# HG changeset patch
# User peterjc
# Date 1618612410 0
# Node ID 4863b1dbe8f012799fd687d24b96bbab8cc6895b
# Parent  f61366a4a14e5228b2927390e37b7a8b24c6f2fa
"Update all the pico_galaxy tools on main Tool Shed"

diff -r f61366a4a14e -r 4863b1dbe8f0 tools/clinod/README.rst
--- a/tools/clinod/README.rst	Tue May 16 08:50:43 2017 -0400
+++ b/tools/clinod/README.rst	Fri Apr 16 22:33:30 2021 +0000
@@ -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.
 ======= ======================================================================
 
 
@@ -103,7 +109,7 @@
 
     $ planemo shed_upload --tar_only tools/clinod/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ 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
diff -r f61366a4a14e -r 4863b1dbe8f0 tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Tue May 16 08:50:43 2017 -0400
+++ b/tools/clinod/clinod.xml	Fri Apr 16 22:33:30 2021 +0000
@@ -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>
@@ -6,17 +6,14 @@
     <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>
-        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
+        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
     </inputs>
     <outputs>
         <data name="tabular_file" format="tabular" label="NoD results" />
@@ -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
@@ -63,17 +59,17 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton (2010).
 Characterization and prediction of protein nucleolar localization sequences.
 Nucleic Acids Research 38(21), 7388-7399.
-http://dx.doi.org/10.1093/nar/gkq653
+https://doi.org/10.1093/nar/gkq653
 
 M. S. Scott, P. V. Troshin and G. J. Barton (2011).
 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
 BMC Bioinformatics, 12:317.
-http://dx.doi.org/10.1186/1471-2105-12-317
+https://doi.org/10.1186/1471-2105-12-317
 
 See also http://www.compbio.dundee.ac.uk/www-nod/
 
diff -r f61366a4a14e -r 4863b1dbe8f0 tools/clinod/tool_dependencies.xml
--- a/tools/clinod/tool_dependencies.xml	Tue May 16 08:50:43 2017 -0400
+++ b/tools/clinod/tool_dependencies.xml	Fri Apr 16 22:33:30 2021 +0000
@@ -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>