<?xml version="1.0"?>
<tool id="edu.tamu.cpt.gff.stop_codons" name="Stop Codon Statistics" version="1.0">
	<description>Summarise stop codon usage</description>
	<macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
	</macros>
	<expand macro="requirements"/>
	<command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

$__tool_directory__/stop_stats.py

@GENOME_SELECTOR@
$gff3_data
> $default]]></command>
	<inputs>
		<expand macro="genome_selector" />
		<expand macro="gff3_input" />
	</inputs>
	<outputs>
		<data format="tabular" name="default" label="Stop Codon Usage"/>
	</outputs>
	<tests>
		<test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="miro.fa" />
			<param name="gff3_data" value="miro.gff3" />

			<output name="default" value="stop-stats.tab" />
		</test>
	</tests>
	<help><![CDATA[
.. class:: warningmark

This tool is deprecated. Please use `the new fasta-only tool <root?tool_id=edu.tamu.cpt.fasta.stop_codons>`__.
This change was made to make the tools less complicated and more obvious in
their functionality. Currently this tool makes **assumptions** about your data
which **may be wrong**.

**What it does**

This tool looks for CDS features and outputs summarizes the frequencies
of their stop codons::


	# Name Codon Count
	Ochre  TAA   155
	Amber  TAG   10
	Opal   TGA   111
]]></help>
		<expand macro="citations" />
</tool>