--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylostatistics/SHtest.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,46 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+
+##For debugging command line pass, uncomment next
+#for (my $i=0; $i < @ARGV; $i++){
+#	print "Parameter #$i ".$ARGV[$i]."\n\n";
+#}
+#exit;
+
+my $datatype = shift(@ARGV);		#0 datatype
+my $data_file= shift(@ARGV);		#1 input a phylip file
+my $part_file = shift(@ARGV);		#2 optional partition file
+my $best_tree = shift(@ARGV);		#3 best tree for SH comparison
+my $alt_trees = shift(@ARGV);		#4 Alternative tree(s) for SH comparison
+my $model;
+
+#ADD OPTIONS TO BUILD FULL RAXML COMMANDLINE ARGUMENT
+
+my $build_command;
+#First CALL RAXML THROUGH PATH with 8 threads
+	$build_command = "raxmlHPC-PTHREADS-SSE3 ";
+#Add SH Test Option and Thread number for PThreads
+	$build_command = $build_command."-f h -T 4";
+#Next add call to input phylip file
+	$build_command = $build_command." -s ".$data_file;
+#model is passed directly with xml
+	$model = $datatype;
+	$build_command = $build_command." -m ".$model;
+#Add call to partition file name
+	unless($part_file eq 'None'){
+		$build_command = $build_command." -q ".$part_file;
+	}
+#Next add call to input best tree file
+	$build_command = $build_command." -t ".$best_tree;
+#Next add call to input best tree file
+	$build_command = $build_command." -z ".$alt_trees;
+#name output files galaxy
+	$build_command = $build_command." -n SH";
+
+print "Galaxy COMMAND BUILD WAS: $build_command\n";
+
+#Uncomment to actually call raxml
+system $build_command;
+