<tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0">
    <description>convert formats</description>
    <macros>
        <import>cpt-macros.xml</import>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.9.16">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 $__tool_directory__/cpt_convert_glimmer_to_gff3.py'
'$glimmer'
@GENOME_SELECTOR@
> '$data' ]]>
</command>
    <inputs>
        <param label="Glimmer Output" name="glimmer" type="data" format="tabular,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="ConvGlim_In.fasta"/>
            <param name="glimmer" value="ConvGlim_In.out"/>
            <output name="data" file="ConvGlim_Out.gff3"/>
        </test>
    </tests>
    <help>
	**What it does**

	Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping 
	around over the sequence boundary (as if circular) then it will only convert the upstream fragment and 
	label it as "_truncated" in the resulting GFF.
	</help>
    <expand macro="citations"/>
</tool>