# HG changeset patch
# User cropgeeks
# Date 1487683133 18000
# Node ID 735f690bdb76cadb9f94c49ddbf9b85eec2bbf64
# Parent  8970bd92145824deb6480bab42444032a1361dd0
Uploaded

diff -r 8970bd921458 -r 735f690bdb76 createproject.xml
--- a/createproject.xml	Tue Feb 21 06:37:00 2017 -0500
+++ b/createproject.xml	Tue Feb 21 08:18:53 2017 -0500
@@ -33,6 +33,7 @@
 	</param>
   </inputs>
   <outputs>
+  <!-- label="${tool.name} on ${on_string}: project.flapjack" -->
     <data name="output" format="flapjack" />
 	<data name="html" format="html" />
   </outputs>
diff -r 8970bd921458 -r 735f690bdb76 datatypes_conf.xml
--- a/datatypes_conf.xml	Tue Feb 21 06:37:00 2017 -0500
+++ b/datatypes_conf.xml	Tue Feb 21 08:18:53 2017 -0500
@@ -4,7 +4,9 @@
         <datatype_file name="flapjack.py"/>
     </datatype_files>
     <registration>
-       <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackProjectFormat" mimetype="application/octet-stream" display_in_upload="true"/>
+       <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackProjectFormat" mimetype="application/octet-stream" display_in_upload="true">
+	     <display file="jnlp.xml"/>
+	   </datatype>
 	   <datatype extension="fjmap" type="galaxy.datatypes.flapjack:FlapjackMapFormat" mimetype="text/plain" display_in_upload="true"/>
        <datatype extension="fjgenotype" type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat" mimetype="text/plain" display_in_upload="true"/>
        <datatype extension="fjphenotype" type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat" mimetype="text/plain" display_in_upload="true"/>
diff -r 8970bd921458 -r 735f690bdb76 jnlp.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jnlp.xml	Tue Feb 21 08:18:53 2017 -0500
@@ -0,0 +1,8 @@
+<display id="flapjack_project" version="1.0.0" name="display in Flapjack">
+    <link id="main" name="main">
+        <url>http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bam_file.dbkey)}&amp;hgt.customText=${qp($track.url)}</url>
+        <param type="data" name="bam_file" url="galaxy.bam" />
+        <param type="data" name="bai_file" url="galaxy.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
+        <param type="template" name="track" viewable="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param>
+    </link>
+</display>
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