<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0.1">
  <description>Report CpG rich areas</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>newcpgreport -sequence '$input1' -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile '$out_file1' -minoe $minoe -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="window" type="integer" value="100" label="Window size" />
    <param name="shift" type="integer" value="1" label="Step size (shift)" />
    <param name="minlen" type="integer" value="200" label="Minimum length" />
    <param name="minoe" type="float" value="0.6" label="Minimum average observed to expected ratio" />
    <param name="minpc" type="float" value="50.0" label="Minimum average percentage of G plus C" />
  </inputs>
  <outputs>
    <data name="out_file1" format="newcpgreport" />
  </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://galaxy-iuc.github.io/emboss-5.0-docs/newcpgreport.html
  </help>
  <expand macro="citations" />
</tool>