Mercurial > repos > peterjc > rxlr_venn_workflow

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Uploaded revision to update the citation
author peterjc
date Fri, 25 Oct 2013 10:20:46 -0400
parents 3c280e01b920
children
files Phyca11_example_output.png README.rst repository_dependencies.xml rxlr_venn_workflow.ga
diffstat 4 files changed, 70 insertions(+), 58 deletions(-) [+]
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Binary file Phyca11_example_output.png has changed
--- a/README.rst	Wed Aug 21 13:01:51 2013 -0400
+++ b/README.rst	Fri Oct 25 10:20:46 2013 -0400
@@ -5,57 +5,6 @@
 See http://www.galaxyproject.org for information about the Galaxy Project.
 
 
-Sample Data
-===========
-
-This workflow was developed and run on several Phytophthora species.
-For example, try the "Phyca11" protein set for Phytophthora capsici:
-
-http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
-
-You can upload this directly into Galaxy via this URL. Galaxy will handle
-removing the gzip compression to give you the FASTA protein file which
-has 19,805 protein sequences. The expected results:
-
-* 89 RXLRs using Whisson et al. (2007)
-* 124 RXLRs using Win et al. (2007)
-* 162 RXLRs using Bhattacharjee et al. (2006)
-
-Of these, only 79 sequences pass all three of the RXLR prediction tools,
-while 19643 have no RXLR matches at all.
-
-.. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png
-   :height: 400px
-   :width: 400px
-
-
-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
 ============
 
@@ -70,7 +19,68 @@
 
 Development is being done on github here:
 
-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
+https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow
+
+
+Sample Data
+===========
+
+This workflow was developed and run on several *Phytophthora* species.
+For example, try the "Phyca11" protein set for *Phytophthora capsici*:
+
+http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
+
+You can upload this directly into Galaxy via this URL. Galaxy will handle
+removing the gzip compression to give you the FASTA protein file which
+has 19,805 protein sequences. The expected results:
+
+* 89 RXLRs using Whisson et al. (2007)
+* 124 RXLRs using Win et al. (2007)
+* 162 RXLRs using Bhattacharjee et al. (2006)
+
+Of these, only 79 sequences pass all three of the RXLR prediction tools,
+while 19643 have no RXLR matches at all.
+
+.. image:: Phyca11_example_output.png 
+   :height: 400px
+   :width: 400px
+
+
+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. (2014). Galaxy as a platform for identifying
+candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
+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
+
+For the associated RXLR Galaxy tool, please cite:
+
+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
+
+For the three underlying methods, please cite:
+
+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
 
 
 Dependencies
@@ -99,6 +109,7 @@
           tool to avoid warning about new ``header_lines`` parameter.
         - Added link to Tool Shed in the workflow annotation explaining there
           is a README file with sample data, and a requested citation.
+        - Bundle sample output image for display in this README file.
 ======= ======================================================================
 
 
@@ -107,11 +118,11 @@
 
 This workflow is under source code control here:
 
-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
+https://github.com/peterjc/pico_galaxy/tree/master/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
+    $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png
 
 Check this,
 
@@ -119,3 +130,4 @@
     README.rst
     repository_dependencies.xml
     rxlr_venn_workflow.ga
+    Phyca11_example_output.png
--- a/repository_dependencies.xml	Wed Aug 21 13:01:51 2013 -0400
+++ b/repository_dependencies.xml	Fri Oct 25 10:20:46 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 changeset_revision="6abd809cefdd" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="7de64c8b258d" 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 changeset_revision="abdd608c869b" name="seq_filter_by_id" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="44ab4c0f7683" 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" />
+    <repository changeset_revision="6aae6bc0802d" name="venn_list" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>
--- a/rxlr_venn_workflow.ga	Wed Aug 21 13:01:51 2013 -0400
+++ b/rxlr_venn_workflow.ga	Fri Oct 25 10:20:46 2013 -0400
@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true", 
-    "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_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": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.<br />\n<br />\nThis workflow is <a href=\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_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": "3 RXLR methods, Venn Diagram, overlap FASTA", 
     "steps": {