<tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package">bioconductor-rtracklayer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name'
        &&
        cp annotation_overlap_long.csv '$out_long'
        &&
        cp annotation_overlap.csv '$out_wide'

    ]]></command>
    <inputs>
      <param type="data" name="input1_gff" format="gff" label="First GFF">
        <sanitizer invalid_char="">
          <valid initial="string.ascii_letters,string.digits">
            <add value="_" />
          </valid>
        </sanitizer>
      </param>
      <param type="data" name="input2_gff" format="gff" label="Second GFF">
        <sanitizer invalid_char="">
          <valid initial="string.ascii_letters,string.digits">
            <add value="_" />
          </valid>
        </sanitizer>
      </param>
        <param type="text" name="attribute_name" label="Name of attribute to summarize"/>
    </inputs>
    <outputs>
        <data name="out_long" format="tabular" label="Overlap of annotations
        ${input1_gff.hid} and ${input1_gff.hid} (as matrix)"  />
        <data name="out_wide" format="tabular" label="Overlap of annotations
        ${input1_gff.hid} and ${input1_gff.hid} (as table)"/>
    </outputs>
    <help><![CDATA[
        Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3.
    ]]></help>
</tool>