<tool id="WigScale" name="Scale" version="1.2.0">
  <description>a (Big)Wig file</description>
  <command interpreter="bash">galaxyToolRunner.sh wigmath.Scale -i $input -m $M $chr -o $output</command>
  <inputs>
    <param format="bigwig,wig" name="input" type="data" label="Scale the data in" />
    <param name="M" type="float" value="0" label="Multiply by (leave 0 to scale by 1/mean)" />
    <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Scale chromosomes to 1/mean individually (no effect if scale factor is specified)" />
  </inputs>
  <outputs>
    <data format="wig" name="output" metadata_source="input" />
  </outputs>
  <tests>
    <!--<test>
	    <param name="input" value="wigmath.input1"/>
	    <param name="T" value="0"/>
	    <param name="dbkey" value="sacCer2"/>
	    <output name="output" file="percenter.output1"/>
	  </test>
	  <test>
	    <param name="input" value="wigmath.input1.bw"/>
	    <param name="T" value="0"/>
	    <param name="dbkey" value="sacCer2"/>
	    <output name="output" file="percenter.output1"/>
	  </test>
	  <test>
	    <param name="input" value="wigmath.input2"/>
	    <param name="T" value="2"/>
	    <param name="dbkey" value="sacCer2"/>
	    <output name="output" file="percenter.output2"/>
	  </test>
	  <test>
	    <param name="input" value="wigmath.input2.bw"/>
	    <param name="T" value="2"/>
	    <param name="dbkey" value="sacCer2"/>
	    <output name="output" file="percenter.output2"/>
	  </test>
	  <test>
	    <param name="input" value="wigmath.input3"/>
	    <param name="T" value="1000000"/>
	    <param name="dbkey" value="sacCer2"/>
	    <output name="output" file="percenter.output3"/>
	  </test>
	  <test>
	    <param name="input" value="wigmath.input3.bw"/>
	    <param name="T" value="1000000"/>
	    <param name="dbkey" value="sacCer2"/>
	    <output name="output" file="percenter.output3"/>
	  </test>-->
  </tests>
  
  <help>

This tool will multiply all values in a Wig file by a scale factor. For example, this can be used to normalize to read depth by multiplying by 1/(# reads). By default, the tool will scale to 1/(mean value), which is equivalent to dividing by coverage and multiplying by the size of the genome. The resulting output file should have mean 1.
    
.. 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>