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comparison tools/nlstradamus/nlstradamus.xml @ 2:9ec94203d895 draft

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Uploaded v0.0.7 with automatic installation of the C++ binary.
author peterjc
date Tue, 23 Apr 2013 11:59:14 -0400
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1:f93ad4882338 2:9ec94203d895
1 <tool id="nlstradamus" name="NLStradamus" version="0.0.7">
2 <description>Find nuclear localization signals (NLSs) in protein sequences</description>
3 <command>
4 NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
5 </command>
6 <stdio>
7 <!-- Assume anything other than zero is an error -->
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 </stdio>
11 <inputs>
12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
13 <param name="model" type="select" display="radio" label="Model">
14 <option value="1" selected="True">Two state</option>
15 <option value="2">Four state</option>
16 </param>
17 <param name="algorithm" type="select" display="radio" label="Algorithm">
18 <option value="0">Viterbi</option>
19 <option value="1" selected="True">Posterior with threshold</option>
20 <option value="2">Both</option>
21 </param>
22 <param name="threshold" type="float" label="Posterior theshold" value="0.6">
23 <validator type="in_range" min="0" max="1" message="Threshold value should be between 0 and 1."/>
24 </param>
25 </inputs>
26 <outputs>
27 <data name="tabular_file" format="tabular" label="NLStradamus results" />
28 </outputs>
29 <requirements>
30 <requirement type="binary">NLStradamus</requirement>
31 <requirement type="package" version="1.8">NLStradamus</requirement>
32 </requirements>
33 <tests>
34 <test>
35 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
36 <param name="model" value="1" />
37 <param name="algorithm" value="1" />
38 <param name="threshold" value="0.6" />
39 <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" />
40 </test>
41 <test>
42 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
43 <param name="model" value="2" />
44 <param name="algorithm" value="2" />
45 <param name="threshold" value="0.125"/>
46 <output name="tabular_file" file="empty_nlstradamus.tabular" ftype="tabular" />
47 </test>
48 </tests>
49 <help>
50
51 **What it does**
52
53 This calls the NLStradamus tool for prediction of nuclear localization
54 signals (NLSs), which uses a Hidden Markov Model (HMM).
55
56 The input is a FASTA file of protein sequences, and the output is tabular
57 with six columns (one row per NLS):
58
59 ====== ===================================================================
60 Column Description
61 ------ -------------------------------------------------------------------
62 c1 Sequence identifier
63 c2 Algorithm (posterior or Viterbi)
64 c3 Score (probability between threshold and 1 for posterior algorithm)
65 c4 Start
66 c5 End
67 c6 Sequence of NLS
68 ====== ===================================================================
69
70 -----
71
72 **References**
73
74 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
75 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
76 BMC Bioinformatics. 2009 Jun 29;10(1):202.
77 http://dx.doi.org/10.1186/1471-2105-10-202
78
79 http://www.moseslab.csb.utoronto.ca/NLStradamus
80
81 </help>
82 </tool>