From 0f0364e9fab0c2942395aba21cb20e48b3ae84c7 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Fri, 16 Jan 2015 22:08:29 +0100
Subject: [PATCH] activate SnpSiftDbNSFP and dbnsfp.tabular

---
 config/datatypes_conf.xml.sample | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 786c2fbabc7..44ace07191b 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -113,7 +113,7 @@
       <converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/>
       <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-	    <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/>
+        <converter file="interval_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <!-- <display file="ucsc/interval_as_bed.xml" inherit="True" /> -->
       <display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/>
       <display file="gbrowse/gbrowse_interval_as_bed.xml" inherit="True"/>
@@ -151,11 +151,11 @@
     <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
       <display file="ucsc/maf_customtrack.xml" />
     </datatype>
-	<datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True">
-	  <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-	  <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
-	  <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
-	</datatype>
+    <datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True">
+      <converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
+      <converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
+      <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
+    </datatype>
     <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
     <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true">
       <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
@@ -171,13 +171,17 @@
     <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
     <datatype extension="Roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
     <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
-    	<converter file="sam_to_bam.xml" target_datatype="bam"/>
-    	<converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
-	</datatype>
+        <converter file="sam_to_bam.xml" target_datatype="bam"/>
+        <converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
+    </datatype>
     <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension.  You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/>
     <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
-    <datatype extension="snpeffdb" type="galaxy.datatypes.snpeff:SnpEffDb" display_in_upload="True"/>
-    <datatype extension="snpeffdbv4" type="galaxy.datatypes.snpeff:SnpEffDb" subclass="True" display_in_upload="True"/>
+    <datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="True"/>
+    <datatype extension="snpeffdbv4" type="galaxy.datatypes.text:SnpEffDb" subclass="True" display_in_upload="True"/>
+    <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.txt:SnpSiftDbNSFP" display_in_upload="True"/>
+    <datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True">
+        <converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/>
+    </datatype>
     <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/>
     <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
     <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>