# HG changeset patch
# User peterjc
# Date 1416571243 18000
# Node ID 9f2088ca5f6a35368e5602c83b0f3aa615dd7023
# Parent  f35b2f3ca139de464e687c4b1c42ab1da79e660b
Uploaded v0.0.7 with embedded citations

diff -r f35b2f3ca139 -r 9f2088ca5f6a tools/predictnls/README.rst
--- a/tools/predictnls/README.rst	Fri Oct 11 04:35:15 2013 -0400
+++ b/tools/predictnls/README.rst	Fri Nov 21 07:00:43 2014 -0500
@@ -16,14 +16,14 @@
 http://dx.doi.org/10.1093/embo-reports/kvd092
 
 This wrapper is available from the Galaxy Tool Shed at
-http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
+http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls
 
 
 Automatic Installation
 ======================
 
 This Galaxy tool is self contained, and so should install automatically via the
-Galaxy Tool Shed. See http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls
+Galaxy Tool Shed.
 
 
 Manual Installation
@@ -43,10 +43,10 @@
 
   <tool file="protein_analysis/predictnls.xml" />
 
-If you want to run the unit tests, also add this to tool_conf.xml.sample, and
-copy the test files under test-data, then run::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    ./run_functional_tests.sh -id predictnls
+    ./run_tests.sh -id predictnls
 
 That's it.
 
@@ -63,13 +63,14 @@
         - Use reStructuredText for this README file.
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.7  - Tool definition now embeds citation information.
 ======= ======================================================================
 
 
 Developers
 ==========
 
-This script and related tools are being developed on the following hg branch:
+This script and related tools were initially developed on the following hg branch:
 http://bitbucket.org/peterjc/galaxy-central/src/tools
 
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
diff -r f35b2f3ca139 -r 9f2088ca5f6a tools/predictnls/predictnls.xml
--- a/tools/predictnls/predictnls.xml	Fri Oct 11 04:35:15 2013 -0400
+++ b/tools/predictnls/predictnls.xml	Fri Nov 21 07:00:43 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="predictnls" name="PredictNLS" version="0.0.6">
+<tool id="predictnls" name="PredictNLS" version="0.0.7">
     <description>Find nuclear localization signals (NLSs) in protein sequences</description>
     <command interpreter="python">
       predictnls.py $fasta_file $tabular_file
@@ -94,4 +94,8 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/embo-reports/kvd092</citation>
+    </citations>
 </tool>