# HG changeset patch
# User sanbi-uwc
# Date 1524140749 14400
# Node ID 25b1bbfe9d130aaa844fb47353bce4b8af951f88
# Parent  6e985e2e08027c3f08a36b8ce657489d30664e84
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/gatk2 commit 4551dc00ae1447b86952c0c8e845496c264f3ccb

diff -r 6e985e2e0802 -r 25b1bbfe9d13 unified_genotyper.xml
--- a/unified_genotyper.xml	Wed Jan 25 08:00:49 2017 -0500
+++ b/unified_genotyper.xml	Thu Apr 19 08:25:49 2018 -0400
@@ -151,8 +151,8 @@
         <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk2_annotations">
-            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+            <filter type="multiple_splitter" column="3" separator=","/>
+            <filter type="static_value" value="UnifiedGenotyper" column="3"/>
           </options>
         </param>
         <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
@@ -185,8 +185,8 @@
             help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk2_annotations">
-            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-            <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
+            <filter type="multiple_splitter" column="3" separator=","/>
+            <filter type="static_value" value="UnifiedGenotyper" column="3"/>
           </options>
         </param>
         <param name="sample_ploidy" type="integer" value="2"
diff -r 6e985e2e0802 -r 25b1bbfe9d13 variant_annotator.xml
--- a/variant_annotator.xml	Wed Jan 25 08:00:49 2017 -0500
+++ b/variant_annotator.xml	Thu Apr 19 08:25:49 2018 -0400
@@ -119,8 +119,8 @@
         <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &amp;lt;annotation&amp;gt;" >
           <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
           <options from_data_table="gatk2_annotations">
-            <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-            <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
+            <filter type="multiple_splitter" column="3" separator=","/>
+            <filter type="static_value" value="VariantAnnotator" column="3"/>
           </options>
         </param>
       </when>
@@ -173,8 +173,8 @@
     <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
       <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
       <options from_data_table="gatk2_annotations">
-        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-        <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
+        <filter type="multiple_splitter" column="3" separator=","/>
+        <filter type="static_value" value="VariantAnnotator" column="3"/>
       </options>
     </param>
 
diff -r 6e985e2e0802 -r 25b1bbfe9d13 variant_recalibrator.xml
--- a/variant_recalibrator.xml	Wed Jan 25 08:00:49 2017 -0500
+++ b/variant_recalibrator.xml	Thu Apr 19 08:25:49 2018 -0400
@@ -300,8 +300,8 @@
     <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
       <options from_data_table="gatk2_annotations">
-        <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
-        <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
+        <filter type="multiple_splitter" column="3" separator=","/>
+        <filter type="static_value" value="VariantRecalibrator" column="3"/>
       </options>
     </param>