the intervals of two queries gops_intersect.py $input1 $input2 $output #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): -1 1,4,5,7 --gff1 #else: -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} #end if #if isinstance( $input2.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): -2 1,4,5,7 --gff2 #else: -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} #end if -m $min $returntype Overlapping Intervals Overlapping pieces of Intervals of that intersect for at least

.. class:: infomark **TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- **Screencasts!** See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). .. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc ----- **Syntax** - **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two queries - **Overlapping Intervals** returns entire intervals from the first query that overlap the second query. The returned intervals are completely unchanged, and this option only filters out intervals that do not overlap with the second query. - **Overlapping pieces of Intervals** returns intervals that indicate the exact base pair overlap between the first query and the second query. The intervals returned are from the first query, and all fields besides start and end are guaranteed to remain unchanged. ----- **Example** .. image:: ../static/operation_icons/gops_intersect.gif