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<tool id="regal" name="Read-based evaluation of Genome Assemblies" version="1.0" profile="21.05">
    <description>Assembly statistics from a BED coverage file</description>
    <requirements>
        <requirement type="package" version="0.0.1">assemblyqc</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      regal -c $bed -a $ref -o $json -p $percentiles 
        ]]>
    </command>
    <inputs>
        <param argument="bed" type="data" format="bed" label="BED file" help="BED file containing coverage."/>
        <param argument="ref" type="data" format="fasta" label="FASTA file" help="FASTA file of existing assembly."/>
        <param argument="percentiles" type="text" label="Percentiles" help="Percentiles for assembly statistics (comma delimited)."/>
    </inputs>
    <outputs>
        <data name="json" format="json" label="${tool.name} on ${on_string}: Assembly JSON"></data>
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[

 .. class:: infomark

**Purpose**

Calculate some statistics associated to assembly quality.

------

 .. class:: infomark

**Outputs**

This tool generates a JSON file containing contiguous regions and assembly statistics based on the
reads that were used to produce a given assembly.
    ]]>
    </help>
    <citations>
    </citations>
</tool>