--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/hyphy/hyphy_nj_tree_wrapper.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,58 @@
+#Dan Blankenberg
+#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_filename1 = os.path.abspath(sys.argv[2].strip())
+output_filename2 = os.path.abspath(sys.argv[3].strip())
+distance_metric = sys.argv[4].strip()
+temp_ps_filename = hyphy_util.get_filled_temp_filename("")
+
+#Guess if this is a single or multiple FASTA input file
+found_blank = False
+is_multiple = False
+for line in open(input_filename):
+    line = line.strip()
+    if line == "": found_blank = True
+    elif line.startswith(">") and found_blank:
+        is_multiple = True
+        break
+    else: found_blank = False
+
+NJ_tree_shared_ibf = hyphy_util.get_filled_temp_filename(hyphy_util.NJ_tree_shared_ibf)
+
+#set up NJ_tree file
+NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_tree(NJ_tree_shared_ibf))
+#setup Config file
+config_filename = hyphy_util.get_nj_tree_config_filename(input_filename, distance_metric, output_filename1, temp_ps_filename, NJ_tree_filename)
+if is_multiple: 
+    os.unlink(NJ_tree_filename)
+    os.unlink(config_filename)
+    NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_treeMF(NJ_tree_shared_ibf))
+    config_filename = hyphy_util.get_nj_treeMF_config_filename(input_filename, output_filename1, temp_ps_filename, distance_metric, NJ_tree_filename)
+    print "Multiple Alignment Analyses"
+else: print "Single Alignment Analyses"
+
+
+#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(NJ_tree_filename)
+os.unlink(config_filename)
+
+
+#Convert PS to PDF
+if os.path.getsize(temp_ps_filename)>0: temp = os.popen("ps2pdf %s %s" % (temp_ps_filename, output_filename2), 'r').close()
+os.unlink(temp_ps_filename)