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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="mview_phytab_python" name="phytab_MView" version="1.0">
2 <description>View multiple phytab sequence alignments in HTML</description>
3 <requirements><requirement type="package">mview</requirement></requirements>
4 <command interpreter="python">phytab_mview.py $phytabinput $dna $output "$output.extra_files_path"
5 </command>
6
7 <inputs>
8 <param format="tabular" name="phytabinput" type="data" label="Phytab file of aligned genes to visualize" />
9 <param name="dna" type="select" label="Data type">
10 <option value="dna">DNA</option>
11 <option value="protein">Protein</option>
12 </param>
13 </inputs>
14
15 <outputs>
16 <data format="html" name="output" label="${tool.name} on ${on_string}: Alignment"/>
17 </outputs>
18 <help>
19 **What it does**
20
21 This tool uses the MVIEW package to convert an aligned sequences file in phytab format (ie, phytab_PRANK or phytab_MUSCLE output) to HTML for visualizing each gene's alignment directly in Galaxy.
22
23 ------
24
25 **Input**
26
27 ALIGNED phytab example input (fields are tab-delimited)::
28
29 Species_1 GeneA UniqueID AAAATGCCTA-GTC
30 Species_2 GeneA UniqueID AAATTGCCTA-GTG
31 Species_3 GeneA UniqueID AAAATGGCTAGGAC
32 Species_1 GeneB UniqueID TACGTAG-CTTGATCCTATAA
33 Species_2 GeneB UniqueID TACGTAGTCTAGATCCTATAA
34 Species_3 GeneB UniqueID TACGTAGTCTTGATGGTATAA
35
36 ------
37
38 **Output**
39
40 links to html files for viewing multiple sequence alignments
41
42 ------
43
44 **Additional Information**
45
46 For large datasets, this tool can be slow, as this version runs serially. For a
47 parallel version that sends different genes to different processors, contact
48 ucsb_phylogenetics@lifesci.ucsb.edu
49
50 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
51 bitbucket.org
52
53 ------
54
55 **Citations**
56
57 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.
58
59 Current Osiris Citation is here
60
61 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
62
63 Additional Citations for this tool
64
65 Citation for MView:
66 Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14(4):380-381.
67
68 </help>
69 </tool>