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v0.0.10 internal changes; v0.0.9 citation
author peterjc
date Wed, 05 Aug 2015 12:23:05 -0400
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1 <tool id="nlstradamus" name="NLStradamus" version="0.0.10">
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2 <description>Find nuclear localization signals (NLSs) in protein sequences</description>
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3 <requirements>
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4 <requirement type="binary">NLStradamus</requirement>
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5 <requirement type="package" version="1.8">NLStradamus</requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Assume anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 </stdio>
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12 <command>
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13 NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
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14 </command>
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15 <inputs>
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16 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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17 <param name="model" type="select" display="radio" label="Model">
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18 <option value="1" selected="True">Two state</option>
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19 <option value="2">Four state</option>
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20 </param>
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21 <param name="algorithm" type="select" display="radio" label="Algorithm">
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22 <option value="0">Viterbi</option>
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23 <option value="1" selected="True">Posterior with threshold</option>
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24 <option value="2">Both</option>
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25 </param>
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26 <param name="threshold" type="float" label="Posterior theshold" value="0.6">
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27 <validator type="in_range" min="0" max="1" message="Threshold value should be between 0 and 1."/>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="tabular_file" format="tabular" label="NLStradamus results" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
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36 <param name="model" value="1" />
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37 <param name="algorithm" value="1" />
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38 <param name="threshold" value="0.6" />
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39 <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" />
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40 </test>
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41 <test>
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42 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
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43 <param name="model" value="2" />
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44 <param name="algorithm" value="2" />
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45 <param name="threshold" value="0.125"/>
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46 <output name="tabular_file" file="empty_nlstradamus.tabular" ftype="tabular" />
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47 </test>
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48 </tests>
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49 <help>
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50
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51 **What it does**
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52
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53 This calls the NLStradamus tool for prediction of nuclear localization
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54 signals (NLSs), which uses a Hidden Markov Model (HMM).
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55
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56 The input is a FASTA file of protein sequences, and the output is tabular
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57 with six columns (one row per NLS):
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58
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59 ====== ===================================================================
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60 Column Description
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61 ------ -------------------------------------------------------------------
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62 c1 Sequence identifier
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63 c2 Algorithm (posterior or Viterbi)
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64 c3 Score (probability between threshold and 1 for posterior algorithm)
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65 c4 Start
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66 c5 End
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67 c6 Sequence of NLS
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68 ====== ===================================================================
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69
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70 -----
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71
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72 **References**
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73
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74
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75 If you use this Galaxy tool in work leading to a scientific publication please
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76 cite the following papers:
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77
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78 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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79 Galaxy tools and workflows for sequence analysis with applications
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80 in molecular plant pathology. PeerJ 1:e167
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81 http://dx.doi.org/10.7717/peerj.167
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82
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83 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses (2009).
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84 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
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85 BMC Bioinformatics 10(1):202.
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86 http://dx.doi.org/10.1186/1471-2105-10-202
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87
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88 See also http://www.moseslab.csb.utoronto.ca/NLStradamus
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89
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90 This wrapper is available to install into other Galaxy Instances via the Galaxy
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91 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
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92 </help>
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93 <citations>
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94 <citation type="doi">10.7717/peerj.167</citation>
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95 <citation type="doi">10.1186/1471-2105-10-202</citation>
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96 </citations>
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97 </tool>