Merge pull request #2069 from blankenberg/biom-phinch

Add Phinch as an external display application.
galaxyproject · Apr 4, 2016 · e7d4bc3 · e7d4bc3
2 parents 3ecd4e9 + 55074c8
commit e7d4bc3
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Showing 4 changed files with 18 additions and 1 deletion.
diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
@@ -440,7 +440,9 @@
     <datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true" />
     <datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true" />
     <!-- Metagenomic Datatype -->
-    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json" />
+    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json">
+        <display file="biom/biom_simple.xml" />
+    </datatype>
     <!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
     <datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true" />
 

diff --git a/config/tool_data_table_conf.xml.sample b/config/tool_data_table_conf.xml.sample
@@ -85,4 +85,9 @@
         <columns>value, name, url</columns>
         <file path="tool-data/vcf_iobio.loc" />
     </table>
+    <!-- simple biom servers -->
+    <table name="biom_simple_display" comment_char="#">
+        <columns>value, name, url</columns>
+        <file path="tool-data/biom_simple_display.loc" />
+    </table>
 </tables>
diff --git a/display_applications/biom/biom_simple.xml b/display_applications/biom/biom_simple.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<display id="biom_simple" version="1.0.0" name="view biom at">
+    <dynamic_links from_data_table="biom_simple_display" skip_startswith="#" id="value" name="name">
+        <url>${ url % { 'biom_file_url_qp': $biom_file.qp } }</url>
+        <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" />
+    </dynamic_links>
+</display>
diff --git a/tool-data/biom_simple_display.loc.sample b/tool-data/biom_simple_display.loc.sample
@@ -0,0 +1,3 @@
+# Table used for listing simple BIOM display servers
+#<unique_id>	<display_name>	<url>
+phinch_dan	Phinch	http://www.bx.psu.edu/~dan/Phinch/index.html?biomURL=%(biom_file_url_qp)s