--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/mafft.xml	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,79 @@
+<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>