<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>