--- a/stacks_refmap.xml	Fri Apr 07 11:46:59 2017 -0400
+++ b/stacks_refmap.xml	Thu Apr 27 04:17:01 2017 -0400
@@ -6,54 +6,42 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
-        #from os.path import splitext
-        #import re
+
+        @CLEAN_EXT@
 
-        #if str( $options_usage.rad_analysis_type ) == "genetic":
-            #for $input_parent in $options_usage.parent_alignments:
-                #if $input_parent.is_of_type('sam'):
-                    #set $data_path = splitext($input_parent.element_identifier)[0]
-                    #set $data_path = re.sub(r'\.1$', '', $data_path)
-                    #set $data_path = $data_path + ".sam"
-                #else:
-                    #set $data_path = splitext($input_parent.element_identifier)[0]
-                    #set $data_path = re.sub(r'\.1$', '', $data_path)
-                    #set $data_path = $data_path + ".bam"
+        #if str( $options_usage.rad_analysis_type ) == "genetic"
+            #for $input_parent in $options_usage.parent_alignments
+                #if $input_parent.is_of_type('sam')
+                    #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"
+                #else
+                    #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"
                 #end if
 
-                ln -s "${input_parent}" "${data_path}" &&
+                ln -s '${input_parent}' '${data_path}' &&
             #end for
 
-            #for $input_progeny in $options_usage.progeny_alignments:
+            #for $input_progeny in $options_usage.progeny_alignments
 
-                #if $input_progeny:
-                    #if $input_progeny.is_of_type('sam'):
-                        #set $data_path = splitext($input_progeny.element_identifier)[0]
-                        #set $data_path = re.sub(r'\.1$', '', $data_path)
-                        #set $data_path = $data_path + ".sam"
-                    #else:
-                        #set $data_path = splitext($input_progeny.element_identifier)[0]
-                        #set $data_path = re.sub(r'\.1$', '', $data_path)
-                        #set $data_path = $data_path + ".bam"
+                #if $input_progeny
+                    #if $input_progeny.is_of_type('sam')
+                        #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
+                    #else
+                        #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"
                     #end if
 
-                    ln -s "${input_progeny}" "${data_path}" &&
+                    ln -s '${input_progeny}' '${data_path}' &&
                 #end if
             #end for
-        #else:
-            #for $input_indiv in $options_usage.individual_sample:
+        #else
+            #for $input_indiv in $options_usage.individual_sample
 
-                #if $input_indiv.is_of_type('sam'):
-                    #set $data_path = splitext($input_indiv.element_identifier)[0]
-                    #set $data_path = re.sub(r'\.1$', '', $data_path)
-                    #set $data_path = $data_path + ".sam"
-                #else:
-                    #set $data_path = splitext($input_indiv.element_identifier)[0]
-                    #set $data_path = re.sub(r'\.1$', '', $data_path)
-                    #set $data_path = $data_path + ".bam"
+                #if $input_indiv.is_of_type('sam')
+                    #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
+                #else
+                    #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"
                 #end if
 
-                ln -s "${input_indiv}" "${data_path}" &&
+                ln -s '${input_indiv}' '${data_path}' &&
             #end for
         #end if
 
@@ -65,60 +53,48 @@
 
             -T \${GALAXY_SLOTS:-1}
 
-            #if str( $options_usage.rad_analysis_type ) == "genetic":
-                #for $input_parent in $options_usage.parent_alignments:
-                    #if $input_parent.is_of_type('sam'):
-                        #set $data_path = splitext($input_parent.element_identifier)[0]
-                        #set $data_path = re.sub(r'\.1$', '', $data_path)
-                        #set $data_path = $data_path + ".sam"
-                    #else:
-                        #set $data_path = splitext($input_parent.element_identifier)[0]
-                        #set $data_path = re.sub(r'\.1$', '', $data_path)
-                        #set $data_path = $data_path + ".bam"
+            #if str( $options_usage.rad_analysis_type ) == "genetic"
+                #for $input_parent in $options_usage.parent_alignments
+                    #if $input_parent.is_of_type('sam')
+                        #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"
+                    #else
+                        #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"
                     #end if
 
-                    -p "${data_path}"
+                    -p '${data_path}'
                 #end for
 
                 -A $options_usage.cross_type
 
-                #for $input_progeny in $options_usage.progeny_alignments:
-                    #if $input_progeny:
-                        #if $input_progeny.is_of_type('sam'):
-                            #set $data_path = splitext($input_progeny.element_identifier)[0]
-                            #set $data_path = re.sub(r'\.1$', '', $data_path)
-                            #set $data_path = $data_path + ".sam"
-                        #else:
-                            #set $data_path = splitext($input_progeny.element_identifier)[0]
-                            #set $data_path = re.sub(r'\.1$', '', $data_path)
-                            #set $data_path = $data_path + ".bam"
+                #for $input_progeny in $options_usage.progeny_alignments
+                    #if $input_progeny
+                        #if $input_progeny.is_of_type('sam')
+                            #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"
+                        #else
+                            #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"
                         #end if
 
-                        -r "${data_path}"
+                        -r '${data_path}'
                     #end if
                 #end for
-            #else:
-                #for $input_indiv in $options_usage.individual_sample:
+            #else
+                #for $input_indiv in $options_usage.individual_sample
 
-                    #if $input_indiv.is_of_type('sam'):
-                        #set $data_path = splitext($input_indiv.element_identifier)[0]
-                        #set $data_path = re.sub(r'\.1$', '', $data_path)
-                        #set $data_path = $data_path + ".sam"
-                    #else:
-                        #set $data_path = splitext($input_indiv.element_identifier)[0]
-                        #set $data_path = re.sub(r'\.1$', '', $data_path)
-                        #set $data_path = $data_path + ".bam"
+                    #if $input_indiv.is_of_type('sam')
+                        #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"
+                    #else
+                        #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"
                     #end if
 
-                    -s "${data_path}"
+                    -s '${data_path}'
                 #end for
-                -O "$options_usage.popmap"
+                -O '$options_usage.popmap'
             #end if
 
-            #if str($m):
+            #if str($m)
                 -m $m
             #end if
-            #if str($P):
+            #if str($P)
                 -P $P
             #end if
 
@@ -129,22 +105,29 @@
             -S
 
             ## snp_model
-            #if str( $snp_options.select_model.model_type) == "bounded":
+            #if str( $snp_options.select_model.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"
                 --alpha $snp_options.select_model.alpha
             #end if
 
             -o stacks_outputs
 
-            #if str( $options_usage.rad_analysis_type ) == "genetic":
+            #if str( $options_usage.rad_analysis_type ) == "genetic"
                 @NORM_GENOTYPES_OUTPUT_LIGHT@
             #end if
 
             ## If input is in bam format, stacks will output gzipped files (no option to control this)
             && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
+
+            &&
+
+            stacks_summary.py --stacks-prog ref_map.pl --res-dir stacks_outputs --logfile stacks_outputs/ref_map.log --summary stacks_outputs/summary.html
+            #if str( $options_usage.rad_analysis_type ) == "population":
+                --pop-map '$options_usage.popmap'
+            #end if
     ]]></command>
 
     <inputs>
@@ -178,6 +161,8 @@
     <outputs>
         <data format="txt" name="output_log" label="ref_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/ref_map.log" />
 
+        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
+
         <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
         <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
         <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
@@ -217,6 +202,11 @@
                     <has_text text="ref_map.pl completed" />
                 </assert_contents>
             </output>
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
 
             <!-- catalog -->
             <output name="catalogsnps">
@@ -306,6 +296,11 @@
                     <has_text text="ref_map.pl completed" />
                 </assert_contents>
             </output>
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
 
             <!-- catalog -->
             <output name="catalogsnps">
@@ -395,6 +390,11 @@
                     <has_text text="ref_map.pl completed" />
                 </assert_contents>
             </output>
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
 
             <!-- catalog -->
             <output name="catalogtags">