Mercurial > repos > peterjc > secreted_protein_workflow

--- a/README.txt	Mon Jul 08 11:19:47 2013 -0400
+++ b/README.txt	Mon Jul 08 12:59:49 2013 -0400
@@ -1,27 +1,53 @@
-This Tool Shed Repository contains a workflow for the identification of candidate secreted proteins from a given protein FASATA file.
+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).

-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.
+

-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.
+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, Castelli L, 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.
+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.
+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.
+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 on the main Galaxy Tool Shed:
+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


@@ -32,21 +58,25 @@
  * 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).
+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).


-Development
-===========
+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
+    $ 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
+    $ tar -tzf secreted_protein_workflow.tar.gz
+    README.txt
+    repository_dependencies.xml
+    secreted_protein_workflow.ga