--- a/haplotype_caller.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/haplotype_caller.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,18 +1,14 @@
-<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.0">
+<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.2">
   <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</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 "HaplotypeCaller"
@@ -30,8 +26,9 @@
     #end if
    '
     @DBSNP_OPTIONS@
+    $allow_n_cigar_reads
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
@@ -53,7 +50,7 @@
         #if str($analysis_param_type.comp) != 'None':
             --comp "$analysis_param_type.comp"
         #end if
-        ##  
+        ##
         #if str( $analysis_param_type.annotation ) != "None":
             #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
                 --annotation "${annotation}"
@@ -117,12 +114,7 @@
     <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...-->
@@ -131,14 +123,13 @@
         </param>
       </when>
       <when value="history">
-        <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" />
-        </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" />
-    
+
+    <expand macro="allow_n_cigar_reads" />
     <expand macro="gatk_param_type_conditional" />
 
     <conditional name="analysis_param_type">
@@ -213,8 +204,6 @@
             <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
           </when>
         </conditional>
-
-
         <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph  File to which debug assembly graph information should be written"/>
         <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets  Heterozygosity value used to compute prior likelihoods for any locus"/>
         <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning  The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph">
@@ -254,7 +243,7 @@
   </outputs>
   <tests>
       <test>
-          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 
+          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
           <param name="reference_source_selector" value="history" />
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />