<tool id="dante_ltr_to_library" name="Create representative library from DANTE_LTR output " version="@TOOL_VERSION@" python_template_version="3.5">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        cp '$dante_ltr' dante_ltr.gff3 &&
        dante_ltr_to_library --gff3 dante_ltr.gff3 --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} --min_coverage 3
        &&
        ls -l output
        &&
        mv output/mmseqs2/mmseqs_representative_seq_clean.fasta $dante_ltr_library
    ]]></command>
    <inputs>
        <param type="data" name="dante_ltr" format="gff3"
               label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
        <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
    </inputs>
    <outputs>
        <data name="dante_ltr_library" format="fasta"
              label="Representative library from DANTE_LTR $dante_ltr.hid on reference $reference.hid"/>
    </outputs>
    <help><![CDATA[
        This tool extract representative sequences from LTR-RT library identified
         by DANTE_LTR. Resulting library is suitable for RepeatMasker search.
    ]]></help>
</tool>