<tool id="metaintv" name="binned-average">
  <description>from bigwig</description>
  <command interpreter="python">binnedAverage.py $bwfile $intvfile $nbin $outfile $outplot </command>
  <inputs>
      <param name="intvfile" format="bed" type="data" label="BED file (require strand in column 6)"/>
      <param name="bwfile" format="bigwig" type="data" label="BigWig file"/> 
      <param name="nbin" type="integer" value="20" label="number of bins"/>
                
  </inputs>
  <outputs>
    <data format="tabular" name="outfile" label="${tool.name} on ${on_string}[data]"/>
        <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
  </outputs>
  <help>

.. class:: infomark

Each interval is binned and the average base-resolution score/coverage/density in the bigwig file is added as new columns appended at the end of the original file .

**Example**

If your original data has the following format:

+-----+-----+---+------+
|chrom|start|end|other2|
+-----+-----+---+------+

and you choose to divide each interval into 3 bins and return the mean scores of each bin, your output will look like this:

+-----+-----+---+------+-----+-----+-----+
|chrom|start|end|other2|mean1|mean2|mean3|
+-----+-----+---+------+-----+-----+-----+


</help>
</tool>
