<tool id="edu.tamu.cpt.gff3.require_sd" name="Gff3 Filter: Require SD" version="19.1.0.0">
  <description>ensures CDSs have an SD</description>
  <macros>
    <import>macros.xml</import>
		<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

python $__tool_directory__/gff3_require_sd.py

@GENOME_SELECTOR@
@INPUT_GFF@

> $stdout

]]></command>
  <inputs>
    <expand macro="genome_selector" />
    <expand macro="gff3_input" />
  </inputs>
  <outputs>
    <data format="gff3" name="stdout" label="$gff3_data.name filtered for SD presence"/>
  </outputs>
  <tests>
      <test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="T7_ReqSDIn.fasta" />
			<param name="gff3_data" value="T7_ReqSDIn.gff3" />

          <output name="stdout" file="T7_ReqSDOut.gff3" />
      </test>
      <test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="Miro_ReqSDIn.fa" />
			<param name="gff3_data" value="Miro_ReqSDIn.gff3" />

          <output name="stdout" file="Miro_ReqSDOut.gff3" />
      </test>
  </tests>
  <help><![CDATA[
**What it does**

Ensures every CDS has an upstream Shine-Dalgarno site defined. ShineFind is used to add SD subfeatures to CDSs without one.

.. class:: warningmark 

This tool removes non-CDS type features, and CDS features without an SD site (RBS features are ignored). 

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