--- a/variant_eval.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/variant_eval.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,16 +1,17 @@
-<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0">
+<tool id="gatk2_variant_eval" name="Eval Variants" 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">
    #from binascii import hexlify
 
     gatk2_wrapper.py
    --stdout "${output_log}"
-    #for $var_count, $variant in enumerate( $reference_source.variants ):
-        -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
+    #for $var_count, $variant in enumerate( $reference_source.input_variants ):
+        -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
     #end for
     -p '
     @JAR_PATH@
@@ -24,24 +25,23 @@
         -R "${reference_source.ref_file.fields.path}"
     #end if
    '
-   
+
     #for $rod_binding in $comp_rod_bind:
         -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
         #if str( $rod_binding.comp_known_names ):
             -p '--known_names "${rod_binding.comp_rod_name}"'
         #end if
     #end for
-    
+
     #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
         #if $dbsnp_rod_bind_type.dbsnp_known_names
             -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
         #end if
     #end if
-   
+
     #include source=$standard_gatk_options#
-    
-    
+
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         #for $stratification in $analysis_param_type.stratifications:
@@ -49,39 +49,39 @@
             -o '${ hexlify( $select_string ) }'
         #end for
         -p '
-        
+
         #for $sample in $analysis_param_type.samples:
             --sample "${sample.sample}"
         #end for
-        
+
         #if str( $analysis_param_type.stratification_modules ) != "None":
             #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ):
                 --stratificationModule "${stratification_module}"
             #end for
         #end if
-        
+
         ${analysis_param_type.do_not_use_all_standard_stratifications}
-        
+
         #for $variant_type in $analysis_param_type.only_variants_of_type:
             --onlyVariantsOfType "${variant_type.variant_type}"
         #end for
-        
+
         #if str( $analysis_param_type.eval_modules ) != "None":
             #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ):
                 --evalModule "${eval_module}"
             #end for
         #end if
-        
+
         ${analysis_param_type.do_not_use_all_standard_modules}
-        
+
         #if str( $analysis_param_type.num_samples ) != "0":
             --numSamples "${analysis_param_type.num_samples}"
         #end if
-        
+
         --minPhaseQuality "${analysis_param_type.min_phase_quality}"
-        
+
         --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
-        
+
         #if str( $analysis_param_type.ancestral_alignments ) != "None":
             --ancestralAlignments "${analysis_param_type.ancestral_alignments}"
         #end if
@@ -89,20 +89,18 @@
         #if str( $analysis_param_type.known_cnvs ) != "None":
             -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs"
         #end if
-        
+
         #if str( $analysis_param_type.strat_intervals ) != "None":
             -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals"
         #end if
     #end if
   </command>
   <inputs>
-    
+
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
-          <param name="input_variant" type="data" format="vcf" label="Input variant file" />
-        </repeat>
+        <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;"/>
         <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="input_variant" column="dbkey"/> -->
@@ -111,13 +109,11 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
-          <param name="input_variant" type="data" format="vcf" label="Input variant file" />
-        </repeat>
+        <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&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>
-    
+
     <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;">
       <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
       <param name="comp_rod_name" type="text" value="" label="Comparison ROD name">
@@ -139,10 +135,9 @@
         <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" />
       </when>
     </conditional>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
-    
+
     <expand macro="analysis_type_conditional">
         <repeat name="stratifications" title="Stratification">
           <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &amp;lt;select_exps&amp;gt;">
@@ -155,11 +150,11 @@
           </param>
           <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &amp;lt;select_names&amp;gt;"/>
         </repeat>
-        
+
         <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
           <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
         </repeat>
-        
+
         <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" >
           <option value="AlleleCount" />
           <option value="AlleleFrequency" />
@@ -181,11 +176,11 @@
           <option value="VariantType" />
         </param>
         <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" />
-        
+
         <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
           <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
         </repeat>
-        
+
         <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" >
           <option value="CompOverlap" />
           <option value="CountVariants" />
@@ -200,17 +195,15 @@
           <option value="VariantSummary" />
         </param>
         <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" />
-        
+
         <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &amp;lt;numSamples&amp;gt;"/>
         <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
         <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;"/>
         <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
         <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" />
         <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" />
-        
     </expand>
-    
-    
+
   </inputs>
   <outputs>
     <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" />
@@ -269,7 +262,7 @@
  known_names                           Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets
  stratificationModule                  One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
  doNotUseAllStandardStratifications    Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
- onlyVariantsOfType                    If provided, only variants of these types will be considered during the evaluation, in 
+ onlyVariantsOfType                    If provided, only variants of these types will be considered during the evaluation, in
  evalModule                            One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
  doNotUseAllStandardModules            Do not use the standard modules by default (instead, only those that are specified with the -E option)
  numSamples                            Number of samples (used if no samples are available in the VCF file