diff hyphy_absrel.xml @ 9:cce7b18495e4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
author iuc
date Fri, 27 Mar 2020 13:14:17 -0400
parents f73435dc282b
children 4cc4dbca2f02
line wrap: on
line diff
--- a/hyphy_absrel.xml	Thu Mar 19 10:14:27 2020 -0400
+++ b/hyphy_absrel.xml	Fri Mar 27 13:14:17 2020 -0400
@@ -17,6 +17,8 @@
             #if $log:
                 > '$absrel_log'
             #end if
+            ;
+        @CATCH_MPIERR@
         ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -39,10 +41,10 @@
         </test>
     </tests>
     <help><![CDATA[
-    
+
 aBSREL : Adaptive Branch-Site Random Effects Likelihood
-=======================================================  
-    
+=======================================================
+
 What question does this method answer?
 --------------------------------------
 
@@ -52,7 +54,7 @@
 ------------------------
 
 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) 
+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
 -----------------
@@ -77,7 +79,7 @@
 
 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/aBSREL for an example)
@@ -93,22 +95,22 @@
 ::
 
 
-    --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>
     <expand macro="citations">