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

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/beast.xml	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,36 @@
+<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>