diff hyphy_busted.xml @ 6:f9a193154a55 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"

--- a/hyphy_busted.xml	Mon Feb 17 14:50:45 2020 -0500
+++ b/hyphy_busted.xml	Thu Feb 20 18:16:58 2020 -0500
@@ -33,12 +33,83 @@
         </test>
     </tests>
     <help><![CDATA[
-BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection.
+    
+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. 
+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)? 
+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
+-----------------
+
+BUSTED (branch-site unrestricted statistical test of episodic
+diversification) uses a random effects branch-site model fitted jointly
+to all or a subset of tree branches in order to test for alignment-wide
+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. 
+
+
+Input
+-----
+
+1. A *FASTA* sequence alignment.
+2. A phylogenetic tree in the *Newick* format
+
+Note: the names of sequences in the alignment must match the names of the sequences in the tree.
 
-See the online documentation_ for more information.
+
+Output
+------
+
+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, 
+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)
+
+Further reading
+---------------
+
+http://hyphy.org/methods/selection-methods/#busted
+
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#busted
-    ]]></help>
+Tool options
+------------
+::
+
+
+    --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 
+                            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 
+                            (see http://hyphy.org/tutorials/phylotree/)
+    ]]>
+    </help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msv035</citation>
     </expand>