--- a/tools/clinod/README.rst	Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/README.rst	Thu Nov 20 06:15:49 2014 -0500
@@ -18,35 +18,36 @@
 
 This should be straightforward, Galaxy should automatically download and install
 the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
-Neural Network Simulator (SNNS), and set the $CLINOD to their folder.
+Neural Network Simulator (SNNS), and set the ``$CLINOD`` to their folder.
 
 
 Manual Installation
 ===================
 This wrapper expects the java binary to be on the system PATH, and to be able
-to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used
-/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod
+to access command line NoD as ``$CLINOD/clinod-1.3.jar`` which means if you
+used ``/opt/clinod/clinod-1.3.jar`` set the environment variable ``$CLINOD``
+to ``/opt/clinod``
 
 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
-system path or located next to the JAR file, i.e. /opt/clinod/batchman
+system path or located next to the JAR file, i.e. ``/opt/clinod/batchman``
 
 To install the wrapper copy or move the following files under the Galaxy tools
-folder, e.g. in a tools/clinod folder:
+folder, e.g. in a ``tools/clinod`` folder:
 
-* clinod.xml (the Galaxy tool definition)
-* README.rst (this file)
+* ``clinod.xml`` (the Galaxy tool definition)
+* ``README.rst`` (this file)
 
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
 it next to them. Just add the line::
 
   <tool file="clinod/clinod.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+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 clinod
+    $ ./run_tests.sh -id clinod
 
 That's it.
 
@@ -67,6 +68,8 @@
         - 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  - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
+        - Tool definition now embeds citation information.
 ======= ======================================================================
 
 

--- a/tools/clinod/clinod.xml	Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/clinod.xml	Thu Nov 20 06:15:49 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="binary">java</requirement>
@@ -7,8 +7,7 @@
     <command>
 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
 ##containing both clinod-1.3.jar and the batchman binary:
-java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
-##I want the number of threads to be a Galaxy config option...
+java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
     <stdio>
@@ -25,7 +24,7 @@
     <tests>
         <test>
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
-	    <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
+            <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
         </test>
     </tests>
     <help>
@@ -82,4 +81,9 @@
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
 
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/nar/gkq653</citation>
+        <citation type="doi">10.1186/1471-2105-12-317</citation>
+    </citations>
 </tool>

--- a/tools/clinod/tool_dependencies.xml	Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/tool_dependencies.xml	Thu Nov 20 06:15:49 2014 -0500
@@ -9,7 +9,7 @@
                 </action>
                 <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
                 <action type="shell_command">wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz</action>
-		<action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action>
+                <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action>
                 <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action>
                 <!-- clinod itself is just a JAR file -->
                 <action type="shell_command">wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar</action>