--- a/variant_recalibrator.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/variant_recalibrator.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,16 +1,17 @@
-<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0">
+<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1">
   <description></description>
+  <macros>
+    <import>gatk2_macros.xml</import>
+  </macros>
   <expand macro="requirements">
     <requirement type="package" version="0.9.3">ggplot2</requirement>
   </expand>
-  <macros>
-    <import>gatk2_macros.xml</import>
-  </macros>
+  <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_${var_count}"
     #end for
     -p '
     @JAR_PATH@
@@ -26,14 +27,14 @@
     --tranches_file "${output_tranches}"
     --rscript_file "${output_rscript}"
    '
-    
+
     #set $rod_binding_names = dict()
     #for $rod_binding in $rod_bind:
         #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
             #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
         #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
             #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
-        #else 
+        #else
             #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
@@ -43,9 +44,9 @@
             -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #end if
     #end for
-    
+
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     -p '
     #if str( $annotations ) != "None":
@@ -58,7 +59,7 @@
     #end for
     --mode "${mode}"
     '
-    
+
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
         --maxGaussians "${analysis_param_type.max_gaussians}"
@@ -84,19 +85,16 @@
         #end for
         '
     #end if
-    
-    
+
     &amp;&amp;
     mv "${output_rscript}.pdf" "${output_tranches_pdf}"
-    
+
   </command>
   <inputs>
     <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 recalibrate" />
-        </repeat>
+        <expand macro="input_variants" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk2_picard_indexes">
           <!--  <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
@@ -105,13 +103,11 @@
         </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 recalibrate" />
-        </repeat>
+        <expand macro="input_variants" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
+
     <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;" min="2">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
@@ -182,7 +178,7 @@
                       <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
                   </when>
               </conditional>
-          </when>          
+          </when>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
@@ -300,7 +296,7 @@
           </when>
         </conditional>
     </repeat>
-    
+
     <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
       <options from_data_table="gatk2_annotations">
@@ -308,19 +304,19 @@
         <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
       </options>
     </param>
-    
+
     <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
     </repeat>
-    
+
     <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>
         <option value="BOTH">BOTH</option>
     </param>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
     <expand macro="analysis_type_conditional">
         <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="8" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
         <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="150" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>