# HG changeset patch
# User peterjc
# Date 1496846999 14400
# Node ID 074070ddf4930700ce7aab07651920754ca9a600
# Parent  5f55bebfcf0e7698cd996d365139d04086766f65
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty

diff -r 5f55bebfcf0e -r 074070ddf493 tools/clinod/README.rst
--- a/tools/clinod/README.rst	Thu May 11 18:32:12 2017 -0400
+++ b/tools/clinod/README.rst	Wed Jun 07 10:49:59 2017 -0400
@@ -23,10 +23,11 @@
 
 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``
+This wrapper expects the java binary to availabe via a wapper script named
+``clinod`` on the system ``$PATH``.
+
+Older versions of this tool called the JAR file directly via an environment
+variable as ``$CLINOD/clinod-1.3.jar`` - this is no longer used.
 
 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
@@ -75,6 +76,11 @@
 v0.0.9  - Explicitly record clinod version via ``<version_command>``.
 v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
+v0.1.0  - Calls the JAR file via a wrapper script ``clinod``, in order to use
+          the BioConda package OR the ``tool_dependencies.xml`` system.
+          To do this the Tool Shed XML installation recipe now installs the
+          same wrapper script ``clinod`` used in the BioConda package for
+          calling the JAR file.
 ======= ======================================================================
 
 
diff -r 5f55bebfcf0e -r 074070ddf493 tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Thu May 11 18:32:12 2017 -0400
+++ b/tools/clinod/clinod.xml	Wed Jun 07 10:49:59 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.10">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.1.0">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="package" version="1.3">clinod</requirement>
@@ -6,13 +6,10 @@
     <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"
+clinod | grep -i "^NucleOlar localization sequence Detector"
     </version_command>
     <command detect_errors="aggressive">
-##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='$tabular_file' -t="\${GALAXY_SLOTS:-4}" -f=MEDIUM_TAB -nonols -clean_sequence
+clinod -in='$fasta_file' -out='$tabular_file' -t="\${GALAXY_SLOTS:-4}" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
     <inputs>
@@ -28,7 +25,6 @@
         </test>
     </tests>
     <help>
-
 **What it does**
 
 This calls the command line version of the NoD tool from the Barton Group for
diff -r 5f55bebfcf0e -r 074070ddf493 tools/clinod/tool_dependencies.xml
--- a/tools/clinod/tool_dependencies.xml	Thu May 11 18:32:12 2017 -0400
+++ b/tools/clinod/tool_dependencies.xml	Wed Jun 07 10:49:59 2017 -0400
@@ -12,8 +12,12 @@
                     <!-- clinod requires the SNNS Batch Interpreter v1.0 executable -->
                     <!-- Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz -->
                     <action type="download_file" sha256sum="54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62" target_filename="SNNSv4.3.tar.gz">https://depot.galaxyproject.org/software/SNNS/SNNS_4.3_linux_x64.tar.gz</action>
-                    <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action>
+                    <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</action>
                     <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action>
+                    <!-- Use the BioConda Python wrapper script to put 'clinod' in the install dir -->
+                    <action type="download_file" sha256sum="54de81f6ce9a30cee29a63b400d9a365c4a27d6efffa0096f3adcd91c1ce9066" target_filename="clinod">https://raw.githubusercontent.com/bioconda/bioconda-recipes/487d5fd2d993de578c9380d8da7a0dd0405836e7/recipes/clinod/clinod.py</action>
+                    <action type="shell_command">chmod a+x ./clinod</action>
+                    <action type="move_file"><source>clinod</source><destination>$INSTALL_DIR/</destination></action>
                 </actions>
                 <actions>
                     <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
@@ -37,10 +41,14 @@
 
 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.
+this by downloading SNNS v4.3 which includes the precompiled copy of batchman.
 
 For more details, see:
 http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp
+
+Additionally, to match the BioConda package a wrapper script clinod is also
+installed, see https://anaconda.org/bioconda/clinod and recipe source at
+https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clinod
         </readme>
     </package>
 </tool_dependency>