# HG changeset patch
# User peterjc
# Date 1438786734 14400
# Node ID 9485cdfca57e331bde8960c7d52c062c3b7e67a7
# Parent  4d9a4a43861b190f38ed8754c2b048e33a932055
v0.0.8 internal changes

diff -r 4d9a4a43861b -r 9485cdfca57e tools/clinod/README.rst
--- a/tools/clinod/README.rst	Thu Nov 20 06:15:49 2014 -0500
+++ b/tools/clinod/README.rst	Wed Aug 05 10:58:54 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for Command line NoD predictor (v1.3)
 ====================================================
 
-This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -70,6 +70,8 @@
         - 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.
+v0.0.8  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -82,19 +84,28 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+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/
+    ...
+
+or::
 
-    $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf clinod.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/clinod/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.clinod-1.3.tabular
     tools/clinod/README.rst
     tools/clinod/clinod.xml
     tools/clinod/tool_dependencies.xml
-    test-data/four_human_proteins.fasta
-    test-data/four_human_proteins.clinod-1.3.tabular
 
 
 Licence (MIT)
diff -r 4d9a4a43861b -r 9485cdfca57e tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Thu Nov 20 06:15:49 2014 -0500
+++ b/tools/clinod/clinod.xml	Wed Aug 05 10:58:54 2015 -0400
@@ -1,20 +1,20 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.8">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="binary">java</requirement>
         <requirement type="package" version="1.3">clinod</requirement>
     </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <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="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
     </inputs>
diff -r 4d9a4a43861b -r 9485cdfca57e tools/clinod/tool_dependencies.xml
--- a/tools/clinod/tool_dependencies.xml	Thu Nov 20 06:15:49 2014 -0500
+++ b/tools/clinod/tool_dependencies.xml	Wed Aug 05 10:58:54 2015 -0400
@@ -22,7 +22,7 @@
 Downloads and installs the command line NoD (clinod) JAR file and the binary
 dependency batchman, and sets $CLINOD to the folder used.
 
-We could download, compiles and install the SNNS Batch Interpreter v1.0 executable
+We could download, compile and install the SNNS Batch Interpreter v1.0 executable
 (batchman) from Stuttgart Neural Network Simulator (SNNS) v4.2. However, we simplify
 this by downloading SNNS v4.3 which includes the precompiled copy of batch man.