--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgatools/tools/cgatools_1.5/varfilter_wrapper.pl	Mon Jun 18 20:15:00 2012 -0400
@@ -0,0 +1,56 @@
+#!/usr/bin/perl
+use strict;
+use Getopt::Long;
+use vars qw($opt_reference $opt_input $opt_output @opt_zygosity @opt_vartype  @opt_varscorevaf @opt_varscoreeaf @opt_varquality);
+$| = 1; # set autoflush to screen
+
+# This is a wrapper for the cgatools varfilter function to run cgatools varfilter in Galaxy.
+# The wrapper generates the filter(s) in the correct format to be used with the input file.
+# written 6-1-2012 by bcrain@completegenomics.com
+
+
+#print join("\n", @ARGV), "\n";
+&GetOptions("reference=s", "input=s", "output=s", "zygosity=s@", "vartype=s@", "varscorevaf=s@", "varscoreeaf=s@", "varquality=s@");
+
+my $append = '';
+
+for (my $i = 0; $i <= $#opt_zygosity; $i ++)
+{
+	my $filter = '';
+	unless ($opt_zygosity[$i] eq 'NA') {$filter = $opt_zygosity[$i];}
+	unless ($opt_vartype[$i] eq 'NA')
+	{
+		$filter ne '' and $filter .= ':';
+		$filter .= 'varType=' . $opt_vartype[$i];
+	}
+	unless ($opt_varscorevaf[$i] eq 'x')
+	{
+		$filter ne '' and $filter .= ':';
+		$opt_varscorevaf[$i] =~ s/^x//;
+		$filter .= 'varScoreVAF<' . $opt_varscorevaf[$i];
+	}
+	unless ($opt_varscoreeaf[$i] eq 'x')
+	{
+		$filter ne '' and $filter .= ':';
+		$opt_varscoreeaf[$i] =~ s/^x//;
+		$filter .= 'varScoreEAF<' . $opt_varscoreeaf[$i];
+	}
+	unless ($opt_varquality[$i] eq 'NA')
+	{
+		$filter ne '' and $filter .= ':';
+		$filter .= 'varQuality!=' . $opt_varquality[$i];
+	}
+	
+	if ($filter ne '')
+	{
+		if ($append eq '') {$append = '#' . $filter;}
+		else {$append .= ',' . $filter;}
+	}
+}
+print "cgatools varfilter
+--beta
+--reference $opt_reference
+--output $opt_output
+--input '${opt_input}${append}'\n";
+
+`cgatools varfilter --beta --reference $opt_reference --output $opt_output --input '${opt_input}${append}'`;
\ No newline at end of file