diff hyphy_meme.xml @ 8:3d1f153e2aa1 draft

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

--- a/hyphy_meme.xml	Thu Mar 19 10:16:22 2020 -0400
+++ b/hyphy_meme.xml	Fri Mar 27 13:18:02 2020 -0400
@@ -16,6 +16,8 @@
             --pvalue '$p_value'
             --output '$meme_output'
             > '$meme_log'
+            ;
+        @CATCH_MPIERR@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -39,7 +41,7 @@
     <help><![CDATA[
 MEME: Mixed Effects Model of Evolution
 ======================================
-    
+
 What question does this method answer?
 --------------------------------------
 
@@ -49,13 +51,13 @@
 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. 
-MEME is ideally suited to identify sites under positive selection which 
+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.
+MEME is ideally suited to identify sites under positive selection which
 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
 
-MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection. 
-MEME is therefore our recommended method if maximum power is desired. 
+MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
+MEME is therefore our recommended method if maximum power is desired.
 
 
 Brief description
@@ -99,23 +101,23 @@
 ::
 
 
-    --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
-     
+
 
     ]]></help>
     <expand macro="citations">