--- a/haplotype_caller.xml	Thu May 14 22:47:18 2015 -0400
+++ b/haplotype_caller.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.1">
+<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>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -8,12 +8,7 @@
   <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
+    @INPUT_BAMS@
     -p '
     @JAR_PATH@
     -T "HaplotypeCaller"
@@ -119,12 +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...-->
@@ -133,9 +123,7 @@
         </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>