annotate tools/clinod/clinod.xml @ 3:6a9debe4b860 draft

Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub

<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
    <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
    <requirements>
        <requirement type="binary">java</requirement>
        <requirement type="package" version="1.3">clinod</requirement>
    </requirements>
    <command>
##The Galaxy Tool Shed installation should define $CLINOD to point at folder
##containing both clinod-1.3.jar and the batchman binary:
java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
##I want the number of threads to be a Galaxy config option...
##TODO - Make the -clean_sequence argument a parameter?
    </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"/> 
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="NoD results" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
	    <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>

**What it does**

This calls the command line version of the NoD tool from the Barton Group for
prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an
artificial neural network trained on a set of human NoLSs.

The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded
as a special nuclear localization sequence (NLS).

The input is a FASTA file of protein sequences, and the output is tabular with
four columns (multiple rows per protein):

====== ===================
Column Description
------ -------------------
     1 Sequence identifier
     2 Start of NoLS
     3 End of NoLS
     4 NoLS sequence
====== ===================

If a sequence has no predicted NoLS, then there is no line in the output file
for it.

-----

**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

M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton (2010).
Characterization and prediction of protein nucleolar localization sequences.
Nucleic Acids Research 38(21), 7388-7399.
http://dx.doi.org/10.1093/nar/gkq653

M. S. Scott, P. V. Troshin and G. J. Barton (2011).
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
BMC Bioinformatics, 12:317.
http://dx.doi.org/10.1186/1471-2105-12-317

See also http://www.compbio.dundee.ac.uk/www-nod/

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod

    </help>
</tool>