--- a/stacks_genotypes.xml	Fri Apr 07 11:48:36 2017 -0400
+++ b/stacks_genotypes.xml	Thu Apr 27 04:19:10 2017 -0400
@@ -12,13 +12,13 @@
 
         &&
 
-        #for $input_file in $input_col:
+        #for $input_file in $input_col
             #set $filename = str($input_file.element_identifier)
-            #if not $filename.endswith('.tsv'):
+            #if not $filename.endswith('.tsv')
                 #set $filename = $filename + ".tsv"
             #end if
-            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename):
-                ln -s "${input_file}" "stacks_outputs/${filename}" &&
+            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename)
+                ln -s '${input_file}' 'stacks_outputs/${filename}' &&
             #end if
         #end for
 
@@ -30,34 +30,34 @@
             -t $options_usage.cross_type
             -o $options_usage.map_out.map_out_type
 
-            #if str( $options_usage.map_out.map_out_type ) == "genomic":
+            #if str( $options_usage.map_out.map_out_type ) == "genomic"
                 -e ${options_usage.map_out.enzyme}
             #end if
 
-            #if str($advanced_options.minprogeny):
+            #if str($advanced_options.minprogeny)
                 -r $advanced_options.minprogeny
             #end if
 
-            #if str($advanced_options.mindepth):
+            #if str($advanced_options.mindepth)
                 -m $advanced_options.mindepth
             #end if
 
-            #if str($advanced_options.lnl):
+            #if str($advanced_options.lnl)
                 --lnl_lim $advanced_options.lnl
             #end if
 
-            #if $advanced_options.blacklist:
-                -B "$advanced_options.blacklist"
+            #if $advanced_options.blacklist
+                -B '$advanced_options.blacklist'
             #end if
-            #if $advanced_options.whitelist:
-                -W "$advanced_options.whitelist"
+            #if $advanced_options.whitelist
+                -W '$advanced_options.whitelist'
             #end if
 
-            #if $advanced_options.manual_cor:
-                --corr_path "$advanced_options.manual_cor"
+            #if $advanced_options.manual_cor
+                --corr_path '$advanced_options.manual_cor'
             #end if
 
-            #if $options_autocorr.corrections:
+            #if $options_autocorr.corrections
                 -c
                 --min_hom_seqs $options_autocorr.hom
                 --min_het_seqs $options_autocorr.het
@@ -68,6 +68,10 @@
             -s
 
             @NORM_GENOTYPES_OUTPUT_FULL@
+
+            &&
+
+            stacks_summary.py --stacks-prog genotypes --res-dir stacks_outputs --summary stacks_outputs/summary.html
     ]]></command>
     <inputs>
         <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" />
@@ -85,6 +89,9 @@
                     <option value="rqtl">R/QTL</option>
                     <option value="genomic">Genomic</option>
                 </param>
+                <when value="joinmap"/>
+                <when value="onemap"/>
+                <when value="rqtl"/>
                 <when value="genomic">
                     <param name="enzyme" argument="-e" type="select" label="Restriction enzyme used" help="Only needed for Genomic output format">
                         <expand macro="enzymes"/>
@@ -120,6 +127,8 @@
     </inputs>
     <outputs>
         <expand macro="genotypes_output_full"/>
+
+        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
     </outputs>
 
     <tests>
@@ -143,6 +152,12 @@
             <param name="cross_type" value="CP" />
             <param name="advanced_options|minprogeny" value="1" />
 
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
+
             <!-- genotypes -->
             <output name="out_generic_haplo">
                 <assert_contents>