--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/beast.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,35 @@
+#!/usr/bin/python
+"""
+This program makes a new copy of a BEAST XML config file and changes the name of the log and tree files.
+The names have to be changed since Galaxy does not support dynamic output file names.
+The new XML file name must not be the same as the original!!!
+Script prints unique filename.
+
+
+Usage: python beast.py XMLFILE SAVE_DIRECTORY
+"""
+
+import sys
+import time
+from xml.etree.ElementTree import ElementTree
+
+beastDOM = ElementTree()
+beastDOM.parse(sys.argv[1])
+logs = beastDOM.findall('mcmc/log')
+for log in logs:
+    if log.get('id', False) == "fileLog":
+        log.set('fileName', 'data.log')
+
+logs = beastDOM.findall('mcmc/logTree')
+for log in logs:
+    if log.get('id', False) == "treeFileLog":
+        log.set('fileName', 'data.trees')
+
+if len(sys.argv) > 2:
+    directory = sys.argv[2]
+else:
+    directory = ""
+
+filename = directory + "/" + str(time.time()) + '.xml'
+beastDOM.write(filename)
+print filename