annotate tidecluster_reannotate.xml @ 10:971dbc97e607 draft default tip

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 5269b4297ea690bce0802c3c1cb217f24290f1ec-dirty

<tool id="tc_reannotate" name="TideCluster - Annotate Genome" version="@TOOL_VERSION@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <description>Annotate tandem repeats in genome assembly using similarity-based approach</description>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        tc_reannotate.py
        -s '$ref_seq'
        -f '$fasta_file'
        -c \${GALAXY_SLOTS:-1}
        -o '$output'
    ]]></command>
    <inputs>
        <param type="data" name="ref_seq" format="fasta" label="Reference sequence" help="FASTA file to be annotated by TRC library"/>
        <param type="data" name="fasta_file" format="fasta" label="Tandem repeat library" help="FASTA file with tandem repeat library from TideCluster"/>
    </inputs>
    <outputs>
        <data name="output" format="gff3" label="${tool.name} on ${on_string}: GFF3 Output"/>
    </outputs>
    <help><![CDATA[
        This is a tool for reannotating tandem repeats using a similarity-based approach. This tool runs RepeatMasker using the tandem repeat
        library generated by TAREAN in TideCluster. Resulting RepeatMasker output is processed to retain only high-quality tandem repeat hits.
        Overlapping tandem repeat annotation are merged, and regions shorter than twice the monomer length are excluded from the output.
        Reannotate tandem repeats using similarity-based approach can fill in gaps in annotation provided by TideCluster/TideHunter.
    ]]></help>
    <citations>
        <!-- Add citations here -->
    </citations>
</tool>