Mercurial > repos > peterjc > nlstradamus
annotate tools/nlstradamus/nlstradamus.xml @ 2:9ec94203d895 draft
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author | peterjc |
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date | Tue, 23 Apr 2013 11:59:14 -0400 |
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1 <tool id="nlstradamus" name="NLStradamus" version="0.0.7"> |
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2 <description>Find nuclear localization signals (NLSs) in protein sequences</description> |
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3 <command> |
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4 NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file |
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5 </command> |
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6 <stdio> |
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7 <!-- Assume anything other than zero is an error --> |
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8 <exit_code range="1:" /> |
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9 <exit_code range=":-1" /> |
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10 </stdio> |
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11 <inputs> |
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12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> |
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13 <param name="model" type="select" display="radio" label="Model"> |
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14 <option value="1" selected="True">Two state</option> |
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15 <option value="2">Four state</option> |
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16 </param> |
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17 <param name="algorithm" type="select" display="radio" label="Algorithm"> |
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18 <option value="0">Viterbi</option> |
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19 <option value="1" selected="True">Posterior with threshold</option> |
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20 <option value="2">Both</option> |
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21 </param> |
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22 <param name="threshold" type="float" label="Posterior theshold" value="0.6"> |
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23 <validator type="in_range" min="0" max="1" message="Threshold value should be between 0 and 1."/> |
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24 </param> |
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25 </inputs> |
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26 <outputs> |
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27 <data name="tabular_file" format="tabular" label="NLStradamus results" /> |
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28 </outputs> |
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29 <requirements> |
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30 <requirement type="binary">NLStradamus</requirement> |
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31 <requirement type="package" version="1.8">NLStradamus</requirement> |
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32 </requirements> |
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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 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. |
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75 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. |
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76 BMC Bioinformatics. 2009 Jun 29;10(1):202. |
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77 http://dx.doi.org/10.1186/1471-2105-10-202 |
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78 |
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79 http://www.moseslab.csb.utoronto.ca/NLStradamus |
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80 |
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81 </help> |
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82 </tool> |