<tool id="phytab_mafft" name="phytab MAFFT" force_history_refresh='True'>
    <description> Multiple Sequence Alignment </description>
    <requirements>
        <requirement type="binary">mafft</requirement>
    </requirements>
    <command interpreter="python">
        phytab_mafft.py -s $Strategy -i $input > $mafft_stdout 2>&amp;1
    </command>
    <inputs>
     <param format="fasta,tabular" name="input" type="data" label="Sequence data" help="Format: Fasta or Phytab"/>
     <param name="Strategy" type="select" label="Alignment Strategy">
      <option value="Auto">Auto</option>
      <option value="FFT-NS-1">FFT-NS-1</option>
      <option value="FFT-NS-2">FFT-NS-2</option>
      <option value="FFT-NS-i">FFT-NS-i</option>
      <option value="E-INS-i">E-INS-i</option>
      <option value="L-INS-i">L-INS-i</option>
      <option value="G-INS-i">G-INS-i</option>
      <option value="Q-INS-i">Q-INS-i</option>
    </param>
    </inputs>
    <outputs>
        <data format="txt" name="mafft_stdout" label="${tool.name} on ${on_string}: stdout" />
	<data from_work_dir="data/results.data" format="input" name="seqs_aligned" label="${tool.name} on ${on_string}: Screen Output" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**
This tool runs MAFFT alignment algorithm on when given a single-gene (fasta or phytab) or a multi-gene (phytab) dataset.
Output for single genes is fasta; output for multi-genes is phytab.

------

**Inputs**

FASTA (single-gene) or phytab (single- or multi-gene).

*Algorithm strategies:*

 Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size; may vary between gene partitions in cases of multi-gene input datasets). 

 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).

------

**Outputs**

phytab

------

**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

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**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: MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
Recent developments in the MAFFT multiple sequence alignment program.

MAFFT website: http://mafft.cbrc.jp/alignment/server/index.html
    </help>
</tool>