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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="beast_bayesian172" name="BEAST 1.7.2" version="1.7.2">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description>Bayesian evolutionary analysis by sampling trees.</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <requirements>
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4 <requirement type="package">beast</requirement>
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5 </requirements>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 <command interpreter="bash">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 beast.sh $beast_stdout $xmlconfig $beagle_sse
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8 </command>
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9 <inputs>
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10 <param format="txt" name="xmlconfig" type="data" label="BEAST XML" help="NOTE: If your job fails or your output is empty see the help section below."/>
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11 <param name='beagle_sse' type='boolean' checked='false' truevalue='-beagle_sse' falsevalue='' label='Use Beagle SSE?' help='Beagle will speed up calculations, but may not work on your dataset.'/>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="beast_stdout" label="${tool.name} on ${on_string}: stdout" />
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15 <data format="txt" name="beast_log" label="${tool.name} on ${on_string}: log" from_work_dir="data.log" />
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16 <data format="txt" name="beast_tree" label="${tool.name} on ${on_string}: Assembled Tree" from_work_dir="data.trees" />
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17 </outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 <tests>
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19 </tests>
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20 <help>
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21 **BEAST v1.7.2**
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22
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 This tool takes an xml file configured as a BEAST datafile, and executes BEAST for phylogenetic analysis.
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24
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25 **If the job fails**
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26
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 Make sure your XML file is formatted correctly by running BEAST on you own system first.
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28
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29 **If your output is empty**
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30
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31 This tool requires that your output files be named data.log and data.trees. The tool will try and rename them for you, but it may fail.
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32 To rename them manually look in your XML for the fileLog and treeLog nodes. Change the fileName attribute of each node to data.log and data.trees, respectively.
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33
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34 See BEAST wiki: http://beast.bio.ed.ac.uk/Main_Page
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35 </help>
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36 </tool>