--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/hyphy/hyphy_branch_lengths_wrapper.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,55 @@
+#Dan Blankenberg
+#takes commandline tree def and input multiple fasta alignment file and runs the branch length ananlysis
+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()
+base_freq = sys.argv[5].strip()
+model_options = sys.argv[6].strip()
+
+#Set up Temporary files for hyphy run
+#set up tree file
+tree_filename = hyphy_util.get_filled_temp_filename(tree_contents)
+
+#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
+
+#set up BranchLengths file
+BranchLengths_filename = hyphy_util.get_filled_temp_filename(hyphy_util.BranchLengths)
+if is_multiple: 
+    os.unlink(BranchLengths_filename)
+    BranchLengths_filename = hyphy_util.get_filled_temp_filename(hyphy_util.BranchLengthsMF)
+    print "Multiple Alignment Analyses"
+else: print "Single Alignment Analyses"
+
+#setup Config file
+config_filename = hyphy_util.get_branch_lengths_config_filename(input_filename, nuc_model, model_options, base_freq, tree_filename, output_filename, BranchLengths_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(BranchLengths_filename)
+os.unlink(tree_filename)
+os.unlink(config_filename)