--- a/variant_apply_recalibration.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/variant_apply_recalibration.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,14 +1,15 @@
-<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.0">
+<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1">
   <description></description>
-  <expand macro="requirements" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
-    #for $var_count, $variant in enumerate( $reference_source.variants ):
-        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+    #for $var_count, $variant in enumerate( $reference_source.input_variants ):
+        -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
     #end for
    -p '
    @JAR_PATH@
@@ -24,13 +25,13 @@
     --tranches_file "${reference_source.input_tranches}"
     --out "${output_variants}"
    '
-    
+
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     -p '
     --mode "${mode}"
-    
+
     #for $ignore_filter in $ignore_filters:
         #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
         #if $ignore_filter_name == "custom":
@@ -45,9 +46,7 @@
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
-        </repeat>
+        <expand macro="input_variants" />
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
@@ -58,17 +57,15 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
-          <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
-        </repeat>
+        <expand macro="input_variants" />
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
         <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
           <option value="SNP" selected="True">SNP</option>
           <option value="INDEL">INDEL</option>