<?xml version="1.0"?>
<tool id="edu.tamu.cpt.gff3.remove_annots" name="Remove Annotation Feature" version="19.1.0.1" profile="16.04">
  <description>that's unused in our GFF tools</description>
  <macros>
    <import>macros.xml</import>
		<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/remove_annotations.py
$gff3_data
$remark
$region
> $default]]></command>
  <inputs>
      <expand macro="gff3_input" />
      <param checked="true" label="Remove 'remark' features" name="remark" type="boolean" truevalue="--remark" falsevalue="" />
      <param checked="true" label="Remove 'region' features" name="region" type="boolean" truevalue="--region" falsevalue="" />
  </inputs>
  <outputs>
    <data format="gff3" name="default"/>
  </outputs>
  <tests>
		<test>
			<param name="gff3_data" value="RemoveAnnote_In.gff3" />
			<param name="remark" value="--remark" />
                        <param name="region" value= "--region" />
			<output name="default" file="RemoveAnnote_Out.gff3" />
		</test>
  </tests>
  <help><![CDATA[
**What it does**

For an input GFF3, this tool specifically removes the feature entry with remark and/or region type (column 3) as needed for compatibility 
with certain tools. These feature typically encompasses the entire length of the sequence upon which the GFF3 is based.

Example input:
    Miro	annotation	remark	1	167935	.	.	.	gff-version=3;sequence-region=%28%27Miro%27%2C 0%2C 172788%29

    Miro	cpt		gene	1231	5436	.	.	.	ID=CDS1;

Example output:
    Miro	cpt		gene	1231	5436	.	.	.	ID=CDS1;


      ]]></help>
		<expand macro="citations" />
</tool>