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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="phytab_mafft" name="phytab MAFFT" force_history_refresh='True'>
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2 <description> Multiple Sequence Alignment </description>
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3 <requirements>
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4 <requirement type="binary">mafft</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 phytab_mafft.py -s $Strategy -i $input > $mafft_stdout 2>&amp;1
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8 </command>
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9 <inputs>
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10 <param format="fasta,tabular" name="input" type="data" label="Sequence data" help="Format: Fasta or Phytab"/>
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11 <param name="Strategy" type="select" label="Alignment Strategy">
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12 <option value="Auto">Auto</option>
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13 <option value="FFT-NS-1">FFT-NS-1</option>
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14 <option value="FFT-NS-2">FFT-NS-2</option>
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15 <option value="FFT-NS-i">FFT-NS-i</option>
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16 <option value="E-INS-i">E-INS-i</option>
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17 <option value="L-INS-i">L-INS-i</option>
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18 <option value="G-INS-i">G-INS-i</option>
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19 <option value="Q-INS-i">Q-INS-i</option>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="mafft_stdout" label="${tool.name} on ${on_string}: stdout" />
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24 <data from_work_dir="data/results.data" format="input" name="seqs_aligned" label="${tool.name} on ${on_string}: Screen Output" />
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25 </outputs>
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26 <tests>
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27 </tests>
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28 <help>
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29 **What it does**
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30 This tool runs MAFFT alignment algorithm on when given a single-gene (fasta or phytab) or a multi-gene (phytab) dataset.
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31 Output for single genes is fasta; output for multi-genes is phytab.
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32
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33 ------
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34
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35 **Inputs**
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36
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37 FASTA (single-gene) or phytab (single- or multi-gene).
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38
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39 *Algorithm strategies:*
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40
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41 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).
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42
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43 FFT-NS-1 (Very fast; recommended for more than 2,000 sequences; progressive method).
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44
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45 FFT-NS-2 (Fast; progressive method).
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46
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47 FFT-NS-i (Slow; iterative refinement method).
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48
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49 E-INS-i (Very slow; recommended for less than 200 sequences with multiple conserved domains and long gaps).
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50
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51 L-INS-i (Very slow; recommended for less than 200 sequences with one conserved domain and long gaps).
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52
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53 G-INS-i (Very slow; recommended for less than 200 sequences with global homology).
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54
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55 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).
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56
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57 ------
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58
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59 **Outputs**
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60
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61 phytab
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62
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63 ------
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64
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65 **Additional Information**
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66
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67 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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68
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69 -------
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70
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71 **Citations**
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72
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73 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.
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74
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75 Current Osiris Citation is here
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76
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77 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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78
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79 Additional Citations for this tool
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80
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81 MAFFT: MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
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82 Recent developments in the MAFFT multiple sequence alignment program.
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83
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84 MAFFT website: http://mafft.cbrc.jp/alignment/server/index.html
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85 </help>
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86 </tool>