# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1413918327 18000
# Node ID 4be8e0068bc372e6486fdc9ee91fa105a17cb2e0
# Parent  6d429d880a7507a218400b2131bbec93a416a303
Update loc data to separate version 4 databases

diff -r 6d429d880a75 -r 4be8e0068bc3 snpEff.xml
--- a/snpEff.xml	Mon Oct 20 08:37:01 2014 -0500
+++ b/snpEff.xml	Tue Oct 21 14:05:27 2014 -0500
@@ -94,20 +94,20 @@
             <when value="cached">
                 <param name="genomeVersion" type="select" label="Genome">
                     <!--GENOME    DESCRIPTION-->
-                    <options from_data_table="snpeff_genomedb">
+                    <options from_data_table="snpeff4_genomedb">
                            <filter type="unique_value" column="0" />
                     </options>
                 </param>
                 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
                        <help>These are available for only a few genomes</help>
-                       <options from_data_table="snpeff_annotations">
+                       <options from_data_table="snpeff4_annotations">
                            <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
                            <filter type="unique_value" column="1" />
                        </options>
                 </param>
                 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation">
                        <help>These are available for only a few genomes</help>
-                       <options from_data_table="snpeff_regulationdb">
+                       <options from_data_table="snpeff4_regulationdb">
                            <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
                            <filter type="unique_value" column="1" />
                        </options>
@@ -130,7 +130,7 @@
                 </param>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/>
+                <param name="genome_version" type="text" value="GRCh38.76" label="Snpff Version Name"/>
             </when>
         </conditional>
 
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff4_annotations.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_annotations.loc.sample	Tue Oct 21 14:05:27 2014 -0500
@@ -0,0 +1,5 @@
+## Regulation Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+#genome	annotation_name description
+#GRCh37.71	nextprot	nextprot
+#GRCh37.71	motif	motif
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff4_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_databases.loc.sample	Tue Oct 21 14:05:27 2014 -0500
@@ -0,0 +1,5 @@
+## Available Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+## the Description field in this sample is "Genome : Version" 
+#Version	Description
+#GRCh37.68	Homo sapiens : GRCh37.68
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff4_genomedb.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_genomedb.loc.sample	Tue Oct 21 14:05:27 2014 -0500
@@ -0,0 +1,5 @@
+## Downloaded Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+## the Description field in this sample is "Genome : Version" 
+#Version        Description	data_dir path
+#GRCh37.68      Homo sapiens : GRCh37.68	/home/galaxy/snpEff/data
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff4_regulationdb.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeff4_regulationdb.loc.sample	Tue Oct 21 14:05:27 2014 -0500
@@ -0,0 +1,4 @@
+## Regulation Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+#genome	regulation_name description
+#GRCh37.70	CD4	CD4
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff_annotations.loc.sample
--- a/tool-data/snpeff_annotations.loc.sample	Mon Oct 20 08:37:01 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Regulation Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-#genome	annotation_name description
-#GRCh37.71	nextprot	nextprot
-#GRCh37.71	motif	motif
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff_databases.loc.sample
--- a/tool-data/snpeff_databases.loc.sample	Mon Oct 20 08:37:01 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Available Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version" 
-#Version	Description
-#GRCh37.68	Homo sapiens : GRCh37.68
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff_genomedb.loc.sample
--- a/tool-data/snpeff_genomedb.loc.sample	Mon Oct 20 08:37:01 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Downloaded Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version" 
-#Version        Description	data_dir path
-#GRCh37.68      Homo sapiens : GRCh37.68	/home/galaxy/snpEff/data
diff -r 6d429d880a75 -r 4be8e0068bc3 tool-data/snpeff_regulationdb.loc.sample
--- a/tool-data/snpeff_regulationdb.loc.sample	Mon Oct 20 08:37:01 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-## Regulation Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-#genome	regulation_name description
-#GRCh37.70	CD4	CD4
diff -r 6d429d880a75 -r 4be8e0068bc3 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Oct 20 08:37:01 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Tue Oct 21 14:05:27 2014 -0500
@@ -1,19 +1,19 @@
 <tables>
-    <table name="snpeff_databases" comment_char="#">
+    <table name="snpeff4_databases" comment_char="#">
         <columns>value, name</columns>
-        <file path="tool-data/snpeff_databases.loc" />
+        <file path="tool-data/snpeff4_databases.loc" />
     </table>
-    <table name="snpeff_genomedb" comment_char="#">
+    <table name="snpeff4_genomedb" comment_char="#">
         <columns>value, name, path</columns>
-        <file path="tool-data/snpeff_genomedb.loc" />
+        <file path="tool-data/snpeff4_genomedb.loc" />
     </table>
-    <table name="snpeff_regulationdb" comment_char="#">
+    <table name="snpeff4_regulationdb" comment_char="#">
         <columns>genome, value, name</columns>
-        <file path="tool-data/snpeff_regulationdb.loc" />
+        <file path="tool-data/snpeff4_regulationdb.loc" />
     </table>
-    <table name="snpeff_annotations" comment_char="#">
+    <table name="snpeff4_annotations" comment_char="#">
         <columns>genome, value, name</columns>
-        <file path="tool-data/snpeff_annotations.loc" />
+        <file path="tool-data/snpeff4_annotations.loc" />
     </table>
 </tables>