--- a/samtools_reheader.xml	Fri Dec 18 19:45:43 2015 -0500
+++ b/samtools_reheader.xml	Tue May 09 11:16:51 2017 -0400
@@ -1,12 +1,17 @@
-<tool id="samtools_reheader" name="Reheader" version="2.0">
+<tool id="samtools_reheader" name="Reheader" version="2.0.1">
     <description>copy SAM/BAM header between datasets</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio"></expand>
-  <expand macro="version_command"></expand>
-    <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        samtools reheader
+            '${input_header}'
+            '${input_file}'
+            > '${output}'
+    ]]></command>
     <inputs>
         <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
         <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
@@ -18,15 +23,14 @@
         <test>
             <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
             <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
-            <output name="output" ftype="bam" file="reheader_out.bam"/>
+            <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line -->
         </test>
     </tests>
     <help>
 **What it does**
 
 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
-
     </help>
-    <expand macro="citations"></expand>
+    <expand macro="citations"/>
 </tool>