--- a/stacks_refmap.xml	Wed Feb 27 09:48:50 2019 -0500
+++ b/stacks_refmap.xml	Thu Jun 20 08:11:14 2019 -0400
@@ -30,14 +30,14 @@
 
     <inputs>
         <expand macro="bam_input_macro"/>
-        <param argument="--popmap" type="data" format="tabular,txt" label="Population map" />
+        <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
         <param name="paired_select" type="select" label="Paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input">
             <option value="" selected="true">single/paired</option>
             <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
             <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
         </param>
         <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
-            <expand macro="variant_calling_options_vg"/>
+            <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
         </section>
         <expand macro="in_log"/>
     </inputs>