From d5f735faacedc1beb76d56a3cf3df1c6f29d0fa5 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 21 Nov 2011 16:41:19 -0500
Subject: [PATCH] Remove no longer supported ROD datatypes from GATK tools
 (version 1.3).

---
 tools/gatk/indel_realigner.xml      |  8 ++++----
 tools/gatk/variant_recalibrator.xml | 16 ++++++++--------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/tools/gatk/indel_realigner.xml b/tools/gatk/indel_realigner.xml
index 37504afcc76..fb97635d5fe 100644
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -147,17 +147,17 @@
 	        <option value="custom">Custom</option>
 	      </param>
           <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
           <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
           <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
           </when>
         </conditional>
     </repeat>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 0f6a4237fb0..3e44b0944cd 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -179,7 +179,7 @@
             <option value="custom">Custom</option>
           </param>
           <when value="variant">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -198,7 +198,7 @@
               </conditional>
           </when>
           <when value="comp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
@@ -218,7 +218,7 @@
               </conditional>
           </when>
           <when value="dbsnp">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -237,7 +237,7 @@
               </conditional>
           </when>
           <when value="snps">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -256,7 +256,7 @@
               </conditional>
           </when>
           <when value="hapmap">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -275,7 +275,7 @@
               </conditional>
           </when>
           <when value="omni">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -294,7 +294,7 @@
               </conditional>
           </when>
           <when value="indels">
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>
@@ -314,7 +314,7 @@
           </when>
           <when value="custom">
               <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
-              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
                   <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
                       <option value="is_training_truth_known">Set training/truth/known sites</option>