Hello,
I'd like to add a new datatype to galaxy. This datatype is just an textual interval file, with non-default columns assignment. For example, the chromosome is on column 4, start/end at columns 6/7.
Is there a way to achieve this without inheriting a new class in "/lib/galaxy/datatypes/interval.py" ?
I was hoping for something along the lines of adding the following in "datatypes_conf.xml":
<datatype extension="MyNewType" type="galaxy.datatypes.interval:Interval" mimetype="text/text" display_in_upload="true"> <metadata name="chromCol" value="4" /> <metadata name="startCol" value="6" /> <metadata name="endCol" value="7" /> </datatype>
If this isn't possible yet, and if I may suggest a code fragment, then at "/lib/galaxy/datatypes/registry.py", line 53, I'd add something like: ------------------- for metadata in elem.findall( 'metadata ): name = metadata.get( 'name', None ) value = metadata.get( 'value', None ) if name and value: self.somehow_change_metadata_value ( name, value) -------------------
Thanks, Gordon.