<tool id="edu.tamu.cpt2.util.mga_to_gff3" name="MGA to GFF3" version="19.1.0.0">
    <description/>
    <macros>
        <import>cpt-macros.xml</import>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.9">python</requirement>
        <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
        <requirement type="package" version="1.81">biopython</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@
python '$__tool_directory__/cpt_convert_mga_to_gff3.py'
'$mga'
@GENOME_SELECTOR@
> '$data' ]]>
</command>
    <inputs>
        <param label="MGA Output" name="mga" type="data" format="txt"/>
        <expand macro="genome_selector"/>
    </inputs>
    <outputs>
        <data format="gff3" name="data">
		</data>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="ConvMga_In.fa"/>
            <param name="mga" value="ConvMga_In.out"/>
            <output name="data" file="ConvMga_Out.gff3"/>
        </test>
    </tests>
    <help>
**What it does**

Converts an input MetaGeneAnnotator table to the GFF3 format.
	</help>
    <expand macro="citations"/>
</tool>