<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">

  <description>Looks for inverted repeats in a nucleotide sequence</description>

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

  <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>

  <inputs>

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

      <label>Sequences</label>

    </param>

    <param name="minpallen" size="4" type="text" value="10">

      <label>Minimum length of palindrome</label>

    </param>

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

      <label>Maximum length of palindrome</label>

    </param>

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

      <label>Maximum gap between repeated regions</label>

    </param>

    <param name="nummismatches" size="4" type="text" value="0">

      <label>Number of mismatches allowed</label>

    </param>

    <param name="overlap" type="select">

      <label>Report overlapping matches</label>

      <option value="yes">Yes</option>

      <option value="no">No</option>

    </param>

  </inputs>

  <outputs>

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

  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minpallen" value="10"/>
      <param name="maxpallen" value="100"/>
      <param name="gaplimit" value="100"/>
      <param name="nummismatches" value="0"/>
      <param name="overlap" value="yes"/>
      <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
    </test>
  </tests>

  <help>

.. class:: warningmark

The input dataset needs to be sequences.

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    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.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>