--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Tools/CREF/list_motifs_galaxy.pl	Mon Sep 05 05:53:08 2016 -0400
@@ -0,0 +1,29 @@
+#!/usr/bin/perl -w
+
+
+$|=1;
+use strict; #using this makes debugging your code much easier
+use warnings;
+
+my $line;
+my @cols;
+
+
+if(@ARGV < 2){
+print "\nUsage: list_motifs.pl ame-shorted.txt list-motifs.txt\n\n";
+exit(0);
+}
+open (INPUT, "<$ARGV[0]") || 
+   die "File '$ARGV[0]' not found\n" ;
+
+open (OUTPUT, ">$ARGV[1]") || 
+  die "File '>$ARGV[1]' not found\n" ;
+
+ while (<INPUT>){
+  
+   $line = $_;
+   @cols=split;
+   if ($line =~ /MA/){
+    printf OUTPUT "%s\n", $cols[5];
+   }
+ }
\ No newline at end of file