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<tool id="edu.tamu.cpt.gff3.intersect_and_adjacent" name="Intersect and Adjacent" version="21.0.0">
  <description>Outputs nearby top-level GFF features from two GFF3 files</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.0.2">intervaltree</requirement>
  </expand>
  <command detect_errors="aggressive"><![CDATA[
    python '$__tool_directory__/intersect_and_adjacent.py'
    '$gff3_data_a'
    '$gff3_data_b'
    $window
    $stranding
    --oa '$oa'
    --ob '$ob'
    ]]>
  </command>
  <inputs>
    <param label="GFF3 Annotations A" name="gff3_data_a" type="data" format="gff3"/>
    <param label="GFF3 Annotations B" name="gff3_data_b" type="data" format="gff3"/>
    <param label="Adjacency Window Size" name="window" type="integer" value="0"/>
    <param label="Only allow adjacencies for features on the same strand" name="stranding" type="boolean" checked="false" truevalue="-stranding" falsevalue=""/>
  </inputs>
  <outputs>
    <data format="gff3" name="oa" label="GFF3 Annotations from ${gff3_data_a.name} in ${gff3_data_b.name}"/>
    <data format="gff3" name="ob" label="GFF3 Annotations from ${gff3_data_b.name} in ${gff3_data_a.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="gff3_data_a" value="T7_IntersectAIn.gff3"/>
      <param name="gff3_data_b" value="T7_IntersectBIn.gff3"/>
      <param name="window" value="50"/>
      <param name="stranding" value="-stranding"/>
      <output name="oa" file="T7_IntersectAOut.gff3"/>
      <output name="ob" file="T7_IntersectBOut.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Given two input files, this tool computes the members of A that are within
"Window" nucleotides of a member of B, and vice versa. It then produces
two gff3 outputs, one being the features of GFF A that pass this check,
and the other being the features of GFF B that pass.
]]></help>
  <expand macro="citations-2020"/>
</tool>