Mercurial > repos > peterjc > secreted_protein_workflow

changeset 4:b14c822a37fe draft

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Uploaded v0.0.1d, README file with clearer citation instructions.
author peterjc
date Mon, 19 Aug 2013 11:38:03 -0400
parents 237d3bef3b86
children 5f3cc8229771
files README.rst README.txt repository_dependencies.xml
diffstat 3 files changed, 98 insertions(+), 83 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Aug 19 11:38:03 2013 -0400
@@ -0,0 +1,97 @@
+This is package is a Galaxy workflow for the identification of candidate
+secreted proteins from a given protein FASTA file.
+
+It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
+strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
+on those, and selects only proteins without a predicted trans-membrane helix.
+This workflow was used in Kikuchi et al (2001), and is a simplification of
+the candidate effector protocol described in Jones et al (2009).
+
+See http://www.galaxyproject.org for information about the Galaxy Project.
+
+
+Citation
+========
+
+If you use this workflow directly, or a derivative of it, in work leading
+to a scientific publication, please cite:
+
+Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
+candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
+Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
+Humana Press, Springer. In press.
+
+Also consider citing:
+
+Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
+Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
+http://dx.doi.org/10.1016/j.jmb.2004.05.028
+
+Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001)
+Predicting transmembrane protein topology with a hidden Markov model:
+application to complete genomes. J Mol Biol 305: 567- 580.
+http://dx.doi.org/10.1006/jmbi.2000.4315
+
+
+Additional References
+=====================
+
+Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
+Genomic insights into the origin of parasitism in the emerging plant
+pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219.
+http://dx.doi.org/10.1371/journal.ppat.1002219
+
+Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
+Identification and functional characterization of effectors in expressed
+sequence tags from various life cycle stages of the potato cyst nematode
+Globodera pallida. Mol Plant Pathol 10: 815–28.
+http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
+
+
+Availability
+============
+
+This workflow is available to download and/or install from the main
+Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
+
+Test releases (which should not normally be used) are on the Test Tool Shed:
+
+http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
+
+Development is being done on github here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
+
+
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+
+However, at the time of writing those Galaxy tools have their own
+dependencies required for this workflow which require manual
+installation (SignalP v3.0 and TMHMM v2.0).
+
+
+Developers
+==========
+
+This workflow is under source code control here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
+
+To prepare the tar-ball for uploading to the Tool Shed, I use this:
+
+    $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
+
+Check this,
+
+    $ tar -tzf secreted_protein_workflow.tar.gz 
+    README.rst
+    repository_dependencies.xml
+    secreted_protein_workflow.ga
--- a/README.txt	Mon Jul 08 12:59:49 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-This is package is a Galaxy workflow for the identification of candidate
-secreted proteins from a given protein FASATA file.
-
-It runs SignalP v3.0 and selects only proteins with a strong predicted
-signal peptide, and then runs TMHMM v2.0 on those, and selects only
-proteins without a predicted trans-membrane helix. This workflow was
-used in Kikuchi et al (2001), and is a simplification of the candidate
-effector protocol described in Jones et al (2009).
-
-See http://www.galaxyproject.org for information about the Galaxy Project.
-
-
-References
-==========
-
-Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, et al. (2011)
-Genomic insights into the origin of parasitism in the emerging plant
-pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219.
-http://dx.doi.org/10.1371/journal.ppat.1002219
-
-Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, et al. (2009)
-Identification and functional characterization of effectors in expressed
-sequence tags from various life cycle stages of the potato cyst nematode
-Globodera pallida. Mol Plant Pathol 10: 815–28.
-http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
-
-Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004)
-Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
-http://dx.doi.org/10.1016/j.jmb.2004.05.028
-
-Krogh A, Larsson B, von Heijne G, Sonnhammer E (2001)
-Predicting transmembrane protein topology with a hidden Markov model:
-application to complete genomes. J Mol Biol 305: 567- 580.
-http://dx.doi.org/10.1006/jmbi.2000.4315
-
-
-Availability
-============
-
-This workflow is available to download and/or install from the main
-Galaxy Tool Shed:
-
-http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
-
-Test releases (which should not normally be used) are on the Test Tool Shed:
-
-http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
-
-Development is being done on github here:
-
-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
-
-
-Dependencies
-============
-
-These dependencies should be resolved automatically via the Galaxy Tool Shed:
- * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
- * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
-
-However, at the time of writing those Galaxy tools have their own
-dependencies required for this workflow which require manual
-installation (SignalP v3.0 and TMHMM v2.0).
-
-
-Developers
-==========
-
-This workflow is under source code control here:
-
-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
-
-To prepare the tar-ball for uploading to the Tool Shed, I use this:
-
-    $ tar -cf secreted_protein_workflow.tar.gz README.txt repository_dependencies.xml secreted_protein_workflow.ga
-
-Check this,
-
-    $ tar -tzf secreted_protein_workflow.tar.gz 
-    README.txt
-    repository_dependencies.xml
-    secreted_protein_workflow.ga
--- a/repository_dependencies.xml	Mon Jul 08 12:59:49 2013 -0400
+++ b/repository_dependencies.xml	Mon Aug 19 11:38:03 2013 -0400
@@ -3,5 +3,5 @@
     <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the current latest - but older should be OK -->
     <repository changeset_revision="4cd848c5590b" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     <!-- Revision 2:abdd608c869b on the main tool shed is v0.0.5, the current latest - but older should be OK -->
-    <repository changeset_revision="66d1ca92fb38" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="00153c4efec3" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>