diff README.rst @ 4:3c280e01b920 draft

Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
author peterjc
date Wed, 21 Aug 2013 13:01:51 -0400
parents 1a1ab2f2b5b5
children 4726b640f221
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--- a/README.rst	Mon Aug 19 11:35:52 2013 -0400
+++ b/README.rst	Wed Aug 21 13:01:51 2013 -0400
@@ -5,6 +5,30 @@
 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
 ========
 
@@ -63,6 +87,21 @@
 HMMER v2.0, and the R/Bioconductor package limma).
 
 
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial release to Tool Shed (May, 2013)
+        - Expanded README file to include example data
+v0.0.2  - Updated versions of the tools used, inclulding core Galaxy Filter
+          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.
+======= ======================================================================
+
+
 Developers
 ==========