--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/gblocks.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,30 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+#gblocks.pl [fasta file]
+
+my $infile=shift(@ARGV);
+my $datatype=shift(@ARGV);
+my $gaps=shift(@ARGV);
+my $size=shift(@ARGV);
+my $outfileloc=shift(@ARGV);
+my $htmlfileloc=shift(@ARGV);
+
+
+
+
+##For debugging command line pass, uncomment next
+#for (my $i=0; $i < @ARGV; $i++){
+#	print "Parameter #$i ".$ARGV[$i]."\n\n";
+#}
+
+system "Gblocks $infile $datatype $gaps -b4=$size";
+
+#Gblocks requires output from $input.fas to be written to $input.fas-gb
+#Copy that file to gout where galaxy expects to find the output
+my $outfile = $infile."-gb";
+my $htmlfile = $outfile.".htm";
+system "cat $outfile > $outfileloc";
+system "cat $htmlfile > $htmlfileloc";
+exit;