# HG changeset patch
# User peterjc
# Date 1307482798 14400
# Node ID 0ad90e5eb39026a6d0585121df5c85f1705546ee

Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository

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
@@ -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.
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
@@ -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>