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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="profilemafft" name="profilemafft" version="1.0" force_history_refresh='True'>
2 <description> Add Sequence(s) to existing Multiple Sequence Alignment </description>
3 <requirements>
4 <requirement type="package">mafft</requirement>
5 </requirements>
6 <command interpreter="perl">
7 profilemafft.pl $new_sequences $existing_alignment
8 </command>
9 <inputs>
10 <param format="fasta" name="new_sequences" type="data" label="Sequence(s) in fasta format" help=""/>
11 <param format="fasta" name="existing_alignment" type="data" label="Aligned sequences in fasta format" help=""/>
12 </inputs>
13 <outputs>
14 <data from_work_dir="log.txt" format="txt" name="screen" label="${tool.name} on ${on_string}: Screen Output" />
15 <data from_work_dir="seqs_aligned.fasta" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Full Alignment" />
16 </outputs>
17 <tests>
18 </tests>
19 <help>
20 **What it does**
21
22 This tool runs MAFFT profile alignment to add new sequences to an existing alignment
23
24 ------
25
26 **Inputs**
27
28 FASTA -- aligned sequences
29 FASTA -- new sequences to add to alignment
30
31 ------
32
33 **Outputs**
34
35 aligns new sequences into existing alignment outputting fasta
36
37 ------
38
39 **Additional Information**
40
41 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
42
43 -------
44
45 **Citations**
46
47 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.
48
49 Current Osiris Citation is here
50
51 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
52
53 Additional Citations for this tool
54
55 MAFFT: MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
56 Recent developments in the MAFFT multiple sequence alignment program.
57
58 MAFFT website: http://mafft.cbrc.jp/alignment/server/index.html
59
60 </help>
61 </tool>