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

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

<tool id="tidecluster_annotation" name="TideCluster- Annotate Clusters" version="@TOOL_VERSION@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <description>Annotate tandem repeats clusters identified by TideCluster using custom library of tandem repeats</description>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #set $prefix = 'tidecluster'
        mkdir extracted &&
        unzip '$input_archive' -d extracted && cd extracted &&
        TideCluster.py annotation
        -pr '$prefix'
        -l '$library'
        -c \${GALAXY_SLOTS:-1}
        &&
        cp '${prefix}_annotation.gff3' '$gff3_annotation'
        &&
        cp '${prefix}_annotation.tsv' '$tsv_annotation'
    ]]></command>
    <inputs>
        <param type="data" name="input_archive" format="zip" label="Output archive from previous TideCluster run" help="The zip archive containing the output from a previous TideCluster run."/>
        <param type="data" name="library" format="fasta" label="Library of tandem repeats" help="Path to library of tandem repeats."/>
    </inputs>
    <outputs>
        <data name="gff3_annotation" format="gff3" label="${tool.name} on ${on_string}: GFF3 TideCluster Annotated Output"/>
        <data name="tsv_annotation" format="tsv" label="${tool.name} on ${on_string}: TSV TideCluster Annotated Output"/>
    </outputs>
    <help><![CDATA[
    **TideCluster Annotation Step**

    This step of TideCluster is responsible for annotating the tandem repeats using a library of tandem repeats. The consensus sequences from TideHunter for each cluster are examined by RepeatMasker against a library of tandem repeats. The resulting annotation for each tandem repeat is used to update the information in the GFF3 file.

    **Inputs:**


    - Output archive from previous TideCluster run: The zip archive containing the output from a previous TideCluster run.
    - Library of tandem repeats: FASTA library with tandem repeats, Library must be in RepeatMasker format

    **Outputs:**

    - GFF3 TideCluster Annotated Output: GFF3 file with tandem repeats annotated by RepeatMasker. Attribute Annotation is added to GFF3 file.
    - TSV TideCluster Annotated Output: Summarized annotation for each TRC cluster in a tab-delimited format.
    ]]></help>
    <citations>
        <!-- Add citations here -->
    </citations>
</tool>