<?xml version="1.0"?>
<tool id="circos_aln_to_links" name="Circos: Alignments to links" version="@WRAPPER_VERSION@">
    <description>reformats alignment files to prepare for Circos</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/alignments-to-links.py' '$input' '$input.ext' > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="maf,xmfa,stockholm" label="Alignment file (maf, xmfa, stockholm)" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="alignments/1.maf" ftype="maf" />
            <output name="output" file="alignments/1.tab" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
Converts several standard alignment formats into a format appropriate for Circos plots.
    ]]></help>
    <expand macro="citations" />
</tool>