<tool id="findrepeat" name="Find Repeats" version ="1.8.2">
  <description>Identify repeat elements using Mummer</description>
  <requirements>
    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
    <requirement type="package" version="3.23">mummer</requirement>
  </requirements>
  <command detect_errors="exit_code">
      find-repeats.pl -l $length -p $pid $fasta > $out
  </command>
  <inputs>
    <param name="fasta" type="data"  label="Fasta file" format="fasta"/>
    <param name="length"  label="Minimum length of repeat region" type="integer" value="150"/>
    <param name="pid"   label="Minimum PID of repeat region" type="integer" value="90"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out" />
  </outputs>
  <tests>
    <test>
      <param name="length" value="150"/>
      <param name="pid" value="90"/>
      <param name="fasta" value="find-repeats-input-1.fasta"/>
      <output name="out" file="find-repeats-output-1.tabular"/>
    </test>
  </tests>

  <help>
What it does
============

Searches a fasta reference file for repeats.


Usage
=====

**Parameters**
  - Fasta file:  A fasta reference file to search for repeats.

**Options**
  - Minimum length of repeat region (150).
  - Minimum PID of repeat region (90).
  </help>
<citations>
</citations>
</tool>