From dfb5a988e41c2e62799f97629eb9a9d0e313fb6c Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Wed, 17 Jul 2019 09:54:43 -0400
Subject: [PATCH] Add GEDA for iCn3D

---
 display_applications/icn3d/icn3d_simple.xml              | 7 +++++++
 lib/galaxy/config/sample/datatypes_conf.xml.sample       | 4 +++-
 lib/galaxy/config/sample/tool_data_table_conf.xml.sample | 5 +++++
 tool-data/icn3d_simple_display.loc.sample                | 3 +++
 4 files changed, 18 insertions(+), 1 deletion(-)
 create mode 100644 display_applications/icn3d/icn3d_simple.xml
 create mode 100644 tool-data/icn3d_simple_display.loc.sample

diff --git a/display_applications/icn3d/icn3d_simple.xml b/display_applications/icn3d/icn3d_simple.xml
new file mode 100644
index 00000000000..1d41a423708
--- /dev/null
+++ b/display_applications/icn3d/icn3d_simple.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<display id="icn3d_simple" version="1.0.0" name="view iniCn3D at">
+    <dynamic_links from_data_table="icn3d_simple_display" skip_startswith="#" id="value" name="name">
+        <url>${ url % {  'icn3d_file_type': $icn3d_file.ext, 'icn3d_file_url_qp': $icn3d_file.qp } }</url>
+        <param type="data" name="icn3d_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
+    </dynamic_links>
+</display>
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 3613a6ee58c..37b5df825e0 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -624,7 +624,9 @@
     <datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="true"/>
     <datatype extension="drf" type="galaxy.datatypes.molecules:DRF" display_in_upload="true"/>
     <datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="false"/>
-    <datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="true"/>
+    <datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="true">
+      <display file="icn3d/icn3d_simple.xml"/>
+    </datatype>
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true"/>
diff --git a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
index a3ef84c653c..75c0f96a15c 100644
--- a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
@@ -105,4 +105,9 @@
         <columns>value, name, url</columns>
         <file path="tool-data/intermine_simple_display.loc" />
     </table>
+    <!-- simple iCn3D Structure Viewer servers -->
+    <table name="icn3d_simple_display" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, url</columns>
+        <file path="tool-data/icn3d_simple_display.loc" />
+    </table>
 </tables>
diff --git a/tool-data/icn3d_simple_display.loc.sample b/tool-data/icn3d_simple_display.loc.sample
new file mode 100644
index 00000000000..a0d3d91277b
--- /dev/null
+++ b/tool-data/icn3d_simple_display.loc.sample
@@ -0,0 +1,3 @@
+# Table used for listing simple iCn3D Structure Viewer servers
+#<unique_id>	<display_name>	<url>
+ncbi_icn3d	NCBI	https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?type=%(icn3d_file_type)s&url=%(icn3d_file_url_qp)s