diff hyphy_fel.xml @ 9:8389039f7fbc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"

--- a/hyphy_fel.xml	Thu Mar 19 10:17:07 2020 -0400
+++ b/hyphy_fel.xml	Fri Mar 27 13:19:17 2020 -0400
@@ -17,6 +17,8 @@
             --pvalue '$p_value'
             --output '$fel_output'
             > '$fel_log'
+            ;
+        @CATCH_MPIERR@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -42,7 +44,7 @@
     <help><![CDATA[
 FEL : Fixed effects likelihood
 ==============================
-    
+
 What question does this method answer?
 --------------------------------------
 
@@ -51,9 +53,9 @@
 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. 
+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.
 
@@ -67,7 +69,7 @@
 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. 
+testing.
 
 
 Input
@@ -96,33 +98,33 @@
 
 ::
 
-    --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 
-                            (see http://hyphy.org/tutorials/phylotree/)    
-                        
+                            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>