# HG changeset patch
# User peterjc
# Date 1438791785 14400
# Node ID 1458e60f3fd074331e3b87d62130e44d07014e3c
# Parent  b2e648e55ed7a759e36869ad0d35dab76e56cbf9
v0.0.10 internal changes; v0.0.9 citation

diff -r b2e648e55ed7 -r 1458e60f3fd0 tools/nlstradamus/README.rst
--- a/tools/nlstradamus/README.rst	Wed Sep 18 06:15:33 2013 -0400
+++ b/tools/nlstradamus/README.rst	Wed Aug 05 12:23:05 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
 =========================================================
 
-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 (MIT licence).
 
@@ -35,25 +35,24 @@
 
 Manual Installation
 ===================
-This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
-PATH.
+This wrapper expects the compiled C++ binary "NLStradamus" to be on the ``$PATH``.
 
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a tools/protein_analysis folder:
 
-* nlstradamus.xml (the Galaxy tool definition)
-* nlstradamus.txt (this README file)
+* ``nlstradamus.xml`` (the Galaxy tool definition)
+* ``nlstradamus.txt`` (this README file)
 
-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 (matching the chosen install path)::
+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 (matching the chosen install path)::
 
   <tool file="protein_analysis/nlstradamus.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 nlstradamus
+    $ ./run_tests.sh -id nlstradamus
 
 That's it.
 
@@ -77,33 +76,47 @@
         - Adopted standard MIT licence.
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.9  - Tool definition now embeds citation information.
+v0.0.10 - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
 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
 
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus
 
-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/nlstradamus/
+    ...
+
+or::
 
-    $ tar -czf nlstradmus.tar.gz tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/nlstradamus/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf nlstradmus.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/nlstradamus/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    test-data/empty.fasta
+    test-data/empty_nlstradamus.tabular
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.nlstradamus.tabular
     tools/nlstradamus/README.rst
     tools/nlstradamus/nlstradamus.xml
     tools/nlstradamus/tool_dependencies.xml
     test-data/four_human_proteins.fasta
-    test-data/four_human_proteins.nlstradamus.tabular
-    test-data/empty.fasta
-    test-data/empty_nlstradamus.tabular
 
 
 Licence (MIT)
diff -r b2e648e55ed7 -r 1458e60f3fd0 tools/nlstradamus/nlstradamus.xml
--- a/tools/nlstradamus/nlstradamus.xml	Wed Sep 18 06:15:33 2013 -0400
+++ b/tools/nlstradamus/nlstradamus.xml	Wed Aug 05 12:23:05 2015 -0400
@@ -1,13 +1,17 @@
-<tool id="nlstradamus" name="NLStradamus" version="0.0.8">
+<tool id="nlstradamus" name="NLStradamus" version="0.0.10">
     <description>Find nuclear localization signals (NLSs) in protein sequences</description>
-    <command>
-      NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
-    </command>
+    <requirements>
+        <requirement type="binary">NLStradamus</requirement>
+        <requirement type="package" version="1.8">NLStradamus</requirement>
+    </requirements>
     <stdio>
         <!-- Assume anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <command>
+      NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
+    </command>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
         <param name="model" type="select" display="radio" label="Model">
@@ -26,16 +30,12 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="NLStradamus results" />
     </outputs>
-    <requirements>
-        <requirement type="binary">NLStradamus</requirement>
-        <requirement type="package" version="1.8">NLStradamus</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
             <param name="model" value="1" />
             <param name="algorithm" value="1" />
-	    <param name="threshold" value="0.6" />
+            <param name="threshold" value="0.6" />
             <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" />
         </test>
         <test>
@@ -90,4 +90,8 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1186/1471-2105-10-202</citation>
+    </citations>
 </tool>
diff -r b2e648e55ed7 -r 1458e60f3fd0 tools/nlstradamus/tool_dependencies.xml
--- a/tools/nlstradamus/tool_dependencies.xml	Wed Sep 18 06:15:33 2013 -0400
+++ b/tools/nlstradamus/tool_dependencies.xml	Wed Aug 05 12:23:05 2015 -0400
@@ -4,7 +4,7 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8.tar.gz</action>
-		<!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did not -->
+                <!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did not -->
                 <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action>
                 <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action>
                 <action type="set_environment">