annotate phylogenies/beast.xml @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

<tool id="beast_bayesian172" name="BEAST 1.7.2" version="1.7.2">
	<description>Bayesian evolutionary analysis by sampling trees.</description>
	<requirements>
		<requirement type="package">beast</requirement>
	</requirements>
	<command interpreter="bash">
		beast.sh $beast_stdout $xmlconfig $beagle_sse 
	</command>
	<inputs>
		<param format="txt" name="xmlconfig" type="data" label="BEAST XML" help="NOTE: If your job fails or your output is empty see the help section below."/>
	<param name='beagle_sse' type='boolean' checked='false' truevalue='-beagle_sse' falsevalue='' label='Use Beagle SSE?' help='Beagle will speed up calculations, but may not work on your dataset.'/>
	</inputs>
	<outputs>
		<data format="txt" name="beast_stdout" label="${tool.name} on ${on_string}: stdout" />
		<data format="txt" name="beast_log" label="${tool.name} on ${on_string}: log" from_work_dir="data.log" />
		<data format="txt" name="beast_tree" label="${tool.name} on ${on_string}: Assembled Tree" from_work_dir="data.trees" />
	</outputs>
	<tests>
	</tests>
	<help>
	**BEAST v1.7.2**
	
	This tool takes an xml file configured as a BEAST datafile, and executes BEAST for phylogenetic analysis.
	
	**If the job fails**

	Make sure your XML file is formatted correctly by running BEAST on you own system first.

	**If your output is empty**
	
	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.
	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.

	See BEAST wiki: http://beast.bio.ed.ac.uk/Main_Page
	</help>
</tool>