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

<tool id="gops_basecoverage_1" name="Base Coverage">
  <description>of all intervals</description>
  <command interpreter="python"> $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
    <param format="interval" name="input1" type="data">
      <label>Compute coverage for</label>
    <data format="txt" name="output" />
  <code file=""/>
      <param name="input1" value="1.bed" />
      <output name="output" file="gops_basecoverage_out.txt" />     
      <param name="input1" value="gops_bigint.interval" />
      <output name="output" file="gops_basecoverage_out2.txt" />     

.. 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.

This operation counts the total bases covered by a set of intervals.  Bases that are covered by more than one interval are **not** counted more than once towards the total.



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

.. _Screencasts: