<tool id="beast" name="Beast" version="1.1" force_history_refresh="True">
  <description>Bayesian MCMC analysis of molecular sequences.</description>
  <version_command>beast 2> /dev/null | grep -e "v[0-9]\.*" | awk '{print $2}' | awk -F, '{print $1}' | sed 's/^.//'</version_command>
  <command interpreter="python">beast.py -T 4 -r $strict -s $seed -i $inputxml -o $operators -l $log -t $trees -d $trees.id -p $__new_file_path__</command>
  <inputs>
    <param format="xml" name="inputxml" type="data">
      <label>Input XML File</label>
    </param>
    <param name="strict" type="boolean" checked="no" truevalue="-strict" falsevalue="" display="checkboxes">
        <label>Fail on non-conforming BEAST XML</label>
    </param>
    <param name="seed" size="8" type="integer" value="12345" label="Random Seed">
    </param>
    <param name="errors" size="4" type="integer" value="1000" label="Maxium number of numerical errors before stopping">
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="operators" label="${tool.name} on ${on_string}: Operators " from_work_dir="mcmc.operators"/>
    <data format="txt" name="log" label="${tool.name} on ${on_string}: Log" from_work_dir="beast.log"/>
    <data format="nexus" name="trees" label="${tool.name} on ${on_string}: Trees" />
  </outputs>
<help>
.. class:: warningmark

The input dataset needs to be in BEAST XML format. The names of the log output files configured in the xml file should have the '.log' extension and the trees file(s) should have the '.tree' extension for the best presentation.

If the random seed is not chosen "12345" will be used.

-----

**BEAST v1.7.1, 2002-2012**

Bayesian Evolutionary Analysis Sampling Trees

Designed and developed by


Alexei J. Drummond - 
Department of Computer Science, 
University of Auckland, 
alexei@cs.auckland.ac.nz

Andrew Rambaut - 
Institute of Evolutionary Biology, 
University of Edinburgh, 
a.rambaut@ed.ac.uk

Marc A. Suchard - David Geffen School of Medicine, 
University of California, Los Angeles, 
msuchard@ucla.edu

Downloads, Help and Resources: http://beast.bio.ed.ac.uk

Source code distributed under the GNU Lesser General Public License:
http://code.google.com/p/beast-mcmc

BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian
Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter,
Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus,
Chieh-Hsi Wu, Walter Xie

Thanks to: Roald Forsberg, Beth Shapiro and Korbinian Strimmer
</help>
</tool>