--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/hyphy/hyphy_dnds_wrapper.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,55 @@
+#Guru
+#takes fasta alignments, a distance metric and builds neighbor joining trees
+import os, sys
+from galaxy import eggs
+from galaxy.tools.util import hyphy_util
+
+#Retrieve hyphy path, this will need to be the same across the cluster
+tool_data = sys.argv.pop()
+HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
+HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )
+
+#Read command line arguments
+input_filename = os.path.abspath(sys.argv[1].strip())
+output_filename = os.path.abspath(sys.argv[2].strip())
+tree_contents = sys.argv[3].strip()
+nuc_model = sys.argv[4].strip()
+analysis = sys.argv[5].strip()
+
+if tree_contents == "":
+    print >> sys.stderr, "Please specify a valid tree definition."
+    sys.exit()
+        
+tree_filename = hyphy_util.get_filled_temp_filename(tree_contents)
+
+if analysis == "local":
+    fitter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.SimpleLocalFitter)
+else:
+    fitter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.SimpleGlobalFitter)
+
+tabwriter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.TabWriter)
+FastaReader_filename = hyphy_util.get_filled_temp_filename(hyphy_util.FastaReader)
+#setup Config file
+config_filename = hyphy_util.get_dnds_config_filename(fitter_filename, tabwriter_filename, "Universal", tree_filename, input_filename, nuc_model, output_filename, FastaReader_filename)
+
+#Run Hyphy
+hyphy_cmd = "%s BASEPATH=%s USEPATH=/dev/null %s" % (HYPHY_EXECUTABLE, HYPHY_PATH, config_filename)
+hyphy = os.popen(hyphy_cmd, 'r')
+#print hyphy.read()
+hyphy.close()
+
+#remove temporary files
+os.unlink(fitter_filename)
+os.unlink(tabwriter_filename)
+os.unlink(tree_filename)
+os.unlink(FastaReader_filename)
+os.unlink(config_filename)
+
+if nuc_model == "000000":
+    model = "F81"
+elif nuc_model == "010010":
+    model = "HKY85"
+else:
+    model = "REV"
+    
+print "Analysis: %s; Model: %s; Tree: %s" %(analysis, model, tree_contents)