<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">

  <description>Report CpG rich areas</description>

  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>

  <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>

  <inputs>

    <param format="data" name="input1" type="data">

      <label>Sequence</label>

    </param>

    <param name="window" size="4" type="text" value="100">

      <label>Window Size</label>

    </param>

    <param name="shift" size="4" type="text" value="1">

      <label>Step size (shift)</label>

    </param>

    <param name="minlen" size="4" type="text" value="200">

      <label>Minimum length</label>

    </param>

    <param name="minoe" size="4" type="text" value="0.6">

      <label>Minimum average observed to expected ratio</label>

    </param>

    <param name="minpc" size="4" type="text" value="50.0">

      <label>Minimum average percentage of G plus C</label>

    </param>

  </inputs>

  <outputs>

    <data format="newcpgreport" name="out_file1" />

  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="100"/>
      <param name="shift" value="1"/>
      <param name="minlen" value="200"/>
      <param name="minoe" value="0.6"/>
      <param name="minpc" value="50.0"/>
      <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/>
    </test>
  </tests>

  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html



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**Citation**



If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>