Mercurial > repos > peterjc > secreted_protein_workflow

--- a/README.rst	Wed Aug 21 12:31:56 2013 -0400
+++ b/README.rst	Fri Oct 25 10:22:35 2013 -0400
@@ -10,11 +10,28 @@
 See http://www.galaxyproject.org for information about the Galaxy Project.


+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/pico_galaxy/tree/master/workflows/secreted_protein_workflow
+
+
 Sample Data
 ===========

 This workflow was developed and run on several nematode species. For example,
-try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011):
+try the protein set for *Bursaphelenchus xylophilus* (Kikuchi et al. 2011):

 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz

@@ -30,12 +47,16 @@
 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
+Cock, P.J.A. and Pritchard, L. (2014). 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.
+Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds.
+Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7.
+http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7

-Also consider citing:
+Peter J.A. Cock, Björn A. Grüning, 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, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
@@ -52,33 +73,16 @@

 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.
+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.
+*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
 ============

@@ -112,7 +116,7 @@

 This workflow is under source code control here:

-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
+https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow

 To prepare the tar-ball for uploading to the Tool Shed, I use this:
--- a/repository_dependencies.xml	Wed Aug 21 12:31:56 2013 -0400
+++ b/repository_dependencies.xml	Fri Oct 25 10:22:35 2013 -0400
@@ -1,7 +1,7 @@
 <?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 changeset_revision="4cd848c5590b" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="ee10017fcd80" 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="00153c4efec3" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="8a34c565a473" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>
--- a/secreted_protein_workflow.ga	Wed Aug 21 12:31:56 2013 -0400
+++ b/secreted_protein_workflow.ga	Fri Oct 25 10:22:35 2013 -0400
@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2013).",
+    "annotation": "Runs SignalP v3.0 and TMHMM v2.0 to look for secreted proteins.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow\" target=\"_blank\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2014).",
     "format-version": "0.1",
     "name": "Find secreted proteins with TMHMM and SignalP",
     "steps": {