the intervals of two queries side-by-sidegops_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
.. 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