# HG changeset patch
# User peterjc
# Date 1492790820 14400
# Node ID 6abe3913c881438dd4e51b1854e7aa254d30a6bf
# Parent  64cc41c3456d42f90ebdb894d2189b9be005a61b
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty

diff -r 64cc41c3456d -r 6abe3913c881 tools/seq_primer_clip/README.rst
--- a/tools/seq_primer_clip/README.rst	Thu Feb 09 11:27:30 2017 -0500
+++ b/tools/seq_primer_clip/README.rst	Fri Apr 21 12:07:00 2017 -0400
@@ -69,8 +69,10 @@
         - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
         - Fixed input file help text.
-v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed).
+v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
         - Explicit dependency on ``galaxy_sequence_utils``.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only)
 ======= ======================================================================
 
 
diff -r 64cc41c3456d -r 6abe3913c881 tools/seq_primer_clip/seq_primer_clip.xml
--- a/tools/seq_primer_clip/seq_primer_clip.xml	Thu Feb 09 11:27:30 2017 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Fri Apr 21 12:07:00 2017 -0400
@@ -3,16 +3,12 @@
     <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_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    <version_command>
+python $__tool_directory__/seq_primer_clip.py --version
+    </version_command>
+    <command detect_errors="aggresive">
+python $__tool_directory__/seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>