--- a/crossmap_vcf.xml	Fri Oct 20 11:34:06 2017 -0400
+++ b/crossmap_vcf.xml	Thu May 24 19:09:50 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@-0">
+<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -22,9 +22,7 @@
 '${input_file}'
 '${seq_source.input_fasta}'
 
-'${output}'
-
-&& mv '${output}.unmap' '$output_unmapped'
+output
     ]]></command>
 
     <inputs>
@@ -59,8 +57,8 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="vcf" label="${tool.name} on ${on_string}" />
-        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" />
+        <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
+        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />
     </outputs>
 
     <tests>
@@ -107,7 +105,6 @@
   you run CrossMap).
 - In the output VCF file, whether the chromosome IDs contain “chr” or not
   depends on the format of the input VCF file.
-
     ]]></help>
 
     <citations>