Mercurial > repos > peterjc > tmhmm_and_signalp

--- a/tools/protein_analysis/LICENSE	Thu May 23 12:49:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
-
-License for TMHMM 2.0, SignalP 3.0, WoLF PSORT and PSORTb wrappers for
-Galaxy (note that tools themselves are copyright and licensed separately)
-and the RXLR motif tool for Galaxy.
-
-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.
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/protein_analysis/LICENSE.txt	Tue Sep 10 08:55:19 2013 -0400
@@ -0,0 +1,26 @@
+These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
+
+License for TMHMM 2.0, SignalP 3.0, WoLF PSORT and PSORTb wrappers for
+Galaxy (note that tools themselves are copyright and licensed separately)
+and the RXLR motif tool for Galaxy.
+
+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.
+
--- a/tools/protein_analysis/README	Thu May 23 12:49:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,170 +0,0 @@
-This package contains Galaxy wrappers for a selection of standalone command
-line protein analysis tools:
-
-* SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
-  Sequence Analysis at the Technical University of Denmark,
-  http://www.cbs.dtu.dk/cbs/
-
-* WoLF PSORT v0.2 from http://wolfpsort.org/
-
-* PSORTb v3 from http://www.psort.org/downloads/index.html
-
-Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
-
-To use these Galaxy wrappers you must first install the command line tools.
-At the time of writing they are all free for academic use, or open source.
-
-These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
-See the included LICENCE file for details (an MIT style open source licence).
-
-The wrappers are available from the Galaxy Tool Shed
-http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
-
-
-Requirements
-============
-
-First install those command line tools you wish to use the wrappers for:
-
-1. Install the command line version of SignalP 3.0 and ensure "signalp" is
-   on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
-
-2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
-   the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
-
-3. Install the command line version of Promoter 2.0 and ensure "promoter" is
-   on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
-
-4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
-   is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
-   directory, run runWolfPsortSummary, and then change back to the original
-   directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
-
-5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
-   but put it on the path under the name hmmsearch2 (allowing it to co-exist
-   with HMMER 3), or edit rlxr_motif.py accordingly.
-
-Verify each of the tools is installed and working from the command line
-(when logged in as the Galaxy user if appropriate).
-
-
-Manual Installation
-===================
-
-1. Create a folder tools/protein_analysis under your Galaxy installation.
-   This folder name is not critical, and can be changed if desired - you
-   must update the paths used in tool_conf.xml to match.
-
-2. Copy/move the following files (from this archive) there:
-
-tmhmm2.xml (Galaxy tool definition)
-tmhmm2.py (Python wrapper script)
-
-signalp3.xml (Galaxy tool definition)
-signalp3.py (Python wrapper script)
-
-promoter2.xml (Galaxy tool definition)
-promoter2.py (Python wrapper script)
-
-psortb.xml (Galaxy tool definition)
-psortb.py (Python wrapper script)
-
-wolf_psort.xml (Galaxy tool definition)
-wolf_psort.py (Python wrapper script)
-
-rxlr_motifs.xml (Galaxy tool definition)
-rxlr_motifs.py (Python script)
-
-seq_analysis_utils.py (shared Python code)
-LICENCE
-README (this file)
-
-3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
-   also tool_conf.xml.sample (to run the tests) to include the new tools
-   by adding:
-
-  <section name="Protein sequence analysis" id="protein_analysis">
-    <tool file="protein_analysis/tmhmm2.xml" />
-    <tool file="protein_analysis/signalp3.xml" />
-    <tool file="protein_analysis/psortb.xml" />
-    <tool file="protein_analysis/wolf_psort.xml" />
-    <tool file="protein_analysis/rxlr_motifs.xml" />
-  </section>
-  <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
-    <tool file="protein_analysis/promoter2.xml" />
-  </section>
-
-   Leave out the lines for any tools you do not wish to use in Galaxy.
-
-4. Copy/move the test-data files (from this archive) to Galaxy's
-   subfolder test-data.
-
-5. Run the Galaxy functional tests for these new wrappers with:
-
-./run_functional_tests.sh -id tmhmm2
-./run_functional_tests.sh -id signalp3
-./run_functional_tests.sh -id Psortb
-./run_functional_tests.sh -id rxlr_motifs
-
-Alternatively, this should work (assuming you left the name and id as shown in
-the XML file tool_conf.xml.sample):
-
-./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
-
-To check the section ID expected, use ./run_functional_tests.sh -list
-
-6. Restart Galaxy and check the new tools are shown and work.
-
-
-History
-=======
-
-v0.0.1 - Initial release
-v0.0.2 - Corrected some typos in the help text
-       - Renamed test output file to use Galaxy convention of *.tabular
-v0.0.3 - Check for tmhmm2 silent failures (no output)
-       - Additional unit tests
-v0.0.4 - Ignore comment lines in tmhmm2 output.
-v0.0.5 - Explicitly request tmhmm short output (may not be the default)
-v0.0.6 - Improvement to how sub-jobs are run (should be faster)
-v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
-         SignalP webservice.
-v0.0.8 - Added WoLF PSORT wrapper to the suite.
-v0.0.9 - Added our RXLR motifs tool to the suite.
-v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
-       - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
-v0.1.1 - Fixed an error in the header of the tabular output from Promoter
-v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
-       - Use SGE style $NSLOTS for thread count (otherwise default to 4)
-v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
-v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
-         contributed by Konrad Paszkiewicz.
-v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
-         files accidentally included previously via a wildcard).
-v0.2.2 - Include missing test files.
-v0.2.3 - Added unit tests for WoLF PSORT.
-v0.2.4 - Added unit tests for Promoter 2
-v0.2.5 - Link to Tool Shed added to help text and this documentation.
-       - More unit tests.
-       - Fixed bug with RXLR tool and empty FASTA files.
-
-
-
-Developers
-==========
-
-This script and other tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-This incorporates the previously used hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
-
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
-
-This simplifies ensuring a consistent set of files is bundled each time,
-including all the relevant test files.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/protein_analysis/README.txt	Tue Sep 10 08:55:19 2013 -0400
@@ -0,0 +1,184 @@
+This package contains Galaxy wrappers for a selection of standalone command
+line protein analysis tools:
+
+* SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
+  Sequence Analysis at the Technical University of Denmark,
+  http://www.cbs.dtu.dk/cbs/
+
+* WoLF PSORT v0.2 from http://wolfpsort.org/
+
+* PSORTb v3 from http://www.psort.org/downloads/index.html
+
+Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
+
+To use these Galaxy wrappers you must first install the command line tools.
+At the time of writing they are all free for academic use, or open source.
+
+These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
+See the included LICENCE file for details (an MIT style open source licence).
+
+The wrappers are available from the Galaxy Tool Shed
+http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
+
+Citation
+========
+
+If you use any of these Galaxy tools in work leading to a scientific
+publication, in addition to citing the invididual underlying tools, please cite:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Full reference information is included in the help text for each tool.
+
+
+Requirements
+============
+
+First install those command line tools you wish to use the wrappers for:
+
+1. Install the command line version of SignalP 3.0 and ensure "signalp" is
+   on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
+
+2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
+   the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
+
+3. Install the command line version of Promoter 2.0 and ensure "promoter" is
+   on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
+
+4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
+   is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
+   directory, run runWolfPsortSummary, and then change back to the original
+   directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
+
+5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
+   but put it on the path under the name hmmsearch2 (allowing it to co-exist
+   with HMMER 3), or edit rlxr_motif.py accordingly.
+
+Verify each of the tools is installed and working from the command line
+(when logged in as the Galaxy user if appropriate).
+
+
+Manual Installation
+===================
+
+1. Create a folder tools/protein_analysis under your Galaxy installation.
+   This folder name is not critical, and can be changed if desired - you
+   must update the paths used in tool_conf.xml to match.
+
+2. Copy/move the following files (from this archive) there:
+
+tmhmm2.xml (Galaxy tool definition)
+tmhmm2.py (Python wrapper script)
+
+signalp3.xml (Galaxy tool definition)
+signalp3.py (Python wrapper script)
+
+promoter2.xml (Galaxy tool definition)
+promoter2.py (Python wrapper script)
+
+psortb.xml (Galaxy tool definition)
+psortb.py (Python wrapper script)
+
+wolf_psort.xml (Galaxy tool definition)
+wolf_psort.py (Python wrapper script)
+
+rxlr_motifs.xml (Galaxy tool definition)
+rxlr_motifs.py (Python script)
+
+seq_analysis_utils.py (shared Python code)
+LICENCE
+README (this file)
+
+3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
+   also tool_conf.xml.sample (to run the tests) to include the new tools
+   by adding:
+
+  <section name="Protein sequence analysis" id="protein_analysis">
+    <tool file="protein_analysis/tmhmm2.xml" />
+    <tool file="protein_analysis/signalp3.xml" />
+    <tool file="protein_analysis/psortb.xml" />
+    <tool file="protein_analysis/wolf_psort.xml" />
+    <tool file="protein_analysis/rxlr_motifs.xml" />
+  </section>
+  <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
+    <tool file="protein_analysis/promoter2.xml" />
+  </section>
+
+   Leave out the lines for any tools you do not wish to use in Galaxy.
+
+4. Copy/move the test-data files (from this archive) to Galaxy's
+   subfolder test-data.
+
+5. Run the Galaxy functional tests for these new wrappers with:
+
+./run_functional_tests.sh -id tmhmm2
+./run_functional_tests.sh -id signalp3
+./run_functional_tests.sh -id Psortb
+./run_functional_tests.sh -id rxlr_motifs
+
+Alternatively, this should work (assuming you left the name and id as shown in
+the XML file tool_conf.xml.sample):
+
+./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
+
+To check the section ID expected, use ./run_functional_tests.sh -list
+
+6. Restart Galaxy and check the new tools are shown and work.
+
+
+History
+=======
+
+v0.0.1 - Initial release
+v0.0.2 - Corrected some typos in the help text
+       - Renamed test output file to use Galaxy convention of *.tabular
+v0.0.3 - Check for tmhmm2 silent failures (no output)
+       - Additional unit tests
+v0.0.4 - Ignore comment lines in tmhmm2 output.
+v0.0.5 - Explicitly request tmhmm short output (may not be the default)
+v0.0.6 - Improvement to how sub-jobs are run (should be faster)
+v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
+         SignalP webservice.
+v0.0.8 - Added WoLF PSORT wrapper to the suite.
+v0.0.9 - Added our RXLR motifs tool to the suite.
+v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
+       - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
+v0.1.1 - Fixed an error in the header of the tabular output from Promoter
+v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
+       - Use SGE style $NSLOTS for thread count (otherwise default to 4)
+v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
+v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
+         contributed by Konrad Paszkiewicz.
+v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
+         files accidentally included previously via a wildcard).
+v0.2.2 - Include missing test files.
+v0.2.3 - Added unit tests for WoLF PSORT.
+v0.2.4 - Added unit tests for Promoter 2
+v0.2.5 - Link to Tool Shed added to help text and this documentation.
+       - More unit tests.
+       - Fixed bug with RXLR tool and empty FASTA files.
+       - Fixed typo in the RXLR tool help text.
+       - Updated citation information (Cock et al. 2013).
+
+
+Developers
+==========
+
+This script and other tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+This incorporates the previously used hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
+
+For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+$ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
+
+This simplifies ensuring a consistent set of files is bundled each time,
+including all the relevant test files.
--- a/tools/protein_analysis/promoter2.xml	Thu May 23 12:49:18 2013 -0400
+++ b/tools/protein_analysis/promoter2.xml	Tue Sep 10 08:55:19 2013 -0400
@@ -67,12 +67,20 @@

 **References**

-Knudsen.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Knudsen (1999).
 Promoter2.0: for the recognition of PolII promoter sequences.
-Bioinformatics, 15:356-61, 1999.
+Bioinformatics, 15:356-61.
 http://dx.doi.org/10.1093/bioinformatics/15.5.356

-http://www.cbs.dtu.dk/services/Promoter/output.php
+See also http://www.cbs.dtu.dk/services/Promoter/output.php

 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
--- a/tools/protein_analysis/psortb.xml	Thu May 23 12:49:18 2013 -0400
+++ b/tools/protein_analysis/psortb.xml	Tue Sep 10 08:55:19 2013 -0400
@@ -83,6 +83,14 @@

 **References**

+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
 PSORTb 3.0: Improved protein subcellular localization prediction with
@@ -90,7 +98,7 @@
 prokaryotes, Bioinformatics 26(13):1608-1615
 http://dx.doi.org/10.1093/bioinformatics/btq249

-http://www.psort.org/documentation/index.html
+See also http://www.psort.org/documentation/index.html

 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
--- a/tools/protein_analysis/rxlr_motifs.xml	Thu May 23 12:49:18 2013 -0400
+++ b/tools/protein_analysis/rxlr_motifs.xml	Tue Sep 10 08:55:19 2013 -0400
@@ -74,9 +74,9 @@
 Looks for the oomycete motif RXLR as described in Bhattacharjee et al. (2006).

 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
-a SignalP Neural Network (NN) predicted clevage site giving a signal peptide
+a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
-after but within 100 amino acids of the clevage site.
+after but within 100 amino acids of the cleavage site.
 SignalP is run truncating the sequences to the first 70 amino acids, which was
 the default on the SignalP webservice used in Bhattacharjee et al. (2006).

@@ -86,9 +86,9 @@
 Looks for the protein motif RXLR as described in Win et al. (2007).

 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
-a SignalP Neural Network (NN) predicted clevage site giving a signal peptide
+a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
-after the clevage site and start between amino acids 30 and 60.
+after the cleavage site and start between amino acids 30 and 60.
 SignalP is run truncating the sequences to the first 70 amino acids, to match
 the methodology of Torto et al. (2003) followed in Win et al. (2007).

@@ -135,6 +135,14 @@

 **References**

+If you use this Galaxy tool in work leading to a scientific publication please
+cite Cock et al. (2013) and the appropriate method paper(s):
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch
 A translocation signal for delivery of oomycete effector proteins into host plant cells.
 Nature 450:115-118, 2007.
--- a/tools/protein_analysis/signalp3.xml	Thu May 23 12:49:18 2013 -0400
+++ b/tools/protein_analysis/signalp3.xml	Tue Sep 10 08:55:19 2013 -0400
@@ -168,23 +168,31 @@

 **References**

-Bendtsen, Nielsen, von Heijne, and Brunak.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Bendtsen, Nielsen, von Heijne, and Brunak (2004).
 Improved prediction of signal peptides: SignalP 3.0.
-J. Mol. Biol., 340:783-795, 2004.
+J. Mol. Biol., 340:783-795.
 http://dx.doi.org/10.1016/j.jmb.2004.05.028

-Nielsen, Engelbrecht, Brunak and von Heijne.
+Nielsen, Engelbrecht, Brunak and von Heijne (1997).
 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
-Protein Engineering, 10:1-6, 1997.
+Protein Engineering, 10:1-6.
 http://dx.doi.org/10.1093/protein/10.1.1

-Nielsen and Krogh.
+Nielsen and Krogh (1998).
 Prediction of signal peptides and signal anchors by a hidden Markov model.
 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
-AAAI Press, Menlo Park, California, pp. 122-130, 1998.
+AAAI Press, Menlo Park, California, pp. 122-130.
 http://www.ncbi.nlm.nih.gov/pubmed/9783217

-http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
+See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php

 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
--- a/tools/protein_analysis/tmhmm2.xml	Thu May 23 12:49:18 2013 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Tue Sep 10 08:55:19 2013 -0400
@@ -96,17 +96,25 @@

 **References**

-Krogh, Larsson, von Heijne, and Sonnhammer.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Krogh, Larsson, von Heijne, and Sonnhammer (2001).
 Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
-J. Mol. Biol. 305:567-580, 2001.
+J. Mol. Biol. 305:567-580.
 http://dx.doi.org/10.1006/jmbi.2000.4315

-Sonnhammer, von Heijne, and Krogh.
+Sonnhammer, von Heijne, and Krogh (1998).
 A hidden Markov model for predicting transmembrane helices in protein sequences.
-In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press, 1998.
+In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press.
 http://www.ncbi.nlm.nih.gov/pubmed/9783223

-http://www.cbs.dtu.dk/services/TMHMM/
+See also http://www.cbs.dtu.dk/services/TMHMM/

 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
--- a/tools/protein_analysis/wolf_psort.xml	Thu May 23 12:49:18 2013 -0400
+++ b/tools/protein_analysis/wolf_psort.xml	Tue Sep 10 08:55:19 2013 -0400
@@ -128,16 +128,24 @@

 **References**

-Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai,
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007).
 WoLF PSORT: Protein Localization Predictor.
-Nucleic Acids Research, 35(S2), W585-W587, 2007.
+Nucleic Acids Research, 35(S2), W585-W587.
 http://dx.doi.org/10.1093/nar/gkm259

-Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai.
+Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006).
 Protein Subcellular Localization Prediction with WoLF PSORT.
-Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006.
+Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48.

-http://wolfpsort.org
+See also http://wolfpsort.org

 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp