# HG changeset patch
# User peterjc
# Date 1494521306 14400
# Node ID 515fc5316fdb700e2d76b9d46c16fa46dd0276f5
# Parent  b0ac04e1efe075bb6250f9a443656b9506e4200e
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty

diff -r b0ac04e1efe0 -r 515fc5316fdb tools/samtools_idxstats/README.rst
--- a/tools/samtools_idxstats/README.rst	Wed May 10 12:48:16 2017 -0400
+++ b/tools/samtools_idxstats/README.rst	Thu May 11 12:48:26 2017 -0400
@@ -54,6 +54,8 @@
 v0.0.3  - Embed samtools citation in tool XML.
 v0.0.4  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.5  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r b0ac04e1efe0 -r 515fc5316fdb tools/samtools_idxstats/samtools_idxstats.xml
--- a/tools/samtools_idxstats/samtools_idxstats.xml	Wed May 10 12:48:16 2017 -0400
+++ b/tools/samtools_idxstats/samtools_idxstats.xml	Thu May 11 12:48:26 2017 -0400
@@ -1,15 +1,14 @@
-<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4">
+<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.5">
     <description>samtools idxstats</description>
     <requirements>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">samtools_idxstats.py --version</version_command>
-    <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
+    <version_command>
+python $__tool_directory__/samtools_idxstats.py --version
+    </version_command>
+    <command  detect_errors="aggressive">
+python $__tool_directory__/samtools_idxstats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular'
+    </command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Input BAM file" />
     </inputs>