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"> $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
    <param format="interval" name="input1" type="data">
      <label>Merge overlaping regions of</label>
    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
      <label>Output 3 column bed</label>
    <data format="input" name="output" metadata_source="input1" />
  <code file="">
    <hook exec_after_process="exec_after_merge" />
      <param name="input1" value="1.bed" />
      <output name="output" file="gops-merge.dat" />
      <param name="returntype" value="true" />
      <param name="input1" value="2_mod.bed" ftype="interval"/>
      <output name="output" file="gops_merge_diffCols.dat" />
      <param name="returntype" value="true" />
      <param name="input1" value="gops_bigint.interval" />
      <output name="output" file="gops_merge_out2.bed" />
      <param name="returntype" value="true" />

.. 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.



See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).

.. _Screencasts:


This operation merges all overlapping intervals into single intervals.


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