Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison alignment/phytab_aliscorecut.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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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 > $aliscorecut_stdout 2>&1 | |
8 </command> | |
9 <inputs> | |
10 <param format="txt" name="sequence" type="data" label="Aligned sequence" help="This should be an aligned sqeuence from UCSB Muscle."/> | |
11 </inputs> | |
12 <outputs> | |
13 <data format="txt" name="aliscorecut_stdout" label="${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> |