--- a/flankbed.xml	Wed Jun 18 15:07:04 2014 -0400
+++ b/flankbed.xml	Thu Jun 19 10:12:00 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_flankbed" name="FlankBed" version="0.2.0">
+<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -11,13 +11,15 @@
         $strand
         -g $genome
         -i $inputA
-        &gt; $output
+
         #if $addition.addition_select == 'b':
-        -b $addition.b
+            -b $addition.b
         #else:
-        -l $addition.l
-        -r $addition.r
+            -l $addition.l
+            -r $addition.r
         #end if
+
+        &gt; $output
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
@@ -25,8 +27,6 @@
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
         <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
         <expand macro="addition" />
-
-        
     </inputs>
     <outputs>
         <data format="bed" name="output"  label=""/>