| Next changeset 1:f93ad4882338 (2013-04-17) |
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Commit message:
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository |
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added:
tools/protein_analysis/nlstradamus.txt tools/protein_analysis/nlstradamus.xml |
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| diff -r 000000000000 -r 0ad90e5eb390 tools/protein_analysis/nlstradamus.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/nlstradamus.txt Tue Jun 07 17:39:58 2011 -0400 |
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| @@ -0,0 +1,84 @@ +Galaxy wrapper for NLStradamus v1.7 (C++ version) +================================================= + +This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +NLStradamus is a command line tools for predicting nuclear localization +signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM). + +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 + +Early versions of NLStradamus did not have a native tabular output format, this +was added in version 1.7. Additionally a fast C++ implementation was added at +this point (early versions of NLStradamus came as a perl script only). This +wrapper expects the compiled C++ binary "NLStradamus" to be on the system PATH. + +To install the wrapper installed the following files under the Galaxy tools +folder, e.g. in a tools/protein_analysis folder: + +* nlstradamus.xml (the Galaxy tool definition) +* nlstradamus.txt (this README file) + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +tool. If you are using other protein analysis tools like TMHMM or SignalP, put +it next to them. Just add the line: + +<tool file="protein_analysis/nlstradamus.xml" /> + +That's it. + + +History +======= + +v0.0.3 - Initial public release + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradum.xml tools/protein_analysis/nlstradum.txt + +Check this worked: + +$ tar -tzf nlstradmus.tar.gz +filter/seq_filter_by_id.py +filter/seq_filter_by_id.txt +filter/seq_filter_by_id.xml + + +Licence (MIT/BSD style) +======================= + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. + +NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus +is available and licenced separately. |
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| diff -r 000000000000 -r 0ad90e5eb390 tools/protein_analysis/nlstradamus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/nlstradamus.xml Tue Jun 07 17:39:58 2011 -0400 |
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| @@ -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> |