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comparison beast.xml @ 3:95b13782906c draft

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author malex
date Thu, 26 Apr 2012 11:11:47 -0400
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2:1914e55fee82 3:95b13782906c
1 <tool id="beast" name="Beast" version="1.1" force_history_refresh="True">
2 <description>Bayesian MCMC analysis of molecular sequences.</description>
3 <version_command>beast 2> /dev/null | grep -e "v[0-9]\.*" | awk '{print $2}' | awk -F, '{print $1}' | sed 's/^.//'</version_command>
4 <command interpreter="python">beast.py -T 4 -r $strict -s $seed -i $inputxml -o $operators -l $log -t $trees -d $trees.id -p $__new_file_path__</command>
5 <inputs>
6 <param format="xml" name="inputxml" type="data">
7 <label>Input XML File</label>
8 </param>
9 <param name="strict" type="boolean" checked="no" truevalue="-strict" falsevalue="" display="checkboxes">
10 <label>Fail on non-conforming BEAST XML</label>
11 </param>
12 <param name="seed" size="8" type="integer" value="12345" label="Random Seed">
13 </param>
14 <param name="errors" size="4" type="integer" value="1000" label="Maxium number of numerical errors before stopping">
15 </param>
16 </inputs>
17 <outputs>
18 <data format="txt" name="operators" label="${tool.name} on ${on_string}: Operators " from_work_dir="mcmc.operators"/>
19 <data format="txt" name="log" label="${tool.name} on ${on_string}: Log" from_work_dir="beast.log"/>
20 <data format="nexus" name="trees" label="${tool.name} on ${on_string}: Trees" />
21 </outputs>
22 <help>
23 .. class:: warningmark
24
25 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.
26
27 If the random seed is not chosen "12345" will be used.
28
29 -----
30
31 **BEAST v1.7.1, 2002-2012**
32
33 Bayesian Evolutionary Analysis Sampling Trees
34
35 Designed and developed by
36
37
38 Alexei J. Drummond -
39 Department of Computer Science,
40 University of Auckland,
41 alexei@cs.auckland.ac.nz
42
43 Andrew Rambaut -
44 Institute of Evolutionary Biology,
45 University of Edinburgh,
46 a.rambaut@ed.ac.uk
47
48 Marc A. Suchard - David Geffen School of Medicine,
49 University of California, Los Angeles,
50 msuchard@ucla.edu
51
52 Downloads, Help and Resources: http://beast.bio.ed.ac.uk
53
54 Source code distributed under the GNU Lesser General Public License:
55 http://code.google.com/p/beast-mcmc
56
57 BEAST developers:
58 Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian
59 Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter,
60 Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus,
61 Chieh-Hsi Wu, Walter Xie
62
63 Thanks to: Roald Forsberg, Beth Shapiro and Korbinian Strimmer
64 </help>
65 </tool>