Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

diff phylogenies/beast_treeannotator.pl @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/beast_treeannotator.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,23 @@
+#!/usr/bin/perl
+
+my $treeannotator_path = '/home/galaxy/pkgs/BEAST172/bin/treeannotator';
+
+my $input = $ARGV[0];
+my $burnin = $ARGV[1];
+my $Node_heights = $ARGV[2];
+
+my $node_opt;
+
+if($Node_heights eq "0") {
+	$node_opt = "keep";
+}
+elsif($Node_heights eq "1") {
+	$node_opt = "median";
+}
+elsif($Node_heights eq "2") {
+	$node_opt = "mean";
+}
+
+my $run = qx/$treeannotator_path -heights $node_opt -burnin $burnin $input out.tre 2>log.txt/;
+
+print $run;