--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/phytab_mafft.xml	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,86 @@
+<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
+
+-------
+
+**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>