From e5201f86327572e400c2fc86c55d9a9fec1b94aa Mon Sep 17 00:00:00 2001
From: dcnorris <dcnorris@uncc.edu>
Date: Mon, 14 Apr 2014 10:05:03 -0400
Subject: [PATCH] adding support for the visualization of gtf file format in
 IGB

---
 datatypes_conf.xml.sample        |  1 +
 display_applications/igb/gtf.xml | 17 +++++++++++++++++
 2 files changed, 18 insertions(+)
 create mode 100644 display_applications/igb/gtf.xml

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 3b6be66144e..89b57430e55 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -99,6 +99,7 @@
     <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
         <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
         <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
+	<display file="igb/gtf.xml" />
     </datatype>
     <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
     <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" />
diff --git a/display_applications/igb/gtf.xml b/display_applications/igb/gtf.xml
new file mode 100644
index 00000000000..3804f339fe2
--- /dev/null
+++ b/display_applications/igb/gtf.xml
@@ -0,0 +1,17 @@
+<display id="igb_gtf" version="1.0.0" name="display in IGB">
+    
+	<link id="View" name="View">
+		<url>$bioviz</url>
+		<param type="data" name="gtf_file_for_name" viewable="False"/>
+		<param type="template" name="niceName" viewable="False" strip="True">
+			#import re
+			#set nm=$gtf_file_for_name.name
+			${re.sub('\W',"_",nm)}
+		</param>
+		<param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" />
+		
+		<param type="template" name="bioviz" strip="True" >
+     		http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&amp;loadresidues=false&amp;feature_url_0=${gtf_file.url}&amp;sym_name_0=${niceName}&amp;sym_method_0=${gtf_file.url}&amp;query_url=${gtf_file.url}&amp;server_url=galaxy
+        </param>
+	</link>
+</display>
\ No newline at end of file