comparison galaxy-conf/InterpolateDiscontinuousData.xml @ 20:9d56b5b85740 draft

Reuploaded to see if tools get loaded correctly this time.

20:9d56b5b85740

<tool id="WigInterpolate" name="Interpolate" version="1.1.0">
  <description>missing values in a (Big)Wig file</description>
  <command interpreter="sh">galaxyToolRunner.sh converters.InterpolateDiscontinousData -i $input -t $type -m $max -o $output</command>
  <inputs>
      <param format="bigwig,wig" name="input" type="data" label="Interpolate missing values in" />
      <param name="type" type="select" label="Interpolation type">
      	<option value="nearest">Nearest</option>
      	<option value="linear">Linear</option>
      	<option value="cubic">Cubic</option>
      </param>
      <param name="max" type="integer" value="1000" label="Maximum span of missing values to interpolate (bp)"/>
  </inputs>
  <outputs>
      <data format="wig" name="output" metadata_source="input" />
  </outputs>
  
  <help>

This tool will attempt to interpolate missing values (NaN) in a Wig file that result when converting discontinuous microarray probe data to Wig format. Stretches of missing data that extend longer than the allowed maximum will be left as NaN.

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**Interpolation types**

- **Nearest** uses the value of the nearest base pair that has data
- **Linear** uses a linear interpolant between the values of the nearest two probes
- **Cubic** uses a cubic interpolant between the values of the nearest two probes

For more information, see Wikipedia_.

.. _Wikipedia: http://en.wikipedia.org/wiki/Interpolation

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.. class:: infomark

**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use the Converters -> IntervalToWig tool to convert Bed, BedGraph, or GFF-formatted microarray data to Wig format, then use this tool to interpolate the missing values between probes.

  </help>
</tool>