view galaxy-conf/GaussianSmooth.xml @ 14:f58706d4d421 draft

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author timpalpant
date Sat, 19 May 2012 10:40:16 -0400
parents 81d5b81fb3c2
children 3e477c7e0e73
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<tool id="GaussianSmoother" name="Gaussian smooth" version="1.0.0">
  <description>a (Big)Wig file</description>
  <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
  <inputs>
      <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" />
      <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian in base pairs" />
  </inputs>
  <outputs>
      <data format="wig" name="output" metadata_source="input" />
  </outputs>
  <tests>
    <!--<test>
	    <param name="input" value="test.wig"/>
	    <param name="dbkey" value="sacCer2"/>
	    <param name="S" value="20"/>
	    <param name="W" value="3"/>
	    <output name="output" file="smoother.output1"/>
	  </test>
	  <test>
	    <param name="input" value="test.bw"/>
	    <param name="dbkey" value="sacCer2"/>
	    <param name="S" value="20"/>
	    <param name="W" value="3"/>
	    <output name="output" file="smoother.output1"/>
	  </test>
	  <test>
	    <param name="input" value="test.wig"/>
	    <param name="dbkey" value="sacCer2"/>
	    <param name="S" value="10"/>
	    <param name="W" value="2"/>
	    <output name="output" file="smoother.output2"/>
	  </test>
	  <test>
	    <param name="input" value="test.bw"/>
	    <param name="dbkey" value="sacCer2"/>
	    <param name="S" value="10"/>
	    <param name="W" value="2"/>
	    <output name="output" file="smoother.output2"/>
	  </test>
	  <test>
	    <param name="input" value="test.wig"/>
	    <param name="dbkey" value="sacCer2"/>
	    <param name="S" value="50"/>
	    <param name="W" value="1"/>
	    <output name="output" file="smoother.output3"/>
	  </test>
	  <test>
	    <param name="input" value="test.bw"/>
	    <param name="dbkey" value="sacCer2"/>
	    <param name="S" value="5"/>
	    <param name="W" value="1"/>
	    <output name="output" file="smoother.output3"/>
	  </test>-->
  </tests>
  
<help>
  
This tool smooths genomic data with an area-preserving Gaussian_ filter. The Gaussian filter is computed out to +/- 3 standard deviations.

.. _Gaussian: http://en.wikipedia.org/wiki/Gaussian_filter
  
.. 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 "edit attributes" to set the correct format if it was not detected correctly.

</help>
</tool>