# HG changeset patch
# User ucsb-phylogenetics
# Date 1340569018 14400
# Node ID eb55013e0f28bb250c2b21d515e18e395e25fff0
# Parent  5b23f3eb3f0989de863a3e2e2aca48fb7f943cc7
Added tree annotator from BEAST.

diff -r 5b23f3eb3f09 -r eb55013e0f28 ucsb_phylogenetics/treeannotator/treeannotator.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsb_phylogenetics/treeannotator/treeannotator.pl	Sun Jun 24 16:16:58 2012 -0400
@@ -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; 
diff -r 5b23f3eb3f09 -r eb55013e0f28 ucsb_phylogenetics/treeannotator/treeannotator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsb_phylogenetics/treeannotator/treeannotator.xml	Sun Jun 24 16:16:58 2012 -0400
@@ -0,0 +1,42 @@
+<tool id="beast_tree_annotator172" name="Tree Annotator (BEAST 1.7.2)" version="1.0.2">
+	<description>Runs BEAST 1.7.2 Tree Annotator</description>
+	<requirements>
+		<requirement type="binary">BEAST 1.7.2</requirement>
+	</requirements>
+	<command interpreter="perl">treeannotator.pl $input $burnin $node_heights</command>
+	<inputs>
+		<param name="input" type="data" format="trees" label="Input file" />
+		<param name="burnin" value="0" type="integer" label="Burnin" />
+		<param name="node_heights" type="select" label="Node heights" >
+			<option value="0">Keep</option>
+			<option value="1">Median</option>
+			<option value="2">Mean</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data from_work_dir="out.tre" />
+	</outputs>
+
+	<help>
+		TreeAnnotator is a part of BEAST 1.7.2.
+		
+		http://beast.bio.ed.ac.uk/Main_Page
+		
+		This program assists in summarizing the information from a sample of trees produced by BEAST onto a single “target” tree. 
+		The summary information includes the posterior probabilities of the nodes in the target tree, the posterior estimates and HPD limits of the node heights and (in the case of a relaxed molecular clock model) the rates.
+		
+		Burnin: This option allows you to select the amount of burn-in, i.e., the number of samples that will be discarded at the start of the run, so that you are only analysing the part of the trace that is in equilibrium.
+		
+		Node heights: This option allows you select how the node heights are summarised on the target tree. You can choose to keep the heights that the target tree has, or rescale it to reflect the posterior mean/median node heights for the clades contained in the target tree.
+		
+		http://beast.bio.ed.ac.uk/TreeAnnotator
+		
+		Citations:
+		
+		http://mbe.oxfordjournals.org/content/early/2012/02/25/molbev.mss075.abstract
+		Drummond AJ, Suchard MA, Xie D and Rambaut A "Bayesian phylogenetics with BEAUti and the BEAST 1.7" "Molecular Biology And Evolution" "in press"
+		
+		
+		
+	</help>
+</tool>
diff -r 5b23f3eb3f09 -r eb55013e0f28 ucsb_phylogenetics/treeannotator/treeannotator_README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsb_phylogenetics/treeannotator/treeannotator_README.txt	Sun Jun 24 16:16:58 2012 -0400
@@ -0,0 +1,51 @@
+TreeAnnotator is a part of BEAST 1.7.2.
+	
+http://beast.bio.ed.ac.uk/Main_Page
+		
+		
+
+This program assists in summarizing the information from a sample of trees produced by BEAST onto a single “target” tree. 
+		
+The summary information includes the posterior probabilities of the nodes in the target tree, the posterior estimates and HPD limits of the node heights and (in the case of a relaxed molecular clock model) the rates.
+		
+		
+http://beast.bio.ed.ac.uk/TreeAnnotator
+		
+		
+
+Citations:
+		
+		
+http://mbe.oxfordjournals.org/content/early/2012/02/25/molbev.mss075.abstract
+		
+Drummond AJ, Suchard MA, Xie D and Rambaut A "Bayesian phylogenetics with BEAUti and the BEAST 1.7" "Molecular Biology And Evolution" "in press"
+
+Galaxy XML and Perl wrapper written by: Roger Ngo and Todd H.Oakley, UCSB
+
+Tree Annotator is a part of BEAST 1.7.2. It is required that BEAST 1.7.2 be installed
+in your Galaxy user account in order for the Perl wrapper to execute properly.
+
+Required files included in this package:
+
+* treeannotator.pl - Perl wrapper script for BEAST 1.7.2 Tree Annnotator
+* treeannotator.xml - Galaxy XML tool for the Perl wrapper script.
+* treeannotator_README.txt - Documentation file
+
+To install this wrapper:
+
+1. First modify the $treeannotator_path in the treeannotator.pl script to reflect your
+installation of BEAST 1.7.2.
+
+The default variable is: my $treeannotator_path = '/home/galaxy/pkgs/BEAST172/bin/treeannotator';
+
+2. Copy treeannotator.pl and treeannotator.xml to a folder in /galaxy-dist/tools
+
+3. Add the XML to the tool_conf.xml file in /galaxy-dist/ 
+
+4. Restart Galaxy with
+
+./run.sh --stop-daemon
+
+and then
+
+./run.sh --reload --daemon
\ No newline at end of file
diff -r 5b23f3eb3f09 -r eb55013e0f28 ucsb_phylogenetics/trimmingreads/TrimmingReads.xml
--- a/ucsb_phylogenetics/trimmingreads/TrimmingReads.xml	Sun Jun 24 16:02:29 2012 -0400
+++ b/ucsb_phylogenetics/trimmingreads/TrimmingReads.xml	Sun Jun 24 16:16:58 2012 -0400
@@ -1,5 +1,8 @@
-<tool id="trimming_reads" name="TrimmingReads">
+<tool id="trimming_reads" name="TrimmingReads" version="1.0.1">
 	<description>Runs TrimmingReads</description>
+	<requirements>
+		<requirement type="binary">IlluQC Toolkit</requirement>
+	</requirements>
 	<command interpreter="perl">TrimmingReads.pl -i $input -l $l_int -o out.fastq -r $r_int -q $q_int -n $len_int</command>
 	<inputs>
 		<param name="input" label="Input file" type="data" format="fastq"/>