--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/jmodeltest.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,57 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use Cwd;
+
+my $jmodeltest_path = '/home/galaxy/pkgs/jmodeltest';
+my $jmodeltest_tool = '/home/galaxy/galaxy-dist/tools/jmodeltest';
+
+my $galaxyPath = getcwd();
+
+my $input = $ARGV[0];
+my $likelihoodStyle = $ARGV[1];
+my $likelihood = $ARGV[2];
+my $criterion = $ARGV[3];
+my $extension = $ARGV[4];
+
+# open increment file
+open my $file, '<', $jmodeltest_tool."\/increment.txt";
+	my $increment = <$file>;
+	$increment = int($increment);
+close $file;
+
+# get the current increment
+my $temp = $increment;
+
+# update the increment
+open(UPDATE, '>'.$jmodeltest_tool."\/increment.txt");
+	$increment = $increment + 1;
+	print UPDATE $increment;
+close(UPDATE);
+
+chdir("$jmodeltest_path");
+
+if($likelihoodStyle eq "-t") {
+	#only need to copy input file
+	qx/cp $input input.$temp.$extension/;
+	
+	#print qx/ls/;
+	
+	qx/java -jar jModelTest.jar -d input.$temp.$extension $likelihoodStyle $likelihood -$criterion > $galaxyPath\/output.txt 2> $galaxyPath\/err_log.txt/;		
+	qx/rm input.$temp.*/;
+}
+elsif($likelihoodStyle eq "-u") {
+	#copy input file
+	qx/cp $input input.$temp.$extension/;
+	#copy likelihood tree
+	qx/cp $likelihood likelihood.$temp.tre/;
+	qx/java -jar jModelTest.jar -d input.$temp.$extension $likelihoodStyle likelihood.$temp.tre -$criterion > $galaxyPath\/output.txt 2> $galaxyPath\/err_log.txt/;		
+
+	# clean up
+	qx/rm input.$temp.*/;
+	qx/rm likelihood.$temp.tre/;
+
+}
+
+chdir("$galaxyPath");
\ No newline at end of file