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annotate alignment/prank.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 <tool id="prank" name="PRANK" version="1.0" force_history_refresh='True'> |
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2 <description> Phylogeny Aware Multiple Sequence Alignment </description> |
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3 <requirements> |
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4 <requirement type="package">prank</requirement> |
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5 </requirements> |
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6 <command interpreter="perl"> |
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7 prank.pl $input1 $format $missing |
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8 </command> |
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9 <inputs> |
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10 <param format="fasta" name="input1" type="data" label="Sequences in FASTA format" help=""/> |
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11 <param name="format" type="select" label="Output format"> |
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12 <option value="fasta">fasta</option> |
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13 </param> |
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14 <param name='missing' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='-F |
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15 option when sequences have terminal missing data'/> |
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16 </inputs> |
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17 <outputs> |
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18 <data from_work_dir="output.1.fas" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Alignment" /> |
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19 <data from_work_dir="output.2.fas" format="fasta" name="seqs_aligned2" label="${tool.name} on ${on_string}: Alignment" /> |
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20 </outputs> |
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21 <tests> |
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22 </tests> |
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23 <help> |
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24 **What it does** |
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25 |
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26 "PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel |
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27 algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, |
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28 PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the |
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29 evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be |
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30 aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences." |
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31 From the PRANK website: http://code.google.com/p/prank-msa/wiki/PRANK?tm=6 |
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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 |
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38 |
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39 ------ |
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40 |
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41 **Outputs** |
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42 |
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43 FASTA |
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44 |
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45 ------- |
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46 |
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47 **Additional Information** |
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48 |
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49 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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50 |
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51 ------- |
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52 |
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53 **Citations** |
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54 |
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55 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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56 |
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57 Current Osiris Citation is here |
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58 |
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59 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html |
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60 |
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61 Additional Citations for this tool |
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62 |
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63 PRANK was developed by Ari Löytynoja and Nick Goldman and is maintained at http://code.google.com/p/prank-msa/ |
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64 |
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65 The WebCite online citation for PRANK is available here: |
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66 http://www.webcitation.org/query.php?url=http://tinyurl.com/prank-msa&refdoi=10.1186/1471-2105-11-579 |
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67 </help> |
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68 </tool> |