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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_muscle" name="phytab MUSCLE" version="1.0">
2 <description>MUSCLE: Multiple sequence alignment. Input can be FASTA or phytab format.</description>
3 <requirements>
4 <requirement type="package">muscle</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_muscle.py -i $data > $muscle_stdout 2>&amp;1
8 </command>
9 <inputs>
10 <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in fasta or phytab format"/>
11 </inputs>
12 <outputs>
13 <data format="txt" name="muscle_stdout" label="${tool.name} on ${on_string}: stdout" />
14 <data format="tabular" name="muscle_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
15 </outputs>
16 <tests>
17 </tests>
18 <help>
19 **What it does**
20
21 Uses MUSCLE to perform multiple sequence alignment on multiple gene families in parallel.
22
23 ------
24
25 **Inputs**
26
27 Can take as input fasta or phytab format. Phytab allows alignment in parallel of multiple separate gene families/paralogs. See:
28 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
29
30 ------
31
32 **Outputs**
33
34 Either a fasta file or phytab file of aligned sequences
35
36 -------
37
38 **Additional Information**
39
40 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
41
42 -------
43
44 **Citations**
45
46 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.
47
48 Current Osiris Citation is here
49
50 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
51
52 Additional Citations for this tool
53
54 Runs MUSCLE 3.8 Multiple Sequence Alignment
55 See MUSCLE help: http://www.drive5.com/muscle/muscle_userguide3.8.html
56
57 </help>
58 </tool>
59
60