# HG changeset patch
# User iuc
# Date 1444771358 14400
# Node ID 669a23f1f4b5be19cc2dca398556b51babd898e3
# Parent  86007c982f00f3d4f3641e4699f65c41ad34ad9c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e

diff -r 86007c982f00 -r 669a23f1f4b5 depth_of_coverage.xml
--- a/depth_of_coverage.xml	Thu May 14 22:47:18 2015 -0400
+++ b/depth_of_coverage.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
   <description>on BAM files</description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -8,12 +8,7 @@
   <command interpreter="python">gatk2_wrapper.py
    ##--max_jvm_heap_fraction "1"
    --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_${i}" ##hardcode galaxy ext type as bam_index
-       #end if
-   #end for
+   @BAM_INPUTS@
    -p '
    @JAR_PATH@
     -T "DepthOfCoverage"
@@ -129,12 +124,7 @@
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-            </param>
-        </repeat>
+        <expand macro="input_bams_cached" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk2_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
@@ -143,9 +133,8 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file" />
-        </repeat>
+
+        <expand macro="input_bams_history" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
diff -r 86007c982f00 -r 669a23f1f4b5 gatk2_macros.xml
--- a/gatk2_macros.xml	Thu May 14 22:47:18 2015 -0400
+++ b/gatk2_macros.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -24,11 +24,31 @@
         -d "--dbsnp:${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}"
     #end if
   </token>
+  <token name="@BAM_INPUTS@">
+   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
+       -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}"
+       #if str( $input_bam.metadata.bam_index ) != "None":
+           -d "" "${input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
+       #end if
+   #end for
+  </token>
+  <xml name="input_variants" token_help="-input,--input &amp;lt;input&amp;gt;">
+    <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" min="1" help="@HELP@"/>
+  </xml>
+  <xml name="input_bams_history">
+    <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"/>
+  </xml>
+  <xml name="input_bams_cached">
+    <param name="input_bams" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" min="1" multiple="True">
+      <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>
+  </xml>
   <template name="standard_gatk_options">
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
-        #for $pedigree in $gatk_param_type.pedigree:
-            -p '--pedigree "${pedigree.pedigree_file}"'
+        #for $pedigree in $gatk_param_type.pedigree_files:
+            -p '--pedigree "${pedigree}"'
         #end for
         #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
@@ -51,12 +71,12 @@
             #end for
             '
         #end for
-        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
-            -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+        #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_intervals ):
+            -d "--intervals" "${input_interval}" "${input_interval.ext}" "input_intervals_${interval_count}"
         #end for
-        
-        #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
-            -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+
+        #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_exclude_intervals ):
+            -d "--excludeIntervals" "${input_interval}" "${input_interval.ext}" "input_exlude_intervals_${interval_count}"
         #end for
 
         -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
@@ -84,7 +104,7 @@
             #end if
         #end for
     #end if
-    
+
     #if str( $reference_source.reference_source_selector ) == "history":
         -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
     #end if
@@ -100,9 +120,7 @@
         <!-- Do nothing here -->
       </when>
       <when value="advanced">
-        <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
-            <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
-        </repeat>
+        <param name="pedigree_files" type="data" format="txt" label="Pedigree files for samples" multiple="True" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;"/>
         <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
             <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
         </repeat>
@@ -212,13 +230,9 @@
               </when>
             </conditional>
         </repeat>
-        <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
-          <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
-        </repeat>
-        <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
-          <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
-        </repeat>
-        
+        <param name="input_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;" />
+        <param name="input_exclude_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;" />
+
         <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
@@ -282,7 +296,7 @@
           <option value="ALL" selected="True">ALL</option>
           <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
         </param>
-        
+
         <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
           <conditional name="read_group_black_list_type">
             <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
@@ -297,7 +311,7 @@
             </when>
           </conditional>
         </repeat>
-        
+
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
         <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
@@ -327,7 +341,7 @@
   </xml>
 
   <xml name="allow_n_cigar_reads">
-    <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue="" 
+    <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue=""
         label="Allow N in CIGAR strings" help="This is required for RNA-seq data. (-U ALLOW_N_CIGAR_READS)" />
   </xml>
 
diff -r 86007c982f00 -r 669a23f1f4b5 haplotype_caller.xml
--- 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>
diff -r 86007c982f00 -r 669a23f1f4b5 unified_genotyper.xml
--- a/unified_genotyper.xml	Thu May 14 22:47:18 2015 -0400
+++ b/unified_genotyper.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.1">
+<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.2">
   <description>SNP and indel caller</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
+    @BAM_INPUTS@
     -p '
     @JAR_PATH@
     -T "UnifiedGenotyper"
@@ -89,12 +84,7 @@
     <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...-->
@@ -103,10 +93,7 @@
         </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>
diff -r 86007c982f00 -r 669a23f1f4b5 variant_apply_recalibration.xml
--- a/variant_apply_recalibration.xml	Thu May 14 22:47:18 2015 -0400
+++ b/variant_apply_recalibration.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.0">
+<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1">
   <description></description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -8,8 +8,8 @@
   <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@
@@ -46,9 +46,7 @@
     <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 annotate"/>
-        </repeat>
+        <expand macro="input_variants" />
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
@@ -59,9 +57,7 @@
         </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 annotate" />
-        </repeat>
+        <expand macro="input_variants" />
         <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
         <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
diff -r 86007c982f00 -r 669a23f1f4b5 variant_eval.xml
--- a/variant_eval.xml	Thu May 14 22:47:18 2015 -0400
+++ b/variant_eval.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0">
+<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1">
   <description></description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -10,8 +10,8 @@
 
     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_${var_count}"
     #end for
     -p '
     @JAR_PATH@
@@ -100,9 +100,7 @@
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
-          <param name="input_variant" type="data" format="vcf" label="Input variant file" />
-        </repeat>
+        <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;"/>
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk2_picard_indexes">
             <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
@@ -111,9 +109,7 @@
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
-        <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;">
-          <param name="input_variant" type="data" format="vcf" label="Input variant file" />
-        </repeat>
+        <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
diff -r 86007c982f00 -r 669a23f1f4b5 variant_recalibrator.xml
--- a/variant_recalibrator.xml	Thu May 14 22:47:18 2015 -0400
+++ b/variant_recalibrator.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0">
+<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1">
   <description></description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -10,8 +10,8 @@
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${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@
@@ -94,9 +94,7 @@
     <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"/> -->
@@ -105,9 +103,7 @@
         </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>
diff -r 86007c982f00 -r 669a23f1f4b5 variant_select.xml
--- a/variant_select.xml	Thu May 14 22:47:18 2015 -0400
+++ b/variant_select.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.0">
+<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.2">
   <description>from VCF files</description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -50,12 +50,12 @@
     ##start tool specific options
     #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced':
         -p '
-          #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat:
-              --exclude_sample_file "${exclude_sample_file.exclude_sample_file}"
+          #for $esf in $analysis_param_type.exclude_sample_file:
+              --exclude_sample_file "${esf}"
           #end for
 
-          #for $sample_file in $analysis_param_type.sample_file_repeat:
-              --sample_file "${ample_file.sample_file}"
+          #for $sf in $analysis_param_type.sample_file:
+              --sample_file "${sf}"
           #end for
 
           #if $analysis_param_type.input_keep_ids:
@@ -143,15 +143,11 @@
 
     <expand macro="analysis_type_conditional">
 
-        <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;">
-            <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/>
-        </repeat>
+        <param name="exclude_sample_file" type="data" format="txt" multiple="True" label="Exclude Samples by file" help="File containing a list of samples (one per line) to exclude (-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;)"/>
 
-        <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
-            <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" />
-        </repeat>
+        <param name="sample_file" type="data" format="txt" multiple="True" label="Samples by file"  help="File containing a list of samples (one per line) to include (-sf,--sample_file &amp;lt;sample_file&amp;gt;)"/>
 
-        <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
+        <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
 
         <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />