--- a/haplotype_caller.xml	Tue Apr 28 22:56:25 2015 -0400
+++ b/haplotype_caller.xml	Mon May 04 22:47:06 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.1">
   <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description>
-  <expand macro="requirements" />
-  <expand macro="version_command" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
@@ -33,7 +33,7 @@
     @DBSNP_OPTIONS@
     $allow_n_cigar_reads
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
@@ -55,7 +55,7 @@
         #if str($analysis_param_type.comp) != 'None':
             --comp "$analysis_param_type.comp"
         #end if
-        ##  
+        ##
         #if str( $analysis_param_type.annotation ) != "None":
             #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
                 --annotation "${annotation}"
@@ -216,8 +216,6 @@
             <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
           </when>
         </conditional>
-
-
         <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph  File to which debug assembly graph information should be written"/>
         <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets  Heterozygosity value used to compute prior likelihoods for any locus"/>
         <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning  The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph">
@@ -257,7 +255,7 @@
   </outputs>
   <tests>
       <test>
-          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 
+          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
           <param name="reference_source_selector" value="history" />
           <param name="ref_file" value="phiX.fasta" ftype="fasta" />
           <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />