# HG changeset patch
# User damion
# Date 1429825659 14400
# Node ID 79a4a86981d33ccca9a26b931a295bbc4618d866
# Parent  671667722d3d7fd4369d98b6200e07bbc56cebc0
Uploaded

diff -r 671667722d3d -r 79a4a86981d3 README.md
--- a/README.md	Fri Mar 20 14:27:19 2015 -0400
+++ b/README.md	Thu Apr 23 17:47:39 2015 -0400
@@ -9,6 +9,8 @@
 
 The original command line ffp-phylogeny code is at http://ffp-phylogeny.sourceforge.net/ .  This tool uses Aaron Petkau's modified version: https://github.com/apetkau/ffp-3.19-custom .  Aaron has quite a good writeup of the technique as well at https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny .
 
+**Installation Note** : Your Galaxy server will need the groff package to be installed on it first (to generate ffp-phylogeny man pages).  A cryptic error will occur if it isn't: "troff: fatal error: can't find macro file s".  This is different from the "groff-base" package.
+
 This Galaxy tool prepares a mini-pipeline consisting of **[ffpry | ffpaa | ffptxt] > [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree**  .  The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output a distance matrix rather than a Newick (.nhx) formatted tree file.
 
 Each sequence or text file has a profile containing tallies of each feature found.  A feature is a string of valid characters of given length. 
diff -r 671667722d3d -r 79a4a86981d3 ffp_phylogeny.py
--- a/ffp_phylogeny.py	Fri Mar 20 14:27:19 2015 -0400
+++ b/ffp_phylogeny.py	Thu Apr 23 17:47:39 2015 -0400
@@ -245,7 +245,7 @@
 			help='Enables pearson correlation coefficient matrix and any of the binary distance measures to be turned into similarity matrixes.')
 		
 		parser.add_option('-f', '--filter', type='choice', dest='filter', default='none',
-			choices=['none','f','n','e','freq','norm','evd'],
+			choices=['none','count','f','n','e','freq','norm','evd'],
 			help='Choice of [f=raw frequency|n=normal|e=extreme value (Gumbel)] distribution: Features are trimmed from the data based on lower/upper cutoff points according to the given distribution.')
 
 		parser.add_option('-L', '--lower', type='float', dest='lower', 
diff -r 671667722d3d -r 79a4a86981d3 ffp_phylogeny.xml
--- a/ffp_phylogeny.xml	Fri Mar 20 14:27:19 2015 -0400
+++ b/ffp_phylogeny.xml	Thu Apr 23 17:47:39 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.03">
+<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.04">
 	<description>An alignment free comparison tool for phylogenetic analysis and text comparison</description>
 	<requirements>
 		<requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement>
@@ -44,7 +44,7 @@
 				-a
 			#end if			
 		#end if
-		#if $phylogeny.phylo_type == 'filter'
+		#if $phylogeny.phylo_type == 'filt'
 			-f "$phylogeny.filt.filter_type"
 			-L "$phylogeny.filt.lower"
 			-U "$phylogeny.filt.upper" 
diff -r 671667722d3d -r 79a4a86981d3 test.txt
--- a/test.txt	Fri Mar 20 14:27:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-(2010EL_1798_v2_fa:8.45000000e-05,(2010EL_1786_v2_fa:7.20000000e-05,
-2010EL_1796_v2_fa:1.25000000e-04):1.65000000e-05,2010EL_1749_v2_fa:1.11500000e-04);