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<tool id="umicount" name="umicount" version="0.1">
    <description>Runs umicount</description>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">
        dedup_fingerprint.py -f "${input}" > "${output}"
    </command>
    <inputs>
        <param name="input" format="bed" label="Select Paired BED file" type="data" />
    </inputs>
    <outputs>
        <data format="bed" name="output" label="Unicount output for ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param ftype="bed" name="input" value="paired.bed" />
            <output file="cagescan_fragments.bed" ftype="bed" name="output" />
        </test>
    </tests>
    <help>
<![CDATA[
Runs umicount (https://raw.githubusercontent.com/mmendez12/umicount)

See http://umicount.readthedocs.org/en/latest/introduction.html for more details.
]]>
    </help>
    <citations>
        <citation type="bibtex">
            @misc{
                umicount_bibtex,
                author = {Mickaël Mendez},
                title = {umicount on GitHub},
                url = {https://github.com/mmendez12/umicount}
            }
        </citation>
        <citation type="bibtex">
            @misc{
                umicount_docs,
                author = {Mickaël Mendez},
                title = {umicount documentation on readthedocs},
                url = {http://umicount.readthedocs.org}
            }
        </citation>
    </citations>
</tool>