the intervals of two queries side-by-side gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill Join with with min overlap Only records that are joined (INNER JOIN) All records of first query (fill null with ".") All records of second query (fill null with ".") All records of both queries (fill nulls with ".")

.. 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** specifies the minimum overlap between intervals that allows them to be joined. - **Return only records that are joined** returns only the records of the first query that join to a record in the second query. This is analogous to an INNER JOIN. - **Return all records of first query (fill null with ".")** returns all intervals of the first query, and any intervals that do not join an interval from the second query are filled in with a period(.). This is analogous to a LEFT JOIN. - **Return all records of second query (fill null with ".")** returns all intervals of the second query, and any intervals that do not join an interval from the first query are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** - **Return all records of both queries (fill nulls with ".")** returns all records from both queries, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** ----- **Example** If **First query** is:: chr1 10 100 Query1.1 chr1 500 1000 Query1.2 chr1 1100 1250 Query1.3 and **Second query** is:: chr1 20 80 Query2.1 chr1 2000 2204 Query2.2 chr1 2500 3000 Query2.3 The four return options will generate: - **Return only records that are joined**:: chr1 10 100 Query1.1 chr1 20 80 Query2.1 - **Return all records of first query**:: chr1 10 100 Query1.1 chr1 20 80 Query2.1 chr1 500 1000 Query1.2 . . . . chr1 1100 1250 Query1.3 . . . . - **Return all records of second query**:: chr1 10 100 Query1.1 chr1 20 80 Query2.1 . . . . chr1 2000 2204 Query2.2 . . . . chr1 2500 3000 Query2.3 - **Return all records of both queries**:: chr1 10 100 Query1.1 chr1 20 80 Query2.1 chr1 500 1000 Query1.2 . . . . chr1 1100 1250 Query1.3 . . . . . . . . chr1 2000 2204 Query2.2 . . . . chr1 2500 3000 Query2.3