# HG changeset patch
# User greg
# Date 1508945220 14400
# Node ID 77fcf796be0e17b71d24db576679ed6d8bb17a1e
# Parent  763a50c4f9fc6bbc1a023708bc5e18bd44f628c5
Uploaded

diff -r 763a50c4f9fc -r 77fcf796be0e gene_family_aligner.xml
--- a/gene_family_aligner.xml	Thu Oct 19 08:54:15 2017 -0400
+++ b/gene_family_aligner.xml	Wed Oct 25 11:27:00 2017 -0400
@@ -47,6 +47,7 @@
         #end if
     #end if
 #end if
+&>proc.log
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
@@ -134,14 +135,15 @@
         <test>
             <param name="input">
                 <collection type="list">
-                <element name="3722.faa" value="3722.faa"/>
-                <element name="3722.fna" value="3722.fna"/>
-                <element name="38889.faa" value="38889.faa"/>
-                <element name="38889.fna" value="38889.fna"/>
-                <element name="39614.faa" value="39614.faa"/>
-                <element name="39614.fna" value="39614.fna"/>
+                    <element name="3722.faa" value="3722.faa"/>
+                    <element name="3722.fna" value="3722.fna"/>
+                    <element name="38889.faa" value="38889.faa"/>
+                    <element name="38889.fna" value="38889.fna"/>
+                    <element name="39614.faa" value="39614.faa"/>
+                    <element name="39614.fna" value="39614.fna"/>
                 </collection>
             </param>
+            <param name="codon_alignments" value="yes"/>
             <output_collection name="primary_faa" type="list">
                 <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/>
                 <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/>