Mercurial > repos > peterjc > nlstradamus
view tools/nlstradamus/nlstradamus.xml @ 2:9ec94203d895 draft
Uploaded v0.0.7 with automatic installation of the C++ binary.
author | peterjc |
---|---|
date | Tue, 23 Apr 2013 11:59:14 -0400 |
parents | |
children | b2e648e55ed7 |
line wrap: on
line source
<tool id="nlstradamus" name="NLStradamus" version="0.0.7"> <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> <stdio> <!-- Assume anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <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> <requirement type="package" version="1.8">NLStradamus</requirement> </requirements> <tests> <test> <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="model" value="1" /> <param name="algorithm" value="1" /> <param name="threshold" value="0.6" /> <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" /> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta" /> <param name="model" value="2" /> <param name="algorithm" value="2" /> <param name="threshold" value="0.125"/> <output name="tabular_file" file="empty_nlstradamus.tabular" ftype="tabular" /> </test> </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): ====== =================================================================== Column Description ------ ------------------------------------------------------------------- c1 Sequence identifier c2 Algorithm (posterior or Viterbi) c3 Score (probability between threshold and 1 for posterior algorithm) c4 Start c5 End c6 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://dx.doi.org/10.1186/1471-2105-10-202 http://www.moseslab.csb.utoronto.ca/NLStradamus </help> </tool>