# HG changeset patch
# User iuc
# Date 1608753847 0
# Node ID b8bdfac5a32646185fd139f2be11b69a6c1ddc27
# Parent  ba548f24669a30c164ddf5a50ba9df10abb85b89
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8f76cb8602f79412152a92b267ee016605ae6b8e"

diff -r ba548f24669a -r b8bdfac5a326 hyphy_relax.xml
--- a/hyphy_relax.xml	Thu Nov 19 22:02:32 2020 +0000
+++ b/hyphy_relax.xml	Wed Dec 23 20:04:07 2020 +0000
@@ -9,10 +9,13 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' relax_input.fa &&
         ln -s '$input_nhx' relax_input.nhx &&
+
+        export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
         hyphy relax
             --alignment ./relax_input.fa
             --tree ./relax_input.nhx
             --models '$analysisType'
+            --code '$gencodeid'
             #if $treeAnnotations == "2":
                 --test TEST
                 --reference REFERENCE
@@ -51,7 +54,7 @@
 What question does this method answer?
 --------------------------------------
 
-Is there ev- idence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST)
+Is there evidence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST)
 relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically.
 We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address,
 or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation.
diff -r ba548f24669a -r b8bdfac5a326 macros.xml
--- a/macros.xml	Thu Nov 19 22:02:32 2020 +0000
+++ b/macros.xml	Wed Dec 23 20:04:07 2020 +0000
@@ -107,7 +107,7 @@
             <yield/>
         </citations>
     </xml>
-    <token name="@VERSION@">2.5.23</token>
+    <token name="@VERSION@">2.5.24</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">hyphy</requirement>