--- a/snpEff.xml	Wed Apr 29 11:56:04 2015 -0400
+++ b/snpEff.xml	Mon May 04 22:37:25 2015 -0400
@@ -1,22 +1,23 @@
 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
     <description>Variant effect and annotation</description>
-    <expand macro="requirements" />
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
 <![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 
-        -c \$SNPEFF_JAR_PATH/snpEff.config 
+        java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
+        -c \$SNPEFF_JAR_PATH/snpEff.config
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
         #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
           -spliceSiteSize $spliceSiteSize
         #end if
         #if $filterIn and $filterIn.__str__ != 'no_filter':
-          $filterIn 
+          $filterIn
         #end if
         #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
-          $filterHomHet 
+          $filterHomHet
         #end if
         #if $annotations and $annotations.__str__ != '':
           #echo " "
@@ -33,15 +34,15 @@
           -interval $intervals
         #end if
         #if $statsFile:
-          -stats $statsFile 
+          -stats $statsFile
         #end if
         #if $offset.__str__ != 'default':
-          ${offset} 
+          ${offset}
         #end if
         #if $chr.__str__.strip() != '':
-          -chr "$chr" 
+          -chr "$chr"
         #end if
-          $noLog 
+          $noLog
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
@@ -63,7 +64,7 @@
             -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
           #end if
           ${snpDb.snpeff_db.metadata.genome_version}
-        #else 
+        #else
           -download
           $snpDb.genome_version
         #end if
@@ -252,7 +253,6 @@
             <filter>generate_stats == True</filter>
         </data>
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <!-- Check that an effect was added in out VCF -->
         <!-- Check for a HTML header indicating that this was successful -->
@@ -262,7 +262,7 @@
             <has_text text="SnpEff: Variant analysis" />
             </assert_contents>
         </output>
-        --> 
+        -->
         <!-- Setting filterOut throws exception in twilltestcase.py
         <test>
         <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
@@ -281,7 +281,7 @@
             </assert_contents>
         </output>
         </test>
-        --> 
+        -->
 
         <test>
         <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>