Mercurial > repos > peterjc > nlstradamus
annotate tools/protein_analysis/nlstradamus.xml @ 0:0ad90e5eb390
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:39:58 -0400 |
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children | f93ad4882338 |
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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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1 <tool id="nlstradamus" name="NLStradamus" version="0.0.3"> |
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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 <inputs> |
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7 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> |
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8 <param name="model" type="select" display="radio" label="Model"> |
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9 <option value="1" selected="True">Two state</option> |
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10 <option value="2">Four state</option> |
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11 </param> |
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12 <param name="algorithm" type="select" display="radio" label="Algorithm"> |
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13 <option value="0">Viterbi</option> |
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14 <option value="1" selected="True">Posterior with threshold</option> |
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15 <option value="2">Both</option> |
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16 </param> |
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17 <param name="threshold" type="float" label="Posterior theshold" value="0.6"> |
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18 <validator type="in_range" min="0" max="1" message="Threshold value should be between 0 and 1."/> |
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19 </param> |
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20 </inputs> |
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21 <outputs> |
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22 <data name="tabular_file" format="tabular" label="NLStradamus results" /> |
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23 </outputs> |
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24 <requirements> |
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25 <requirement type="binary">NLStradamus</requirement> |
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26 </requirements> |
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27 <tests> |
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28 </tests> |
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29 <help> |
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30 |
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31 **What it does** |
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32 |
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33 This calls the NLStradamus tool for prediction of nuclear localization |
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34 signals (NLSs), which uses a Hidden Markov Model (HMM). |
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35 |
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36 The input is a FASTA file of protein sequences, and the output is tabular |
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37 with six columns (one row per NLS): |
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38 |
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39 * Sequence identifier |
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40 * Algorithm (posterior or Viterbi) |
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41 * Score (probability between threshold and 1 for posterior algorithm) |
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42 * Start |
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43 * End |
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44 * Sequence of NLS |
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45 |
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46 ----- |
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47 |
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48 **References** |
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49 |
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50 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. |
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51 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. |
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52 BMC Bioinformatics. 2009 Jun 29;10(1):202. |
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53 |
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54 http://www.moseslab.csb.utoronto.ca/NLStradamus |
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55 |
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56 </help> |
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57 </tool> |