--- a/hyphy_relax.xml	Thu Nov 19 21:53:06 2020 +0000
+++ b/hyphy_relax.xml	Wed Dec 23 19:54:44 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.