--- a/unified_genotyper.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/unified_genotyper.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,18 +1,14 @@
-<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.0">
+<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.2">
   <description>SNP and indel caller</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 $i, $input_bam in enumerate( $reference_source.input_bams ):
-        -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-        #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-            -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
-        #end if
-    #end for
+    @BAM_INPUTS@
     -p '
     @JAR_PATH@
     -T "UnifiedGenotyper"
@@ -32,7 +28,7 @@
     --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"
    '
     @DBSNP_OPTIONS@
-
+    $allow_n_cigar_reads
     #include source=$standard_gatk_options#
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
@@ -88,44 +84,38 @@
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-            </param>
-        </repeat>
+        <expand macro="input_bams_cached" />
         <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_bam" column="dbkey"/> does not yet work in a repeat...--> 
+            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
           </options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file" >
-            </param>
-        </repeat>
+        <expand macro="input_bams_history" />
         <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="dbsnp_param" />
-    
+
     <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &amp;lt;genotype_likelihoods_model&amp;gt;">
       <option value="BOTH" selected="True">BOTH</option>
       <option value="SNP">SNP</option>
       <option value="INDEL">INDEL</option>
     </param>
-    
+
     <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &amp;lt;standard_min_confidence_threshold_for_calling&amp;gt;" />
     <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &amp;lt;standard_min_confidence_threshold_for_emitting&amp;gt;" />
 
-    
+    <expand macro="allow_n_cigar_reads" />
     <expand macro="gatk_param_type_conditional" />
-    
+
     <expand macro="analysis_type_conditional">
-        <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &amp;lt;heterozygosity&amp;gt;" />
-        <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &amp;lt;pcr_error_rate&amp;gt;" />
+        <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus"
+            help="-hets,--heterozygosity &amp;lt;heterozygosity&amp;gt;" />
+        <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods"
+            help="-pcr_error,--pcr_error_rate &amp;lt;pcr_error_rate&amp;gt;" />
         <conditional name="genotyping_mode_type">
           <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &amp;lt;genotyping_mode&amp;gt;">
             <option value="DISCOVERY" selected="True">DISCOVERY</option>
@@ -191,14 +181,16 @@
             <!-- <option value="none">none</option> -->
         </param>
     <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
-        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
+        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude"
+            help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&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">
             <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
             <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
           </options>
         </param>
-        <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" />
+        <param name="sample_ploidy" type="integer" value="2"
+            label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" />
     </expand>
   </inputs>
   <outputs>
@@ -235,8 +227,8 @@
           <param name="doContextDependentGapPenalties" />
           <!-- <param name="annotation" value="" />
           <param name="group" value="" /> -->
-          <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> 
-          <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> 
+          <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" />
+          <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" />
           <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" />
       </test>
   </tests>