--- a/bcftools_gtcheck.xml	Sat Mar 11 17:59:29 2017 -0500
+++ b/bcftools_gtcheck.xml	Thu Apr 13 17:43:41 2017 -0400
@@ -12,16 +12,17 @@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
 #set $section = $sec_default
 #set $genotypes_vcf = None
 #if $section.genotypes:
   #if $section.genotypes.is_of_type('vcf')
     #set $genotypes_vcf = 'genotypes.vcf.gz'
-    bgzip -c "$section.genotypes" > $genotypes_vcf &&
+    bgzip -c '$section.genotypes' > $genotypes_vcf &&
     bcftools index $genotypes_vcf &&
   #elif $section.genotypes.is_of_type('bcf')
     #set $genotypes_vcf = 'genotypes.bcf'
-    ln -s "$ection.genotypes" $genotypes_vcf &&
+    ln -s '$ection.genotypes' $genotypes_vcf &&
     #if $section.genotypes.metadata.bcf_index:
       ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
     #else
@@ -40,27 +41,27 @@
 #end if
 
 #if $section.genotypes:
-  --genotypes "${section.genotypes}"
+  --genotypes '${section.genotypes}'
 #end if
 
 ${section.all_sites}
 
 #if $section.GTs_only:
-  --GTs-only "${section.GTs_only}"
+  --GTs-only '${section.GTs_only}'
 #end if
 
 ${section.homs_only}
 
 #if $section.plot:
-  --plot "${section.plot}"
+  --plot '${section.plot}'
 #end if
 
 #if $section.query_sample:
-  --query-sample "${section.query_sample}"
+  --query-sample '${section.query_sample}'
 #end if
 
 #if $section.target_sample:
-  --target-sample "${section.target_sample}"
+  --target-sample '${section.target_sample}'
 #end if
 
 #set $section = $sec_restrict
@@ -70,7 +71,7 @@
 ## Primary Input/Outputs
 
 @INPUT_FILE@
-> "$output_file"
+> '$output_file'
 ]]>
     </command>
     <inputs>
@@ -96,11 +97,10 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="GTs_only" value="" />
+            <param name="GTs_only" value="99" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
-                    <has_text_matching expression="CN\t1174\t14\t75.57\tNA00002\tNA00001"/>
+                    <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/>
                 </assert_contents>
             </output>
         </test>