change extension to "ucsc.net" and improve description

ahmedhamidawan · May 3, 2024 · d4aa9c4 · d4aa9c4
1 parent 6f527a0
commit d4aa9c4
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -988,8 +988,8 @@
     <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true" description="geospatial vector data format for geographic information system"/>
     <!-- Flexible Image Transport System (FITS) used in Astronomy https://fits.gsfc.nasa.gov/ https://fits.gsfc.nasa.gov/rfc4047.txt -->
     <datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
-    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true"/>
-    <datatype extension="net" type="galaxy.datatypes.chain:Net" display_in_upload="true"/>
+    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
+    <datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
   </registration>
   <sniffers>
     <!--

diff --git a/lib/galaxy/datatypes/chain.py b/lib/galaxy/datatypes/chain.py
@@ -133,7 +133,7 @@ class Net(data.Text):
     """Class describing a net format alignment file"""
 
     edam_format = "format_3983"
-    file_ext = "net"
+    file_ext = "ucsc.net"
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
@@ -153,7 +153,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname( '1.chain' )
         >>> Net().sniff( fname )
         False
-        >>> fname = get_test_fname( '1.net' )
+        >>> fname = get_test_fname( '1.ucsc.net' )
         >>> Net().sniff( fname )
         True
         >>>

diff --git a/lib/galaxy/datatypes/test/1.net → lib/galaxy/datatypes/test/1.ucsc.net b/lib/galaxy/datatypes/test/1.net → lib/galaxy/datatypes/test/1.ucsc.net