<?xml version="1.0"?>
<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>
		<import>cpt-macros.xml</import>
  </macros>
  <requirements>
      			<requirement type="package" version="3.7">python</requirement>
			<requirement type="package" version="1.79">biopython</requirement>
			<requirement type="package" version="1.1.3">cpt_gffparser</requirement>  
      <requirement type="package" version="3.0.2">intervaltree</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
$__tool_directory__/intersect_and_adjacent.py
"$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>