# HG changeset patch
# User greg
# Date 1507919070 14400
# Node ID c2b9081064f0879d3d84dccc7a9e8d253f30c144
# Parent  9c9c2ea494ba2f190cfb25929377ab17d68cb428
Uploaded

diff -r 9c9c2ea494ba -r c2b9081064f0 gene_family_aligner.xml
--- a/gene_family_aligner.xml	Mon Oct 09 08:56:27 2017 -0400
+++ b/gene_family_aligner.xml	Fri Oct 13 14:24:30 2017 -0400
@@ -61,8 +61,8 @@
             </when>
         </conditional>
         <param name="codon_alignments" type="select" label="Codon alignments">
-            <option value="yes" selected="true">Yes</option>
-            <option value="no">No</option>
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
         </param>
         <conditional name="remove_gappy_sequences_cond">
             <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
@@ -135,6 +135,26 @@
     </outputs>
     <tests>
         <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"/>
+                </collection>
+            </param>
+            <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"/>
+                <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/>
+            </output_collection>
+            <output_collection name="primary_fna" type="list">
+                <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
+                <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
+                <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
+            </output_collection>
         </test>
     </tests>
     <help>
@@ -152,7 +172,7 @@
 
   - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
 
- * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments.  This option requires protein and their corresponding coding sequences to be provided as input data.
+ * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments.  This option requires both protein and their corresponding coding sequence orthogroup fasta files to be present in the GeneFamilyAligner input data that was produced by the GeneFamilyIntegrator.
 
 **Other options**