the intervals of a query gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype Cluster intervals of max distance between intervals min number of intervals per cluster Merge clusters into single intervals Find cluster intervals; preserve comments and order Find cluster intervals; output grouped by clusters Find the smallest interval in each cluster Find the largest interval in each cluster

.. 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** - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered "clustered". **Negative** values for distance are allowed, and are useful for clustering intervals that overlap. - **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the output. - **Merge clusters into single intervals** outputs intervals that span the entire cluster. - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. - **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost. ----- **Example** .. image:: ../static/operation_icons/gops_cluster.gif