--- a/variant_recalibrator.xml	Tue Apr 28 22:56:25 2015 -0400
+++ b/variant_recalibrator.xml	Mon May 04 22:47:06 2015 -0400
@@ -1,12 +1,12 @@
 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0">
   <description></description>
+  <macros>
+    <import>gatk2_macros.xml</import>
+  </macros>
   <expand macro="requirements">
     <requirement type="package" version="0.9.3">ggplot2</requirement>
   </expand>
   <expand macro="version_command" />
-  <macros>
-    <import>gatk2_macros.xml</import>
-  </macros>
   <command interpreter="python">
     gatk2_wrapper.py
     --stdout "${output_log}"
@@ -27,14 +27,14 @@
     --tranches_file "${output_tranches}"
     --rscript_file "${output_rscript}"
    '
-    
+
     #set $rod_binding_names = dict()
     #for $rod_binding in $rod_bind:
         #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
             #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
         #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
             #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
-        #else 
+        #else
             #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
         #end if
         #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
@@ -44,9 +44,9 @@
             -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
         #end if
     #end for
-    
+
     #include source=$standard_gatk_options#
-    
+
     ##start analysis specific options
     -p '
     #if str( $annotations ) != "None":
@@ -59,7 +59,7 @@
     #end for
     --mode "${mode}"
     '
-    
+
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
         -p '
         --maxGaussians "${analysis_param_type.max_gaussians}"
@@ -85,11 +85,10 @@
         #end for
         '
     #end if
-    
-    
+
     &amp;&amp;
     mv "${output_rscript}.pdf" "${output_tranches_pdf}"
-    
+
   </command>
   <inputs>
     <conditional name="reference_source">
@@ -112,7 +111,7 @@
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
+
     <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;" min="2">
         <conditional name="rod_bind_type">
           <param name="rod_bind_type_selector" type="select" label="Binding Type">
@@ -183,7 +182,7 @@
                       <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
                   </when>
               </conditional>
-          </when>          
+          </when>
           <when value="dbsnp">
               <param name="input_rod" type="data" format="vcf" label="ROD file" />
               <conditional name="rod_training_type">
@@ -301,7 +300,7 @@
           </when>
         </conditional>
     </repeat>
-    
+
     <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
       <options from_data_table="gatk2_annotations">
@@ -309,19 +308,19 @@
         <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
       </options>
     </param>
-    
+
     <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
       <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
     </repeat>
-    
+
     <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
         <option value="SNP" selected="True">SNP</option>
         <option value="INDEL">INDEL</option>
         <option value="BOTH">BOTH</option>
     </param>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
     <expand macro="analysis_type_conditional">
         <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="8" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
         <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="150" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>