--- a/stacks_rxstacks.xml	Fri Apr 07 11:48:48 2017 -0400
+++ b/stacks_rxstacks.xml	Thu Apr 27 04:19:22 2017 -0400
@@ -11,12 +11,12 @@
 
         &&
 
-        #for $input_file in $input_col:
+        #for $input_file in $input_col
             #set $ext = ""
-            #if not str($input_file.element_identifier).endswith('.tsv'):
+            #if not str($input_file.element_identifier).endswith('.tsv')
                 #set $ext = ".tsv"
             #end if
-            ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
+            ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
         #end for
 
         rxstacks
@@ -28,32 +28,32 @@
             ## Batch description
             -b 1
 
-            #if str($options_filtering.lnl):
+            #if str($options_filtering.lnl)
                 --lnl_filter
                 --lnl_lim $options_filtering.lnl
             #end if
 
             $options_filtering.lnl_dist
 
-            #if str($options_filtering.conf):
+            #if str($options_filtering.conf)
                 --conf_filter
                 --conf_lim $options_filtering.conf
             #end if
 
-            #if $options_filtering.prune.prune_haplo:
+            #if $options_filtering.prune.prune_haplo == "yes"
                 --prune_haplo
-                #if str($options_filtering.prune.max_haplo):
+                #if str($options_filtering.prune.max_haplo)
                     --max_haplo $options_filtering.prune.max_haplo
                 #end if
             #end if
 
             ## snp_model
-            #if str( $snp_options.select_model.model_type) == "bounded":
+            #if str( $snp_options.select_model.model_type) == "bounded"
                 --model_type bounded
                 --bound_low $snp_options.select_model.bound_low
                 --bound_high $snp_options.select_model.bound_high
                 --alpha $snp_options.select_model.alpha
-            #else if str( $snp_options.select_model.model_type) == "snp":
+            #else if str( $snp_options.select_model.model_type) == "snp"
                 --model_type snp
                 --alpha $snp_options.select_model.alpha
             #else
@@ -73,9 +73,12 @@
             <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/>
 
             <conditional name="prune">
-                <param name="prune_haplo" argument="--prune_haplo" type="boolean" checked="false" label="Prune out non-biological haplotypes unlikely to occur in the population." />
-                <when value="false"></when>
-                <when value="true">
+                <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
                     <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
                 </when>
             </conditional>
@@ -130,7 +133,7 @@
             </param>
             <param name="options_filtering|lnl" value="-10.0" />
             <param name="options_filtering|lnl_dist" value="true" />
-            <param name="options_filtering|prune_haplo" value="true" />
+            <param name="options_filtering|prune_haplo" value="yes" />
             <param name="options_filtering|max_haplo" value="1" />
 
             <output name="output_log">