--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testing_cgatools-982e19c29ec0/cgatools/tools/cgatools_1.6/mkvcf_wrapper.pl	Thu Sep 27 13:37:59 2012 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/perl
+use strict;
+use Getopt::Long;
+use vars qw($opt_reference $opt_output @opt_input $opt_genomes $opt_source $opt_datasource $opt_fields $opt_nocalls $opt_calibration $opt_jctscore $opt_jctside $opt_jctdistance $opt_jctlength $opt_jctpriority $opt_jcttumor);
+$| = 1; # set autoflush to screen
+
+# This is a wrapper for the cgatools mkvcf function to run cgatools mkvcf in Galaxy.
+# written 8-10-2012 by bcrain@completegenomics.com
+
+#print join("\n", @ARGV), "\n";
+&GetOptions("reference=s", "output=s", "input=s@", "genomes=i", "source=s", "datasource=s", "fields=s", "nocalls", "calibration:s", "jctscore=i", "jctside=i", "jctdistance=i", "jctlength=i", "jctpriority", "jcttumor");
+
+my $command = "cgatools mkvcf --beta --reference $opt_reference --output $opt_output --source-names $opt_source";
+
+if ($opt_datasource eq 'in')
+{
+	foreach my $file (@opt_input)
+	{
+		if ($opt_source eq 'masterVar') {$command .= " --master-var ";}
+		elsif ($opt_source eq 'SV') {$command .= " --junction-file ";}
+		else {die "there is an error in the logic: wrong source $opt_source for datasource $opt_datasource.\n";}
+		$command .= $file
+	}
+}
+elsif ($opt_datasource eq 'out')
+{
+	if ($opt_genomes == 1)
+	{
+		if ($opt_input[0] =~ m/masterVar/ and $opt_source eq 'masterVar')
+		{
+			-f $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
+			$command .= " --master-var $opt_input[0]";
+		}
+		elsif ($opt_input[0] =~ m/Junctions/ and $opt_source eq 'SV')
+		{
+			-f $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
+			$command .= " --junction-file $opt_input[0]";
+		}
+		else 
+		{
+			$opt_input[0] =~ s/\/$//;
+			-d $opt_input[0] or die "$opt_input[0] is not a valid directory.\n";
+			$command .= " --genome-root $opt_input[0]";
+		}
+	}
+	else
+	{
+		-T $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
+		my $count = 0;
+		foreach my $file (split /\s+/, `cat $opt_input[0]`)
+		{
+			$count ++;
+			($opt_genomes == 2 and $count > 2) and die "The number of inputs in your list file cannot be greater than the number of genomes selected.\n";
+			if ($file =~ m/masterVar/ and $opt_source eq 'masterVar')
+			{
+				-f $file or die "$file is not a valid file.\n";
+				$command .= " --master-var ";
+			}
+			elsif ($file =~ m/Junctions/ and $opt_source eq 'SV')
+			{
+				-f $file or die "$file is not a valid file.\n";
+				$command .= " --junction-file ";
+			}
+			else 
+			{
+				-d $file or die "$file is not a valid directory.\n";
+				$command .= " --genome-root ";
+			}
+			$command .= $file
+		}
+	}
+}
+else
+{die "there is an error in the logic: wrong datasource $opt_datasource.\n";}
+
+if ($opt_calibration)
+{
+	(-r "$opt_calibration/0.0.0/metrics.tsv" or -r "$opt_calibration/version0.0.0/metrics.tsv") or die "This folder does not contain the calibration data\n";
+	$command .= " --calibration-root $opt_calibration";
+}
+
+$opt_fields eq 'all' or $command .= " --field-names $opt_fields";
+$opt_nocalls and $command .= " --include-no-calls";
+$opt_jctscore and $command .= " --junction-score-threshold $opt_jctscore";
+$opt_jctside and $command .= " --junction-side-length-threshold $opt_jctside";
+$opt_jctdistance and $command .= " --junction-distance-tolerance $opt_jctdistance";
+$opt_jctlength and $command .= " --junction-length-threshold $opt_jctlength";
+$opt_jctpriority and $command .= " --junction-normal-priority";
+$opt_jcttumor and $command .= " --junction-tumor-hc";
+
+my $version = `cgatools | head -1`;
+print "$version\n";
+print "$command \n";
+
+`$command`;
\ No newline at end of file