root/galaxy-central/tools/new_operations/join.xml @ 2

<tool id="gops_join_1" name="Join">
  <description>the intervals of two queries side-by-side</description>
  <command interpreter="python">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</command>
  <inputs>
    <param format="interval" name="input1" type="data" help="First query">
      <label>Join</label>
    </param>
    <param format="interval" name="input2" type="data" help="Second query">
      <label>with</label>
    </param>
    <param name="min" size="4" type="integer" value="1" help="(bp)">
      <label>with min overlap</label>
    </param>
        <param name="fill" type="select" label="Return">
                <option value="none">Only records that are joined (INNER JOIN)</option>
                <option value="right">All records of first query (fill null with ".")</option>
                <option value="left">All records of second query (fill null with ".")</option>
                <option value="both">All records of both queries (fill nulls with ".")</option>
        </param>
   </inputs>
  <outputs>
    <data format="interval" name="output" metadata_source="input1" />
  </outputs>
  <code file="operation_filter.py"/>
  <tests>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="1" />
      <param name="fill" value="none" />
      <output name="output" file="gops-join-none.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="1" />
      <param name="fill" value="right" />
      <output name="output" file="gops-join-right.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="1" />
      <param name="fill" value="left" />
      <output name="output" file="gops-join-left.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="1" />
      <param name="fill" value="both" />
      <output name="output" file="gops-join-both.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="500" />
      <param name="fill" value="none" />
      <output name="output" file="gops-join-none-500.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="100" />
      <param name="fill" value="both" />
      <output name="output" file="gops-join-both-100.dat" />
    </test>
  </tests>
  <help>

.. 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 &quot;.&quot;)** 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 &quot;.&quot;)** 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 &quot;.&quot;)** 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
   

</help>
</tool>