diff README.rst @ 2:3a0c0d1c388f draft

Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.

--- a/README.rst	Mon Aug 19 11:37:04 2013 -0400
+++ b/README.rst	Wed Aug 21 11:58:54 2013 -0400
@@ -4,12 +4,26 @@
 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
 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).
+This workflow was used in Kikuchi et al. (2011), 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.
 
 
+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):
+
+ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.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
+18,074 sequences. The expected result (selecting organism type Eukaryote)
+is a FASTA protein file of 2,297 predicted secreted protein sequences.
+
+
 Citation
 ========
 
@@ -78,6 +92,19 @@
 installation (SignalP v3.0 and TMHMM v2.0).
 
 
+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.
+======= ======================================================================
+
+
 Developers
 ==========