tool id="edu.tamu.cpt.cluster_lcbs" name="Merge LCBs within a given threshold distance" version="@WRAPPER_VERSION@.0">
    <description/>
    <macros>
        <import>macros.xml</import>
        <import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
'python $__tool_directory__/cluster_lcbs.py'
@XMFA_INPUT@
'$threshold'
> '$output'
]]></command>
    <inputs>
        <expand macro="xmfa_input"/>
        <param type="integer" name="threshold" value="50" label="maximum number of nucleotides between LCBs in a cluster"/>
    </inputs>
    <outputs>
        <data format="xmfa" name="output"/>
    </outputs>
    <help><![CDATA[
**What it does**

Merges LCBs near each other into one LCB. Helps with cluttered-looking data due to multiple LCBs.

**WARNING**

Might not work if you have - strand genes. Need to test.

]]></help>
    <!-- TODO -->
    <expand macro="citations"/>
</tool>