# HG changeset patch
# User peterjc
# Date 1494521281 14400
# Node ID 81b90fa846c7742f7ba827acf1f0c99630b5cc06
# Parent  41c56cd5e2ba2fb173e6598585731923ef47bb5a
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty

diff -r 41c56cd5e2ba -r 81b90fa846c7 tools/samtools_depad/README.rst
--- a/tools/samtools_depad/README.rst	Wed May 10 12:47:37 2017 -0400
+++ b/tools/samtools_depad/README.rst	Thu May 11 12:48:01 2017 -0400
@@ -1,14 +1,14 @@
 Galaxy wrapper for samtools depad
 =================================
 
-This wrapper is copyright 2014-2015 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2014-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
 This is a wrapper for part of the command line samtools suite, v0.1.19
 
 This wrapper is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
+http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
 
 
 Automated Installation
@@ -54,6 +54,8 @@
         - Removed unused imports from Python wrapper script.
 v0.0.3  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.4  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r 41c56cd5e2ba -r 81b90fa846c7 tools/samtools_depad/samtools_depad.py
--- a/tools/samtools_depad/samtools_depad.py	Wed May 10 12:47:37 2017 -0400
+++ b/tools/samtools_depad/samtools_depad.py	Thu May 11 12:48:01 2017 -0400
@@ -15,7 +15,7 @@
 
 if "-v" in sys.argv or "--version" in sys.argv:
     # Galaxy seems to invert the order of the two lines
-    print "(Galaxy wrapper v0.0.2)"
+    print "(Galaxy wrapper v0.0.4)"
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
@@ -33,9 +33,9 @@
 
 # Run samtools depad:
 if input_format.lower() == "sam":
-    cmd = "samtools depad -S -T %s %s > %s" % (padded_ref, bam_filename, output_filename)
+    cmd = "samtools depad -S -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename)
 else:
-    cmd = "samtools depad -T %s %s > %s" % (padded_ref, bam_filename, output_filename)
+    cmd = "samtools depad -T '%s' '%s' > '%s'" % (padded_ref, bam_filename, output_filename)
 return_code = os.system(cmd)
 
 if return_code:
diff -r 41c56cd5e2ba -r 81b90fa846c7 tools/samtools_depad/samtools_depad.xml
--- a/tools/samtools_depad/samtools_depad.xml	Wed May 10 12:47:37 2017 -0400
+++ b/tools/samtools_depad/samtools_depad.xml	Thu May 11 12:48:01 2017 -0400
@@ -1,15 +1,14 @@
-<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.3">
+<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.4">
     <description>samtools depad</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_depad.py --version</version_command>
-    <command interpreter="python">samtools_depad.py "$padded_ref" "$input_bam" "$input_bam.ext" "$output_bam"</command>
+    <version_command>
+python $__tool_directory__/samtools_depad.py --version
+    </version_command>
+    <command  detect_errors="aggressive">
+python $__tool_directory__/samtools_depad.py '$padded_ref' '$input_bam' '$input_bam.ext' '$output_bam'
+    </command>
     <inputs>
         <param name="padded_ref" type="data" format="fasta" label="Padded FASTA file (with gap characters)" />
         <param name="input_bam" type="data" format="sam,bam" label="Input SAM or BAM file (mapped against the padded FASTA)" />