# HG changeset patch
# User peterjc
# Date 1494541932 14400
# Node ID 5f55bebfcf0e7698cd996d365139d04086766f65
# Parent  18f705de28ab97b744e3230f01a79bd6c351ee3f
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod commit acaced2b77f2789558b3d4c210ec373f8bdbb7e9-dirty

diff -r 18f705de28ab -r 5f55bebfcf0e tools/clinod/README.rst
--- a/tools/clinod/README.rst	Wed May 10 12:38:05 2017 -0400
+++ b/tools/clinod/README.rst	Thu May 11 18:32:12 2017 -0400
@@ -73,6 +73,8 @@
 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>``.
+v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r 18f705de28ab -r 5f55bebfcf0e tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Wed May 10 12:38:05 2017 -0400
+++ b/tools/clinod/clinod.xml	Thu May 11 18:32:12 2017 -0400
@@ -1,23 +1,18 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.9">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.10">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <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>
     <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>
+    <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="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
+java -jar \$CLINOD/clinod-1.3.jar -in='$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>