# HG changeset patch
# User peterjc
# Date 1494941186 14400
# Node ID 13be788233da04c5624d6a7d0d310a63f3d5082d
# Parent  7a26bb4588066fe3cc8e8612ccefea8320a79d0f
v0.0.5 Internal changes to command line handling

diff -r 7a26bb458806 -r 13be788233da tools/seq_composition/README.rst
--- a/tools/seq_composition/README.rst	Wed May 10 13:03:42 2017 -0400
+++ b/tools/seq_composition/README.rst	Tue May 16 09:26:26 2017 -0400
@@ -42,7 +42,7 @@
 
 You will also need to install Biopython 1.62 or later.
 
-If you wish to run the unit tests, also	move/copy the ``test-data/`` files
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
 under Galaxy's ``test-data/`` folder. Then::
 
     ./run_tests.sh -id seq_composition
@@ -62,6 +62,8 @@
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 v0.0.3  - Python style updates (internal change only).
 v0.0.4  - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
+v0.0.5  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r 7a26bb458806 -r 13be788233da tools/seq_composition/seq_composition.xml
--- a/tools/seq_composition/seq_composition.xml	Wed May 10 13:03:42 2017 -0400
+++ b/tools/seq_composition/seq_composition.xml	Tue May 16 09:26:26 2017 -0400
@@ -1,19 +1,15 @@
-<tool id="seq_composition" name="Sequence composition" version="0.0.4">
+<tool id="seq_composition" name="Sequence composition" version="0.0.5">
     <description>Count bases or amino-acids</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">seq_composition.py --version</version_command>
-    <command interpreter="python">
-seq_composition.py -o "$output_file"
+    <version_command>
+python $__tool_directory__/seq_composition.py --version</version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_composition.py -o '$output_file'
 ##For loop over inputs
 #for i in $input_file
---$i.ext "${i}"
+--$i.ext '${i}'
 #end for
     </command>
     <inputs>