# HG changeset patch
# User iuc
# Date 1587572017 14400
# Node ID cde38657e82c7a47b9e03317450199c834be0186
# Parent  6647e04e92a7bd7ebb4a217231b97cd54b8adf7a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"

diff -r 6647e04e92a7 -r cde38657e82c hyphy_busted.xml
--- a/hyphy_busted.xml	Fri Mar 27 12:30:54 2020 -0400
+++ b/hyphy_busted.xml	Wed Apr 22 12:13:37 2020 -0400
@@ -33,23 +33,23 @@
         </test>
     </tests>
     <help><![CDATA[
-    
+
 BUSTED : Bayesian UnresTricted Test of Episodic Diversification
-===============================================================  
-    
+===============================================================
+
 What question does this method answer?
 --------------------------------------
 
-Is there evidence that some sites in the alignment have been subject to positive diversifying selection, 
-either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? 
-In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. 
+Is there evidence that some sites in the alignment have been subject to positive diversifying selection,
+either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)?
+In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time.
 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.),
 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
 
 Recommended Applications
 ------------------------
 
-1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? 
+1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)?
 2. Testing small or low-divergence alignments (i.e. ~30 sequences) for evidence of positive diversifying selection, where neither branch nor site level methods have sufficient power.
 
 Brief description
@@ -61,7 +61,7 @@
 evidence of episodic diversifying selection. Assuming there is evidence
 of positive selection (i.e. there is an omega > 1), BUSTED will also
 perform a quick evidence-ratio style analysis to explore which
-individual sites may have been subject to selection. 
+individual sites may have been subject to selection.
 
 
 Input
@@ -78,7 +78,7 @@
 
 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
 
-For each tested branch the analysis will infer the appropriate number of selective regimes, 
+For each tested branch the analysis will infer the appropriate number of selective regimes,
 and whether or not there is statistical evidence of positive selection on that branch.
 
 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
@@ -94,19 +94,19 @@
 ::
 
 
-    --code              Which genetic code to use 
+    --code              Which genetic code to use
 
     --branches          Which branches should be tested for selection?
                             All [default] : test all branches
-                            
-                            Internal : test only internal branches (suitable for 
+
+                            Internal : test only internal branches (suitable for
                             intra-host pathogen evolution for example, where terminal branches
                             may contain polymorphism data)
-                            
+
                             Leaves: test only terminal (leaf) branches
-                            
+
                             Unlabeled: if the Newick string is labeled using the {} notation,
-                            test only branches without explicit labels 
+                            test only branches without explicit labels
                             (see http://hyphy.org/tutorials/phylotree/)
     ]]>
     </help>
diff -r 6647e04e92a7 -r cde38657e82c macros.xml
--- a/macros.xml	Fri Mar 27 12:30:54 2020 -0400
+++ b/macros.xml	Wed Apr 22 12:13:37 2020 -0400
@@ -106,7 +106,7 @@
             <yield/>
         </citations>
     </xml>
-    <token name="@VERSION@">2.5.8</token>
+    <token name="@VERSION@">2.5.9</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">hyphy</requirement>