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Commit message:
Uploaded v0.0.5, automated installation |
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added:
tools/clinod/clinod.txt tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml |
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removed:
tools/protein_analysis/clinod.txt tools/protein_analysis/clinod.xml |
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| 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 |
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| @@ -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. |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> + |
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| 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 |
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| @@ -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. |
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| 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 |
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| @@ -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> |