<tool id="seqshuffle" name="shuffle sequences">
  <description>preserving mono-nucleotide frequency</description>
  <command>cat $input | fasta-shuffle-letters > $output  </command>
  <inputs>
     <param name="input" type="data" format="fasta" label="Original FASTA sequence file"/>
  </inputs>
  <outputs>
    <data format="fasta" name="output" />
  </outputs>
  <help>

**Description**

shuffle the position of nucleotides in each sequence, preserving the frequency of nucleotides in that sequence, but do not preserve di-nucleotide frequency. 

  </help>
</tool>