<tool id="EMBOSS: einverted28" name="einverted" version="@VERSION@.1">
  <description>Finds DNA inverted repeats</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="On query" />
    <param name="gap" type="integer" value="12" label="Gap penalty" />
    <param name="threshold" type="integer" value="50" label="Minimum score threshold" />
    <param name="match" type="integer" value="3" label="Match score" />
    <param name="mismatch" type="integer" value="-4" label="Mismatch score" />
    <param name="maxrepeat" type="integer" value="2000" label="Maximum separation between the start of repeat and the end of the inverted repeat" />
  </inputs>
  <outputs>
    <data name="out_file1" format="einverted" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="gap" value="12"/>
      <param name="threshold" value="50"/>
      <param name="match" value="3"/>
      <param name="mismatch" value="-4"/>
      <param name="maxrepeat" value="2000"/>
      <output name="out_file1" file="emboss_einverted_out.einverted"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/einverted.html
  </help>
  <expand macro="citations" />
</tool>