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galaxy-central (ngs) / tools / new_operations / merge.xml

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<tool id="gops_merge_1" name="Merge">
  <description>the overlapping intervals of a dataset</description>
  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
  <inputs>
    <param format="interval" name="input1" type="data">
      <label>Merge overlaping regions of</label>
    </param>
    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
      <label>Output 3 column bed</label>
    </param>
   </inputs>
  <outputs>
    <data format="input" name="output" metadata_source="input1" />
  </outputs>
  <code file="operation_filter.py">
    <hook exec_after_process="exec_after_merge" />
  </code>
  <tests>
    <test>
      <param name="input1" value="1.bed" />
      <output name="output" file="gops-merge.dat" />
      <param name="returntype" value="true" />
    </test>
    <test>
      <param name="input1" value="2_mod.bed" ftype="interval"/>
      <output name="output" file="gops_merge_diffCols.dat" />
      <param name="returntype" value="true" />
    </test>
    <test>
      <param name="input1" value="gops_bigint.interval" />
      <output name="output" file="gops_merge_out2.bed" />
      <param name="returntype" value="true" />
    </test>
  </tests>
  <help>

.. class:: infomark

**TIP:** If your dataset 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://wiki.g2.bx.psu.edu/Learn/Interval%20Operations

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This operation merges all overlapping intervals into single intervals.

**Example**

.. image:: ./static/operation_icons/gops_merge.gif

</help>
</tool>