--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Aug 19 11:35:52 2013 -0400
@@ -0,0 +1,82 @@
+This is package is a Galaxy workflow for comparing three RXLR prediction
+methods with a Venn Diagram, and creates a FASTA file of any proteins
+passing all three methods.
+
+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.
+
+Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
+A translocation signal for delivery of oomycete effector proteins into
+host plant cells. Nature 450:115-118.
+http://dx.doi.org/10.1038/nature06203
+
+Win, J., Morgan, W., Bos, J., et al. (2007)
+Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
+of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
+http://dx.doi.org/10.1105/tpc.107.051037
+
+Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
+The malarial host-targeting signal is conserved in the Irish potato famine
+pathogen. PLoS Pathogens 2(5):e50.
+http://dx.doi.org/10.1371/journal.ppat.0020050
+
+
+Availability
+============
+
+This workflow is available to download and/or install from the main
+Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
+
+Test releases (which should not normally be used) are on the Test Tool Shed:
+
+http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
+
+Development is being done on github here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_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
+* http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
+
+However, at the time of writing those Galaxy tools have their own dependencies
+required for this workflow which require manual installation (SignalP v3.0,
+HMMER v2.0, and the R/Bioconductor package limma).
+
+
+Developers
+==========
+
+This workflow is under source code control here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
+
+To prepare the tar-ball for uploading to the Tool Shed, I use this:
+
+    $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga
+
+Check this,
+
+    $ tar -tzf rxlr_venn_workflow.tar.gz
+    README.rst
+    repository_dependencies.xml
+    rxlr_venn_workflow.ga

--- a/README.txt	Tue May 07 13:53:56 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-This Tool Shed Repository contains a workflow for comparing three RXLR
-prediction methods with a Venn Diagram, and creates a FASTA file of any
-proteins passing all three methods.
-
-
-References
-==========
-
-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.
-http://dx.doi.org/10.1038/nature06203
-
-Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano,
-Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun.
-Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
-of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007.
-http://dx.doi.org/10.1105/tpc.107.051037
-
-Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win,
-Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar.
-The malarial host-targeting signal is conserved in the Irish potato famine
-pathogen. PLoS Pathogens, 2(5):e50, 2006.
-http://dx.doi.org/10.1371/journal.ppat.0020050
-
-
-Availability
-============
-
-This workflow is available on the main Galaxy Tool Shed:
-http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
-
-Development is being done on github here:
-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_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
- * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
-
-However, at the time of writing those Galaxy tools have their own dependencies
-required for this workflow which require manual installation (SignalP v3.0,
-HMMER v2.0, and the R/Bioconductor package limma).

--- a/repository_dependencies.xml	Tue May 07 13:53:56 2013 -0400
+++ b/repository_dependencies.xml	Mon Aug 19 11:35:52 2013 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">
     <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the current latest - but older should be OK -->
-    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tmhmm_and_signalp" owner="peterjc" changeset_revision="6abd809cefdd" />
+    <repository changeset_revision="6abd809cefdd" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://toolshed.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 toolshed="http://toolshed.g2.bx.psu.edu" name="seq_filter_by_id" owner="peterjc" changeset_revision="abdd608c869b" />
-    <!-- Revision 0:baf7031d470e on the main tool shed is v0.0.3, currently the only revision -->
-    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="venn_list" owner="peterjc" changeset_revision="baf7031d470e" />
+    <repository changeset_revision="abdd608c869b" name="seq_filter_by_id" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <!-- Revisiion 2:c96bef0643dc on the main tool shed is v0.0.3, the current latest -->
+    <repository changeset_revision="c96bef0643dc" name="venn_list" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>