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1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.4">
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2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
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3 <command>
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4 java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence
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5 ##I want the number of threads to be a Galaxy config option...
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6 ##TODO - Make the -clean_sequence argument a parameter?
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7 </command>
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8 <stdio>
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9 <!-- Assume anything other than zero is an error -->
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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13 <inputs>
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14 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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15 </inputs>
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16 <outputs>
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17 <data name="tabular_file" format="tabular" label="NoD results" />
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18 </outputs>
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19 <requirements>
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20 <requirement type="binary">java</requirement>
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21 </requirements>
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22 <tests>
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23 <test>
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24 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
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25 <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
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26 </test>
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27 </tests>
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28 <help>
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29
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30 **What it does**
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31
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32 This calls the command line version of the NoD tool from the Barton Group for
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33 prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an
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34 artificial neural network trained on a set of human NoLSs.
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35
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36 The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded
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37 as a special nuclear localization sequence (NLS).
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38
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39 The input is a FASTA file of protein sequences, and the output is tabular with
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40 four columns (multiple rows per protein):
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41
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42 ====== ===================
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43 Column Description
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44 ------ -------------------
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45 1 Sequence identifier
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46 2 Start of NoLS
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47 3 End of NoLS
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48 4 NoLS sequence
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49 ====== ===================
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50
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51 If a sequence has no predicted NoLS, then there is no line in the output file
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52 for it.
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53
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54
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55 **References**
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56
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57 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
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58 Characterization and prediction of protein nucleolar localization sequences.
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59 Nucleic Acids Research 38(21), 7388-7399, 2010.
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60 http://dx.doi.org/10.1093/nar/gkq653
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61
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62 M. S. Scott, P. V. Troshin and G. J. Barton.
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63 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
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64 BMC Bioinformatics, 12:317, 2011.
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65 http://dx.doi.org/10.1186/1471-2105-12-317
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66
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67 http://www.compbio.dundee.ac.uk/www-nod/
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68
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69 </help>
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70 </tool>
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