--- a/bcftools_gtcheck.xml	Wed Jul 13 10:50:59 2016 -0400
+++ b/bcftools_gtcheck.xml	Sat Jan 21 06:52:48 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
     <description>Check sample identity</description>
     <macros>
         <token name="@EXECUTABLE@">gtcheck</token>
@@ -15,16 +15,16 @@
 #set $section = $sec_default
 #set $genotypes_vcf = None
 #if $section.genotypes:
-  #if $section.genotypes.datatype.file_ext == 'vcf'
+  #if $section.genotypes.is_of_type('vcf')
     #set $genotypes_vcf = 'genotypes.vcf.gz'
     bgzip -c "$section.genotypes" > $genotypes_vcf &&
     bcftools index $genotypes_vcf &&
-  #elif $section.genotypes.datatype.file_ext == 'bcf'
+  #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 
+    #else
       bcftools index $genotypes_vcf &&
     #end if
   #end if
@@ -80,10 +80,10 @@
             <expand macro="macro_targets" />
         </section>
         <section name="sec_default" expanded="true" title="Default Options">
-            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" 
+            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
                    help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
             <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
-            <param name="GTs_only" type="integer" label="Gts Only" default="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
+            <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
             <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
             <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
             <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
@@ -96,6 +96,7 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="GTs_only" value="" />
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>