Mercurial > repos > malex > beast

<tool id="beast" name="Beast" version="1.0" 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.

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>
author	malex
date	Tue, 17 Apr 2012 10:52:00 -0400
parents
children	677344fb75c1