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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_aliscorecut" name="phytab AliccoreCut" version="1.0">
2 <description>Runs Aliscore then Alicut on an aligned sequence in phytab format.</description>
3 <requirements>
4 <requirement type="package">aliscore and alicut</requirement>
5 </requirements>
6 <command interpreter="python">
7 aliscorecut.py -i $sequence > $aliscorecut_stdout 2>&amp;1
8 </command>
9 <inputs>
10 <param format="txt" name="sequence" type="data" label="Aligned sequence" help="This should be an aligned sqeuence from UCSB Muscle."/>
11 </inputs>
12 <outputs>
13 <data format="txt" name="aliscorecut_stdout" label="${tool.name} on ${on_string}: stdout" />
14 <data format="tabular" name="aliscorecut_results" label="${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 Aliscore identifies ambiguously aligned regions of a multiple sequence alignment. Alicut deletes sites marked by aliscore. This tool combines both into one tool.
22
23 ------
24
25 **Inputs**
26
27 Aligned sequences in phytab format
28
29 ------
30
31 **Outputs**
32
33 phytab format
34
35 ------
36
37 **Additional information**
38
39 For information on phytab format see: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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
42 bitbucket.org
43
44 ------
45
46 **Citations**
47
48 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
49 citing the following.
50
51 Current Osiris Citation is here
52
53 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
54
55 Additional Citations for this tool
56
57 Aliscore: Kuck P, Meusemann K, Dambach J, Thormann B, von Reumont BM, et al. (2010) Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better
58 resolved trees. Front Zool 7: 10.
59 </help>
60 </tool>