# HG changeset patch
# User peterjc
# Date 1369934793 14400
# Node ID d1aebb0acee73491ad2a956a1fc46efc1880164c
# Parent  221d7dca03a5628914f8db3df699125925802330
Uploaded v0.0.5, automated installation

diff -r 221d7dca03a5 -r d1aebb0acee7 tools/clinod/clinod.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clinod/clinod.txt	Thu May 30 13:26:33 2013 -0400
@@ -0,0 +1,108 @@
+Galaxy wrapper for Command line NoD predictor (v1.3)
+====================================================
+
+This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+Command line NoD predictor is a tool for predicting nucleolar localization
+sequences (NoLSs) in a FASTA file of proteins using a neural network. There
+is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/
+
+This NoD wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
+Neural Network Simulator (SNNS), and set the $CLINOD to their folder.
+
+
+Manual Installation
+===================
+This wrapper expects the java binary to be on the system PATH, and to be able
+to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used
+/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod
+
+Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
+Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
+system path or located next to the JAR file, i.e. /opt/clinod/batchman
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a tools/clinod folder:
+
+* clinod.xml (the Galaxy tool definition)
+* clinod.txt (this README file)
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. If you are using other protein analysis tools like TMHMM or SignalP, put
+it next to them. Just add the line:
+
+<tool file="clinod/clinod.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder.
+
+$ ./run_functional_tests.sh -id clinod
+
+That's it.
+
+
+History
+=======
+
+v0.0.1 - Initial public release
+v0.0.2 - Treat non-zero return codes as errors
+v0.0.3 - Describe output table in help
+v0.0.4 - Added unit test
+v0.0.5 - Link to Tool Shed added to help text and this documentation.
+       - Automated tool installation.
+
+
+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://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+$ tar -czf clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular
+
+Check this worked:
+
+$ tar -tzf clinod.tar.gz
+tools/clinod/clinod.xml
+tools/clinod/clinod.txt
+tools/clinod/tool_dependencies.xml
+test-data/four_human_proteins.fasta
+test-data/four_human_proteins.clinod-1.3.tabular
+
+
+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. Command line
+NoD is available and licenced separately.
diff -r 221d7dca03a5 -r d1aebb0acee7 tools/clinod/clinod.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clinod/clinod.xml	Thu May 30 13:26:33 2013 -0400
@@ -0,0 +1,77 @@
+<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**
+
+M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
+Characterization and prediction of protein nucleolar localization sequences.
+Nucleic Acids Research 38(21), 7388-7399, 2010.
+http://dx.doi.org/10.1093/nar/gkq653
+
+M. S. Scott, P. V. Troshin and G. J. Barton.
+NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
+BMC Bioinformatics, 12:317, 2011.
+http://dx.doi.org/10.1186/1471-2105-12-317
+
+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>
diff -r 221d7dca03a5 -r d1aebb0acee7 tools/clinod/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clinod/tool_dependencies.xml	Thu May 30 13:26:33 2013 -0400
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="clinod" version="1.3">
+        <install version="1.0">
+            <actions>
+                <!-- Set environment variable $CLINOD so wrapper knows where to look -->
+                <action type="set_environment">
+                    <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
+                <action type="shell_command">wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz</action>
+		<action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action>
+                <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action>
+                <!-- clinod itself is just a JAR file -->
+                <action type="shell_command">wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar</action>
+                <!-- Don't need to move it, $INSTALL_DIR is the current directory
+                <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR</destination></action>
+                -->
+            </actions>
+        </install>
+        <readme>
+Downloads and installs the command line NoD (clinod) JAR file and the binary
+dependency batchman, and sets $CLINOD to the folder used.
+
+We could download, compiles and install the SNNS Batch Interpreter v1.0 executable
+(batchman) from Stuttgart Neural Network Simulator (SNNS) v4.2. However, we simplify
+this by downloading SNNS v4.3 which includes the precompiled copy of batch man.
+
+For more details, see:
+http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp
+        </readme>
+    </package>
+</tool_dependency>
+
diff -r 221d7dca03a5 -r d1aebb0acee7 tools/protein_analysis/clinod.txt
--- a/tools/protein_analysis/clinod.txt	Tue Apr 16 13:01:54 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-Galaxy wrapper for Command line NoD predictor (v1.3)
-====================================================
-
-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.
-
-Command line NoD predictor is a tool for predicting nucleolar localization
-sequences (NoLSs) in a FASTA file of proteins using a neural network. There
-is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/
-
-
-Installation
-============
-This wrapper expects the java binary to be on the system PATH, and to be able
-to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if
-you wish to use a different location).
-
-Internally NoD calls the binary batchman from the Stuttgart Neural Network
-Simulator (SNNS) v 4.2 software suite. This binary can either be on the system
-path or located next to the JAR file, i.e. /opt/clinod/batchman
-
-To install the wrapper copy or move the following files under the Galaxy tools
-folder, e.g. in a tools/protein_analysis folder:
-
-* clinod.xml (the Galaxy tool definition)
-* clinod.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/clinod.xml" />
-
-That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial public release
-v0.0.2 - Treat non-zero return codes as errors
-v0.0.3 - Describe output table in help
-v0.0.4 - Added unit test
-
-
-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://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular
-
-Check this worked:
-
-$ tar -tzf clinod.tar.gz
-tools/protein_analysis/clinod.xml
-tools/protein_analysis/clinod.txt
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.clinod-1.3.tabular
-
-
-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. Command line
-NoD is available and licenced separately.
diff -r 221d7dca03a5 -r d1aebb0acee7 tools/protein_analysis/clinod.xml
--- a/tools/protein_analysis/clinod.xml	Tue Apr 16 13:01:54 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.4">
-    <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
-    <command>
-      java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -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>
-    <requirements>
-        <requirement type="binary">java</requirement>
-    </requirements>
-    <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**
-
-M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
-Characterization and prediction of protein nucleolar localization sequences.
-Nucleic Acids Research 38(21), 7388-7399, 2010.
-http://dx.doi.org/10.1093/nar/gkq653
-
-M. S. Scott, P. V. Troshin and G. J. Barton.
-NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
-BMC Bioinformatics, 12:317, 2011.
-http://dx.doi.org/10.1186/1471-2105-12-317
-
-http://www.compbio.dundee.ac.uk/www-nod/
-
-    </help>
-</tool>