<tool id="mafft" name="MAFFT" version="1.0" force_history_refresh='True'>
    <description> Multiple Sequence Alignment </description>
    <requirements>
        <requirement type="package">mafft</requirement>
    </requirements>
    <command interpreter="perl">
        mafft.pl $Strategy $input1
    </command>
    <inputs>
        <param format="fasta" name="input1" type="data" label="Sequences in fasta format" help=""/>
    <param name="Strategy" type="select" label="Alignment Strategy">
      <option value="Auto">Auto</option>
      <option value="FFT-NS-1">FFT-NS-1</option>
      <option value="FFT-NS-2">FFT-NS-2</option>
      <option value="FFT-NS-i">FFT-NS-i</option>
      <option value="E-INS-i">E-INS-i</option>
      <option value="L-INS-i">L-INS-i</option>
      <option value="G-INS-i">G-INS-i</option>
      <option value="Q-INS-i">Q-INS-i</option>
    </param>
    </inputs>
    <outputs>
	<data from_work_dir="seqs_aligned.fasta" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Screen Output" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

MAFFT is a multiple sequence alignment program. It offers a range of multiple alignment methods.
From the MAFFT website: http://mafft.cbrc.jp/alignment/software/

------

**Inputs**
  Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size).

  FFT-NS-1 (Very fast; recommended for more than 2,000 sequences; progressive method). 

  FFT-NS-2 (Fast; progressive method). 

  FFT-NS-i (Slow; iterative refinement method). 

  E-INS-i (Very slow; recommended for less than 200 sequences with multiple conserved domains and long gaps).

  L-INS-i (Very slow; recommended for less than 200 sequences with one conserved domain and long gaps).

  G-INS-i (Very slow; recommended for less than 200 sequences with global homology).

  Q-INS-i (Extremely slow; secondary structure of RNA is considered; recommended for a global alignment of highly diverged ncRNAs with less than 200 sequences × less than 1,000 nucleotides).

------

**Output**

FASTA

------

**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org

-------

**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298) 
Recent developments in the MAFFT multiple sequence alignment program. 
 </help>
</tool>