# HG changeset patch
# User ucsb-phylogenetics
# Date 1340315215 14400
# Node ID 4de3f95726153dba8400f2973914f7ddf9a5fa6d
# Parent  de3ada25282ec2c9f01117483c2a44de4d914a0f
Uploaded

diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic
Binary file phylomatic/phylomatic has changed
diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylomatic/phylomatic.pl	Thu Jun 21 17:46:55 2012 -0400
@@ -0,0 +1,10 @@
+#!/usr/bin/perl
+
+#wrapper written by Roger Ngo and Todd H Oakley, UCSB
+
+my $file1 = $ARGV[0];
+my $file2 = $ARGV[1];
+
+my $run = qx/phylomatic -f $file1 -t $file2 > output.txt 2> errors.txt /;
+
+print $run;
diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylomatic/phylomatic.xml	Thu Jun 21 17:46:55 2012 -0400
@@ -0,0 +1,29 @@
+<tool id="phylomatic" name="Phylomatic">
+	<description>Run Phylomatic</description>
+	<command interpreter="perl">./phylomatic.pl $input1 $input2</command>
+	<inputs>
+		<param name="input1" type="data" format="txt" label="Phylogenetic Tree" />
+		<param name="input2" type="data" format="txt" label="Taxonomy File" />
+	</inputs>
+
+	<outputs>
+		<data from_work_dir="output.txt"/>
+	</outputs>
+	
+	<help>
+	Phylomatic (Part of Phylocom)
+	
+	http://www.phylodiversity.net/phylomatic/phylomatic.html
+	
+	The online software takes your list of taxa, and first tries to match them by genus name to the megatree. 
+	Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. 
+	If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. 
+	Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
+	(http://www.phylodiversity.net/phylomatic/phylomatic_old.html)
+	
+	http://bioinformatics.oxfordjournals.org/content/24/18/2098
+	Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100.
+
+	</help>
+</tool>
+
diff -r de3ada25282e -r 4de3f9572615 phylomatic/phylomatic_README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylomatic/phylomatic_README.txt	Thu Jun 21 17:46:55 2012 -0400
@@ -0,0 +1,50 @@
+Phylomatic (Part of Phylocom)
+
+
+http://www.phylodiversity.net/phylomatic/phylomatic.html
+	
+	
+
+"The online software takes your list of taxa, and first tries to match them by genus name to the megatree. 
+	
+Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. 
+	
+If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. 
+	
+Currently, species are not included in the megatree, and species within a genus are always returned as polytomies.
+	(http://www.phylodiversity.net/phylomatic/phylomatic_old.html)
+"	
+http://bioinformatics.oxfordjournals.org/content/24/18/2098
+	
+
+Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. 
+	Bioinformatics, 24: 2098-2100.
+
+
+Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB
+
+Included in this package:
+
+* phylomatic - binary file
+* phylomatic.pl - wrapper perl script for Galaxy
+* phylomatic.xml - Galaxy tool file
+* phylomatic_README.txt - documentation file
+
+Installation instruction:
+
+1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy
+user account.
+
+2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/
+directory.
+
+3. Add the XML information in tool_conf.xml in /galaxy-dist/
+
+4. Restart Galaxy using:
+
+./run.sh --stop-daemon
+./run.sh --reload --daemon
+
+Known Issues:
+Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper
+script is used to redirect any warnings generated by the binary file to a log file. 
\ No newline at end of file