From bf5568d86ae2e111ab90b9658192ee70faf11fc7 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Mon, 25 Apr 2016 19:30:23 +0100
Subject: [PATCH] Quote some parameters in Trim tool command

Make the tool more robust, see issue #2245.
Also:
- use format_source instead of deprecated format='input';
- explicitly call python in command instead of using the depredated interpreter attribute;
- use CDATA in command.
---
 tools/filters/trimmer.xml | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/tools/filters/trimmer.xml b/tools/filters/trimmer.xml
index 786e29c1766..cf9d176a3d0 100644
--- a/tools/filters/trimmer.xml
+++ b/tools/filters/trimmer.xml
@@ -1,7 +1,9 @@
 <tool id="trimmer" name="Trim" version="0.0.1">
     <description>leading or trailing characters</description>
-    <command interpreter="python">
-    trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1
+    <command>
+<![CDATA[
+python $__tool_directory__/trimmer.py -a -f '$input1' -c $col -s $start -e $end -i '$ignore' $fastq > '$out_file1'
+]]>
     </command>
     <inputs>
         <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
@@ -32,7 +34,7 @@
          </param>   
     </inputs>
     <outputs>
-        <data name="out_file1" format="input" metadata_source="input1"/>
+        <data name="out_file1" format_source="input1" metadata_source="input1"/>
     </outputs>
     <tests>
         <test>
@@ -65,8 +67,6 @@
     </tests>
 
     <help>
-
-
 **What it does**
 
 Trims specified number of characters from a dataset or its field (if dataset is tab-delimited).
@@ -136,7 +136,5 @@ cab done by setting **Remove everything from this position to the end** to 31::
 .. class:: warningmark
 
 **WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example.
-
-
     </help>
 </tool>