diff hyphy_fel.xml @ 6:4eba0baf0278 draft

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

--- a/hyphy_fel.xml	Mon Feb 17 14:54:30 2020 -0500
+++ b/hyphy_fel.xml	Thu Feb 20 18:15:14 2020 -0500
@@ -23,7 +23,7 @@
         <expand macro="gencode"/>
         <expand macro="branches"/>
         <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
-        <param name="include_srv" type="select" label="Include synonymous rate variation">
+        <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
             <option value="Yes">Yes (recommended)</option>
             <option value="No">No</option>
         </param>
@@ -40,12 +40,89 @@
         </test>
     </tests>
     <help><![CDATA[
-FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny.
+FEL : Fixed effects likelihood
+==============================
+    
+What question does this method answer?
+--------------------------------------
+
+Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
+
+Recommended Applications
+------------------------
+
+The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics 
+(or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which 
+represent candidate sites subject to strong selective pressures across the entire phylogeny. 
+
+FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites.
+
+Brief description
+-----------------
+
+FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha)
+and non-synonymous rates (beta), and uses a likelihood ratio test to
+determine if beta != alpha at a site. The estimates aggregate
+information over all branches, so the signal is derived from pervasive
+diversification or conservation. A subset of branches can be selected
+for testing as well, in which case an additional (nuisance) parameter
+will be inferred -- the non-synonymous rate on branches NOT selected for
+testing. 
+
+
+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).
+A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example)
+
+Further reading
+---------------
+
+http://hyphy.org/methods/selection-methods/#FEL
+
+
+Tool options
+------------
+
+::
+
+    --code              Which genetic code to use 
 
-.. _documentation: http://hyphy.org/methods/selection-methods/#fel
-    ]]></help>
+    --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/)    
+                        
+     --pvalue           The significance level used to determine significance
+ 
+     --srv              Include site-to-site synonymous rate variation?
+                            Yes [default] or No
+
+
+
+                            
+]]>
+
+    </help>
+    
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msi105</citation>
     </expand>