--- a/stacks_gstacks.xml	Wed Feb 27 09:56:44 2019 -0500
+++ b/stacks_gstacks.xml	Thu Jun 20 08:15:23 2019 -0400
@@ -172,7 +172,7 @@
                 <option value="snp">snp</option>
             </param>
             <when value="marukilow">
-                <expand macro="variant_calling_options_vg"/>
+                <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
             </when>
             <when value="marukihigh">
                 <expand macro="variant_calling_options_vg"/>
@@ -199,7 +199,7 @@
             </conditional>
             <param name="add_log" value="yes" />
             <param name="add_log_distribs" value="yes" />
-            <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="6"/>
+            <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
             <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/>
             <output_collection name="gstacks_out" type="list" count="2">
                 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
@@ -304,6 +304,7 @@
             </conditional>
             <param name="model_cond|model" value="snp"/>
             <param name="model_cond|gt_alpha" value="0.1" />
+            <param name="model_cond|var_alpha" value="0.1" />
             <param name="add_log" value="yes" />
             <assert_command>
                 <not_has_text text="-I bam_inputs" />
@@ -370,7 +371,9 @@
 
 **Output files**
 
-TODO
+- Assembled contigs and variant sites
+
+- Optional outputs: Read alignments and log.distribs
 
 @STACKS_INFOS@
 ]]>