diff hyphy_absrel.xml @ 6:f73435dc282b draft

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

--- a/hyphy_absrel.xml	Mon Feb 17 14:51:50 2020 -0500
+++ b/hyphy_absrel.xml	Thu Feb 20 18:17:51 2020 -0500
@@ -39,11 +39,77 @@
         </test>
     </tests>
     <help><![CDATA[
-aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
+    
+aBSREL : Adaptive Branch-Site Random Effects Likelihood
+=======================================================  
+    
+What question does this method answer?
+--------------------------------------
+
+Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?
+
+Recommended Applications
+------------------------
+
+1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
+2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) 
+
+Brief description
+-----------------
+
+aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
+random effects branch-site model framework to test whether each branch
+has evolved under positive selection, using a procedure which infers an
+optimal number of rate categories per branch.
+
+
+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.
+
+
+Output
+------
 
-See the online documentation_ for more information.
+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/aBSREL for an example)
+
+Further reading
+---------------
+
+http://hyphy.org/methods/selection-methods/#absrel
+
+
+Tool options
+------------
+::
+
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#absrel
+    --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/msv022</citation>