# HG changeset patch
# User peterjc
# Date 1441104843 14400
# Node ID 77cfe958b5ea0d520329ad6921e65221d2c357c1
# Parent  9485cdfca57e331bde8960c7d52c062c3b7e67a7
v0.0.9 record clinod version

diff -r 9485cdfca57e -r 77cfe958b5ea tools/clinod/README.rst
--- a/tools/clinod/README.rst	Wed Aug 05 10:58:54 2015 -0400
+++ b/tools/clinod/README.rst	Tue Sep 01 06:54:03 2015 -0400
@@ -72,6 +72,7 @@
         - Tool definition now embeds citation information.
 v0.0.8  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.9  - Explicitly record clinod version via ``<version_command>``.
 ======= ======================================================================
 
 
@@ -88,12 +89,12 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
     ...
 
 To just build and check the tar ball, use::
diff -r 9485cdfca57e -r 77cfe958b5ea tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Wed Aug 05 10:58:54 2015 -0400
+++ b/tools/clinod/clinod.xml	Tue Sep 01 06:54:03 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.8">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.9">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="binary">java</requirement>
@@ -9,6 +9,12 @@
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command>
+##The first non-blank line contains the version information, e.g.
+##NucleOlar localization sequence Detector v. 1.3b (13 May 2011)
+##Question: Why don't we have to escape the dollar here?
+java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector"
+    </version_command>
     <command>
 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
 ##containing both clinod-1.3.jar and the batchman binary: