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<tool id="bamtocov" name="BAM to Coverage" version="1.0" profile="21.05">
    <description>Get a BED file of coverage from a BAM</description>
    <requirements>
        <requirement type="package" version="2.7.0">bamtocov</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        bamtocov '$bam' > '$bed'
        ]]>
    </command>
    <inputs>
        <param argument="bam" type="data" format="bam" label="BAM file" help="BAM file to get coverage from."/>
    </inputs>
    <outputs>
        <data name="bed" format="bed" label="${tool.name} on ${on_string}: Coverage"></data>
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[

 .. class:: infomark

**Purpose**

Calculate coverage from a BAM file.

------

 .. class:: infomark

**Outputs**

This tool generates a BED file containing coverage information from the associated BAM file.
    ]]>
    </help>
    <citations>
        <citation type="bibtex">
          @article{birolo2022bamtocov,
              title={BamToCov: an efficient toolkit for sequence coverage calculations},
              author={Birolo, Giovanni and Telatin, Andrea},
              journal={Bioinformatics},
              volume={38},
              number={9},
              pages={2617--2618},
              year={2022},
              publisher={Oxford University Press}
            }
        </citation>
    </citations>
</tool>