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<?xml version="1.0"?>
<tool id="twobit_to_cytoband" name="twoBitToCytoband" version="1.0">
    <description>Creates a cytoband file from a twoBit file</description>

    <macros>
        <import>ucsc_macros.xml</import>
    </macros>

    <expand macro="requirements_twobit" />

    <command detect_errors="exit_code">
<![CDATA[
    twoBitInfo "${twobit_input}" stdout |
        sort -k 1,1 -k 2,2n |
        awk 'BEGIN { OFS="\t" } { print $1, 0, $2, $1, "gneg" }' > "${bed_output}"
]]>
    </command>

    <expand macro="environment_LC_COLLATE" />

    <inputs>
        <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />
    </inputs>
    <outputs>
        <data name="bed_output" format="bed" />
    </outputs>
    <tests>
        <test>
            <!-- Test create Cytoband bed file from a twoBit file -->
            <param name="twobit_input" value="contigs.2bit" ftype="twobit" />
            <output name="bed_output" file="contigs_cytoband.bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool creates a `Cytoband file <http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Cytoband_Track>`_
from a twoBit file to enable quicker navigation of individual scaffolds
in the UCSC Genome Browser.

    ]]></help>

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