Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison alignment/prank.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
---|---|
date | Tue, 11 Mar 2014 12:19:13 -0700 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:5b9a38ec4a39 |
---|---|
1 <tool id="prank" name="PRANK" version="1.0" force_history_refresh='True'> | |
2 <description> Phylogeny Aware Multiple Sequence Alignment </description> | |
3 <requirements> | |
4 <requirement type="package">prank</requirement> | |
5 </requirements> | |
6 <command interpreter="perl"> | |
7 prank.pl $input1 $format $missing | |
8 </command> | |
9 <inputs> | |
10 <param format="fasta" name="input1" type="data" label="Sequences in FASTA format" help=""/> | |
11 <param name="format" type="select" label="Output format"> | |
12 <option value="fasta">fasta</option> | |
13 </param> | |
14 <param name='missing' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='-F | |
15 option when sequences have terminal missing data'/> | |
16 </inputs> | |
17 <outputs> | |
18 <data from_work_dir="output.1.fas" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Alignment" /> | |
19 <data from_work_dir="output.2.fas" format="fasta" name="seqs_aligned2" label="${tool.name} on ${on_string}: Alignment" /> | |
20 </outputs> | |
21 <tests> | |
22 </tests> | |
23 <help> | |
24 **What it does** | |
25 | |
26 "PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel | |
27 algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, | |
28 PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the | |
29 evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be | |
30 aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences." | |
31 From the PRANK website: http://code.google.com/p/prank-msa/wiki/PRANK?tm=6 | |
32 | |
33 ------ | |
34 | |
35 **Inputs** | |
36 | |
37 FASTA | |
38 | |
39 ------ | |
40 | |
41 **Outputs** | |
42 | |
43 FASTA | |
44 | |
45 ------- | |
46 | |
47 **Additional Information** | |
48 | |
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 | |
50 | |
51 ------- | |
52 | |
53 **Citations** | |
54 | |
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. | |
56 | |
57 Current Osiris Citation is here | |
58 | |
59 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
60 | |
61 Additional Citations for this tool | |
62 | |
63 PRANK was developed by Ari Löytynoja and Nick Goldman and is maintained at http://code.google.com/p/prank-msa/ | |
64 | |
65 The WebCite online citation for PRANK is available here: | |
66 http://www.webcitation.org/query.php?url=http://tinyurl.com/prank-msa&refdoi=10.1186/1471-2105-11-579 | |
67 </help> | |
68 </tool> |