# HG changeset patch
# User peterjc
# Date 1492790846 14400
# Node ID a7de1d3c314803b354d8fb31b440981d6371d54d
# Parent  412e708d0172628cf180675a24cb7a4201576d48
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty

diff -r 412e708d0172 -r a7de1d3c3148 tools/seq_rename/README.rst
--- a/tools/seq_rename/README.rst	Fri Feb 03 12:55:57 2017 -0500
+++ b/tools/seq_rename/README.rst	Fri Apr 21 12:07:26 2017 -0400
@@ -82,6 +82,8 @@
 v0.0.8  - Updated to point at Biopython 1.67 (latest version in Tool Shed).
         - Explicit dependency on ``galaxy_sequence_utils``.
         - Python style updates (internal change only).
+v0.0.9  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r 412e708d0172 -r a7de1d3c3148 tools/seq_rename/seq_rename.xml
--- a/tools/seq_rename/seq_rename.xml	Fri Feb 03 12:55:57 2017 -0500
+++ b/tools/seq_rename/seq_rename.xml	Fri Apr 21 12:07:26 2017 -0400
@@ -1,18 +1,14 @@
-<tool id="seq_rename" name="Rename sequences" version="0.0.8">
+<tool id="seq_rename" name="Rename sequences" version="0.0.9">
     <description>with ID mapping from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
         <requirement type="package" version="1.67">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">seq_rename.py --version</version_command>
-    <command interpreter="python">
-seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
+    <version_command>
+python $__tool_directory__/seq_rename.py --version
+</version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_rename.py '$input_tabular' '$old_column' '$new_column' '$input_file' '$input_file.ext' '$output_file'
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />