# HG changeset patch
# User peterjc
# Date 1427729003 14400
# Node ID 8e86daf42b9cc4b33e1f9a75e1a21695df759896
# Parent  2e96bf82b463af378632e1e45f6b3a56f4b132ad
Uploaded with disclaimer and known issues in README

diff -r 2e96bf82b463 -r 8e86daf42b9c README.rst
--- a/README.rst	Mon Mar 30 11:07:48 2015 -0400
+++ b/README.rst	Mon Mar 30 11:23:23 2015 -0400
@@ -14,6 +14,7 @@
 This is an example workflow using the Galaxy wrappers for NCBI BLAST+,
 see https://github.com/peterjc/galaxy_blast
 
+
 Galaxy workflow for counting species of top BLAST hits 
 ======================================================
 
@@ -83,6 +84,37 @@
 Note the nematode count in this image was shown as a mouse-over effect.
 
 
+Disclaimer
+==========
+
+Species assignment by top BLAST hit is not suitable for any in depth
+analysis. It is particularly prone to false positives where contaiminants
+in public datasets are mislabled. See for example Ed Yong (2015),
+"There's No Plague on the NYC Subway. No Platypuses Either.":
+
+http://phenomena.nationalgeographic.com/2015/02/10/theres-no-plague-on-the-nyc-subway-no-platypuses-either/
+
+
+Known Issues
+============
+
+This workflow uses the Galaxy "Count" tool, version 1.0.0, as shipped with
+the current stable release (Galaxy v15.03, i.e. March 2015).
+
+The updated "Count" tool version 1.0.1 includes a fix not to remove spaces
+in the fields being counted. In the example above, while the top hits are
+not affected, minor entries like "cellular slime molds" are shown as
+"cellularslimemolds" instead (look closely at the Pie Chart key)..
+
+The updated "Count" tool version 1.0.1 also adds a new option to sort the
+output, which avoids the additional sorting step in the current version of
+the workflow.
+
+A future update to this workflow will use the revised "Count" tool, once
+this is included in the next stable Galaxy release - or migrated to the
+Galaxy Tool Shed.
+
+
 Availability
 ============