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Uploaded v0.0.7 with automatic installation of the C++ binary.
author peterjc
date Tue, 23 Apr 2013 11:59:14 -0400
parents f93ad4882338
children b2e648e55ed7
files tools/nlstradamus/nlstradamus.txt tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml tools/protein_analysis/nlstradamus.txt tools/protein_analysis/nlstradamus.xml
diffstat 5 files changed, 223 insertions(+), 185 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/nlstradamus/nlstradamus.txt	Tue Apr 23 11:59:14 2013 -0400
@@ -0,0 +1,116 @@
+Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
+=========================================================
+
+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.
+
+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://dx.doi.org/10.1186/1471-2105-10-202
+
+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).
+
+Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
+unchanged.
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the C++ implementation of NLStradamus v1.8, and run the unit tests.
+
+
+Manual Installation
+===================
+This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
+PATH.
+
+To install the wrapper copy or move 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 (matching the chosen install path):
+
+<tool file="protein_analysis/nlstradamus.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. Then:
+
+$ ./run_functional_tests.sh -id nlstradamus
+
+That's it.
+
+
+History
+=======
+
+v0.0.3 - Initial public release
+v0.0.4 - Adding DOI link to reference
+         (Documentation change only)
+v0.0.5 - Assume non-zero return codes are errors
+v0.0.6 - Show output help text using a table
+       - Added unit tests
+v0.0.7 - Automatic installation of the NLStradamus binary when installed
+         via the Galaxy Tool Shed
+
+
+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 nlstradmus.tar.gz tools/nlstradamus/nlstradamus.xml tools/nlstradamus/nlstradamus.txt tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
+
+Check this worked:
+
+$ tar -tzf nlstradmus.tar.gz
+tools/nlstradamus/nlstradamus.xml
+tools/nlstradamus/nlstradamus.txt
+tools/nlstradamus/tool_dependencies.xml
+test-data/four_human_proteins.fasta
+test-data/four_human_proteins.nlstradamus.tabular
+test-data/empty.fasta
+test-data/empty_nlstradamus.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. NLStradamus
+is is available and licenced separately (under the GPL v3 or later).
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/nlstradamus/nlstradamus.xml	Tue Apr 23 11:59:14 2013 -0400
@@ -0,0 +1,82 @@
+<tool id="nlstradamus" name="NLStradamus" version="0.0.7">
+    <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>
+    <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"/> 
+        <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>
+        <requirement type="package" version="1.8">NLStradamus</requirement>
+    </requirements>
+    <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**
+
+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://dx.doi.org/10.1186/1471-2105-10-202
+
+http://www.moseslab.csb.utoronto.ca/NLStradamus
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/nlstradamus/tool_dependencies.xml	Tue Apr 23 11:59:14 2013 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="NLStradamus" version="1.8">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8.tar.gz</action>
+		<!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did not -->
+                <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action>
+                <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+This downloads NLStradamus v1.8 from this folder,
+http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/
+
+The C++ tool is compiled as described in the README_C.txt file, using g++, and included in the $PATH.
+
+The older slower Perl implementation is not installed.
+        </readme>
+    </package>
+</tool_dependency>
+
--- a/tools/protein_analysis/nlstradamus.txt	Wed Apr 17 08:26:25 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
-=========================================================
-
-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.
-
-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://dx.doi.org/10.1186/1471-2105-10-202
-
-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).
-
-Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
-unchanged.
-
-
-Installation
-============
-This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
-PATH.
-
-To install the wrapper copy or move 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" />
-
-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.
-
-That's it.
-
-
-History
-=======
-
-v0.0.3 - Initial public release
-v0.0.4 - Adding DOI link to reference
-         (Documentation change only)
-v0.0.5 - Assume non-zero return codes are errors
-v0.0.6 - Show output help text using a table
-       - Added unit tests
-
-
-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 nlstradmus.tar.gz tools/protein_analysis/nlstradamus.xml tools/protein_analysis/nlstradamus.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
-
-Check this worked:
-
-$ tar -tzf nlstradmus.tar.gz
-tools/protein_analysis/nlstradamus.xml
-tools/protein_analysis/nlstradamus.txt
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.nlstradamus.tabular
-test-data/empty.fasta
-test-data/empty_nlstradamus.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. NLStradamus
-is available and licenced separately.
--- a/tools/protein_analysis/nlstradamus.xml	Wed Apr 17 08:26:25 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-<tool id="nlstradamus" name="NLStradamus" version="0.0.6">
-    <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>
-    <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"/> 
-        <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>
-        <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**
-
-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://dx.doi.org/10.1186/1471-2105-10-202
-
-http://www.moseslab.csb.utoronto.ca/NLStradamus
-
-    </help>
-</tool>