# HG changeset patch
# User bgruening
# Date 1408027472 14400
# Node ID b425a93b4da6797f228a7b93fc0f6c2a74b1f7e1
# Parent  bb468ee178d8be3eef39b18aa2e8211fa5a71d0a
Uploaded

diff -r bb468ee178d8 -r b425a93b4da6 vt_normalize.xml
--- a/vt_normalize.xml	Thu Aug 14 09:57:39 2014 -0400
+++ b/vt_normalize.xml	Thu Aug 14 10:44:32 2014 -0400
@@ -9,7 +9,11 @@
     <command>
 <![CDATA[
         vt @BINARY@
-            -o "${ outfile }"
+            #if $output_format == 'bcf':
+                -o normalised.bcf
+            #else:
+                -o normalised.vcf
+            #end if
             ##-q  do not print options and summary []
             -w $window
 
@@ -25,7 +29,14 @@
                 -r "${reference_source.reference_genome}"
             #end if
 
-            "${ infile }"
+            "${ infile }";
+
+        #if $output_format == 'bcf':
+            mv normalised.bcf "${ outfile }";
+        #else:
+            mv normalised.vcf "${ outfile }";
+        #end if
+
 ]]>
     </command>
     <expand macro="stdio" />
@@ -57,9 +68,18 @@
             <validator type="in_range" min="0"/>
         </param>
 
+        <param name="output_format" type="select" label="Choose the output format" help="">
+            <option value="bcf">BCF</option>
+            <option value="vcf" selected="true">VCF</option>
+        </param>
+
     </inputs>
     <outputs>
-        <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="output_format" value="bcf" format="bcf" />
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>