From 5078b6ea58c886aa13225eb04b67e17e7c42db39 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 6 Dec 2011 09:42:56 -0500
Subject: [PATCH] Update GATK tools handling annotations to allow manually
 specifying additional annotation names to apply.

---
 tools/gatk/unified_genotyper.xml    |  6 ++++++
 tools/gatk/variant_annotator.xml    | 15 +++++++--------
 tools/gatk/variant_recalibrator.xml | 17 ++++++++++++-----
 3 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml
index 9966707ee99..5b1985883f8 100644
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -117,6 +117,9 @@
                 --annotation "${annotation}"
             #end for
         #end if
+        #for $additional_annotation in $analysis_param_type.additional_annotations:
+            --annotation "${additional_annotation.additional_annotation_name}"
+        #end for
         #if str( $analysis_param_type.group ) != "None":
             #for $group in str( $analysis_param_type.group ).split( ','):
                 --group "${group}"
@@ -372,6 +375,9 @@
             <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
           </options>
 	    </param>
+        <repeat name="additional_annotations" title="Additional annotation">
+          <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+        </repeat>
 <!--
         <conditional name="snpEff_rod_bind_type">
           <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
diff --git a/tools/gatk/variant_annotator.xml b/tools/gatk/variant_annotator.xml
index 897c1418cff..72088157d9a 100644
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -36,14 +36,9 @@
             --excludeAnnotation "${annotation}"
         #end for
     #end if
-##    #for $additional_annotation in $additional_annotations:
-##        --annotation "${additional_annotation.additional_annotation_type.additional_annotation_type_selector}"
-##        #for $name, $param in $additional_annotation.additional_annotation_type.iteritems():
-##            #if $name not in [ "__current_case__", "additional_annotation_type_selector" ]:
-##                --${name} "${param}"
-##            #end if
-##        #end for
-##    #end for
+    #for $additional_annotation in $additional_annotations:
+        --annotation "${additional_annotation.additional_annotation_name}"
+    #end for
     ${reference_source.input_variant_bti}
    '
     
@@ -188,6 +183,10 @@
       </when>
     </conditional>
     
+    <repeat name="additional_annotations" title="Additional annotation">
+      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+    </repeat>
+    
     <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data">
       <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
       <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml
index 427e946eb14..4fb8cdcb59d 100644
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -104,6 +104,9 @@
             --use_annotation "${annotation}"
         #end for
     #end if
+    #for $additional_annotation in $additional_annotations:
+        --use_annotation "${additional_annotation.additional_annotation_name}"
+    #end for
     --mode "${mode}"
     '
     
@@ -344,11 +347,15 @@
       </options>
     </param>
     
-        <param name="mode" type="select" label="Recalibration mode">
-          <option value="SNP" selected="True">SNP</option>
-          <option value="INDEL">INDEL</option>
-          <option value="BOTH">BOTH</option>
-        </param>
+    <repeat name="additional_annotations" title="Additional annotation">
+      <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+    </repeat>
+    
+    <param name="mode" type="select" label="Recalibration mode">
+        <option value="SNP" selected="True">SNP</option>
+        <option value="INDEL">INDEL</option>
+        <option value="BOTH">BOTH</option>
+    </param>
     
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">