<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.phage.read_garnier" name="Read Garnier Secondary Structure Prediction" version="1.0">
    <description>read garnier tool output</description>
    <macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
	<command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/reading_garnier_output.py
$tagseq_file


>$output]]></command>
    <inputs>
        <param label="Tagseq" name="tagseq_file" type="data" format="tagseq" />
    </inputs>
    <outputs>
		<data format="tabular" name="output"/>
    </outputs>
    <help><![CDATA[
**What it does**
This program takes output from the garnier tool (as a tagseq file) and converts it into structural predictions for each 
sequence analyzed by the garnier tool. 

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