From 5d6f8c835b779408c2d3c85c1671cd25d39ca4be Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 22 Mar 2013 00:41:08 -0500
Subject: [PATCH] Covert more duplicated GATK wrapper code to macros.

---
 tools/gatk/count_covariates.xml            | 18 +++---------------
 tools/gatk/depth_of_coverage.xml           | 18 +++---------------
 tools/gatk/gatk_macros.xml                 | 20 ++++++++++++++++++++
 tools/gatk/indel_realigner.xml             | 18 +++---------------
 tools/gatk/print_reads.xml                 |  5 +----
 tools/gatk/realigner_target_creator.xml    | 18 +++---------------
 tools/gatk/table_recalibration.xml         | 18 +++---------------
 tools/gatk/unified_genotyper.xml           | 18 +++---------------
 tools/gatk/variant_annotator.xml           |  5 +----
 tools/gatk/variant_apply_recalibration.xml |  5 +----
 tools/gatk/variant_combine.xml             | 18 +++---------------
 tools/gatk/variant_eval.xml                | 18 +++---------------
 tools/gatk/variant_filtration.xml          |  5 +----
 tools/gatk/variant_recalibrator.xml        | 18 +++---------------
 tools/gatk/variant_select.xml              | 19 +++----------------
 tools/gatk/variants_validate.xml           |  5 +----
 16 files changed, 55 insertions(+), 171 deletions(-)

diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml
index 59a42d850fe..c955ce36531 100644
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -83,10 +83,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
@@ -155,15 +152,7 @@
     
     <expand macro="gatk_param_type_conditional" />
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <conditional name="default_read_group_type">
           <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
             <option value="default" selected="True">Don't Set</option>
@@ -227,8 +216,7 @@
         </conditional>
         <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/>
         <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="csv" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
diff --git a/tools/gatk/depth_of_coverage.xml b/tools/gatk/depth_of_coverage.xml
index 7055ed40ff1..20b1800d6d7 100644
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -129,10 +129,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <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">
@@ -175,15 +172,7 @@
     
     <expand macro="gatk_param_type_conditional" />
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
         <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
         <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &amp;lt;maxBaseQuality&amp;gt;" />
@@ -199,8 +188,7 @@
         <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
         <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
         <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
diff --git a/tools/gatk/gatk_macros.xml b/tools/gatk/gatk_macros.xml
index 7fe2393002a..7bd2bc07010 100644
--- a/tools/gatk/gatk_macros.xml
+++ b/tools/gatk/gatk_macros.xml
@@ -273,6 +273,26 @@
       </when>
     </conditional>    
   </xml>
+  <xml name="analysis_type_conditional">
+    <conditional name="analysis_param_type">
+      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <yield />
+      </when>
+    </conditional>
+  </xml>
+  <xml name="reference_source_selector_param">
+    <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+      <option value="cached">Locally cached</option>
+      <option value="history">History</option>
+    </param>
+  </xml>
   <token name="@CITATION_SECTION@">------
 
 **Citation**
diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index c094d51b03f..88bdb878305 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -62,10 +62,7 @@
   <inputs>
     
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
@@ -116,15 +113,7 @@
     
     <expand macro="gatk_param_type_conditional" />
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         
         <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
         <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
@@ -139,8 +128,7 @@
         <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
         <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
         <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/> 
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
diff --git a/tools/gatk/print_reads.xml b/tools/gatk/print_reads.xml
index 0ad5b1b6dff..68667b1434b 100644
--- a/tools/gatk/print_reads.xml
+++ b/tools/gatk/print_reads.xml
@@ -45,10 +45,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <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">
diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml
index 4e97174e825..853ab8f24cb 100644
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -49,10 +49,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
@@ -101,21 +98,12 @@
     
     <expand macro="gatk_param_type_conditional" />
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
         <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
         <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
         <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />
diff --git a/tools/gatk/table_recalibration.xml b/tools/gatk/table_recalibration.xml
index 2be1cc0af67..caf2480cee4 100644
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -66,10 +66,7 @@
   <inputs>
     <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
           <validator type="unspecified_build" />
@@ -95,15 +92,7 @@
     <expand macro="gatk_param_type_conditional" />
     
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <conditional name="default_read_group_type">
           <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
             <option value="default" selected="True">Don't Set</option>
@@ -172,8 +161,7 @@
         <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
         <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
         <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 9cd5ad4c659..39d095cca97 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -94,10 +94,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <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">
@@ -157,15 +154,7 @@
     
     <expand macro="gatk_param_type_conditional" />
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &amp;lt;p_nonref_model&amp;gt;">
           <option value="EXACT" selected="True">EXACT</option>
           <option value="GRID_SEARCH">GRID_SEARCH</option>
@@ -240,8 +229,7 @@
           </options>
         </param>
         <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index b9c2166f876..cb41296ac0d 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -90,10 +90,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
         <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
diff --git a/tools/gatk/variant_apply_recalibration.xml b/tools/gatk/variant_apply_recalibration.xml
index 043c450950e..0fb4d82e1a6 100644
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -43,10 +43,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <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"/>
diff --git a/tools/gatk/variant_combine.xml b/tools/gatk/variant_combine.xml
index 1d1b1f102d6..a18e5023c47 100644
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -54,10 +54,7 @@
   <inputs>
     
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
           <param name="input_variant" type="data" format="vcf" label="Input variant file" />
@@ -93,15 +90,7 @@
     <expand macro="gatk_param_type_conditional" />
     
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
           <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
           <option value="KEEP_IF_ALL_UNFILTERED" />
@@ -115,8 +104,7 @@
         <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
         <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
         
-      </when>
-    </conditional>
+    </expand>
     
     
   </inputs>
diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml
index 62cc50795ac..5055eed3fca 100644
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -102,10 +102,7 @@
   <inputs>
     
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <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" />
@@ -149,15 +146,7 @@
     <expand macro="gatk_param_type_conditional" />
     
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <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;">
             <sanitizer>
@@ -224,8 +213,7 @@
         <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;" />
         
-      </when>
-    </conditional>
+    </expand>
     
     
   </inputs>
diff --git a/tools/gatk/variant_filtration.xml b/tools/gatk/variant_filtration.xml
index 6c0d4412837..ae63e762145 100644
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -48,10 +48,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 917f3d835ed..7aa3c94b293 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -95,10 +95,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <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" />
@@ -327,15 +324,7 @@
     
     <expand macro="gatk_param_type_conditional" />
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <expand macro="analysis_type_conditional">
         <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
         <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>
         <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30" help="-nKM,--numKMeans &amp;lt;numKMeans&amp;gt;"/>
@@ -373,8 +362,7 @@
           </conditional>
         </repeat>
         <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
-      </when>
-    </conditional>
+    </expand>
   </inputs>
   <outputs>
     <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
diff --git a/tools/gatk/variant_select.xml b/tools/gatk/variant_select.xml
index 34407b1f68f..973469f503c 100644
--- a/tools/gatk/variant_select.xml
+++ b/tools/gatk/variant_select.xml
@@ -101,10 +101,7 @@
   </command>
   <inputs>
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
@@ -147,15 +144,7 @@
     <expand macro="gatk_param_type_conditional" />
     
     
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
+    <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"/>
@@ -219,9 +208,7 @@
             <option value="SYMBOLIC">SYMBOLIC</option>
             <option value="NO_VARIATION">NO_VARIATION</option>
         </param>
-        
-      </when>
-    </conditional>
+    </expand>
     
   </inputs>
   <outputs>
diff --git a/tools/gatk/variants_validate.xml b/tools/gatk/variants_validate.xml
index eedca6bece6..89520274099 100644
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -33,10 +33,7 @@
   <inputs>
     
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
-        <option value="history">History</option>
-      </param>
+      <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">