Mercurial > repos > peterjc > nlstradamus
view tools/nlstradamus/nlstradamus.xml @ 4:1458e60f3fd0 draft
v0.0.10 internal changes; v0.0.9 citation
author | peterjc |
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date | Wed, 05 Aug 2015 12:23:05 -0400 |
parents | b2e648e55ed7 |
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<tool id="nlstradamus" name="NLStradamus" version="0.0.10"> <description>Find nuclear localization signals (NLSs) in protein sequences</description> <requirements> <requirement type="binary">NLStradamus</requirement> <requirement type="package" version="1.8">NLStradamus</requirement> </requirements> <stdio> <!-- Assume anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <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> <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** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses (2009). NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics 10(1):202. http://dx.doi.org/10.1186/1471-2105-10-202 See also http://www.moseslab.csb.utoronto.ca/NLStradamus This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus </help> <citations> <citation type="doi">10.7717/peerj.167</citation> <citation type="doi">10.1186/1471-2105-10-202</citation> </citations> </tool>