Mercurial > repos > peterjc > nlstradamus
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/nlstradamus.xml Tue Jun 07 17:39:58 2011 -0400 @@ -0,0 +1,57 @@ +<tool id="nlstradamus" name="NLStradamus" version="0.0.3"> + <description>Find nuclear localization signals (NLSs) in protein sequences</description> + <command> + NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file + </command> + <inputs> + <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> + <param name="model" type="select" display="radio" label="Model"> + <option value="1" selected="True">Two state</option> + <option value="2">Four state</option> + </param> + <param name="algorithm" type="select" display="radio" label="Algorithm"> + <option value="0">Viterbi</option> + <option value="1" selected="True">Posterior with threshold</option> + <option value="2">Both</option> + </param> + <param name="threshold" type="float" label="Posterior theshold" value="0.6"> + <validator type="in_range" min="0" max="1" message="Threshold value should be between 0 and 1."/> + </param> + </inputs> + <outputs> + <data name="tabular_file" format="tabular" label="NLStradamus results" /> + </outputs> + <requirements> + <requirement type="binary">NLStradamus</requirement> + </requirements> + <tests> + </tests> + <help> + +**What it does** + +This calls the NLStradamus tool for prediction of nuclear localization +signals (NLSs), which uses a Hidden Markov Model (HMM). + +The input is a FASTA file of protein sequences, and the output is tabular +with six columns (one row per NLS): + + * Sequence identifier + * Algorithm (posterior or Viterbi) + * Score (probability between threshold and 1 for posterior algorithm) + * Start + * End + * Sequence of NLS + +----- + +**References** + +A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. +NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. +BMC Bioinformatics. 2009 Jun 29;10(1):202. + +http://www.moseslab.csb.utoronto.ca/NLStradamus + + </help> +</tool>