--- a/gemini_burden.xml	Tue Apr 28 22:55:56 2015 -0400
+++ b/gemini_burden.xml	Mon May 04 22:46:38 2015 -0400
@@ -1,11 +1,12 @@
 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
     <description>perform sample-wise gene-level burden calculations</description>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">burden</token>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
 <![CDATA[
         gemini @BINARY@
@@ -26,30 +27,29 @@
 ]]>
 
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="infile" />
 
         <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
         <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
 
-        <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" 
+        <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
             label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
 
-        <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" 
+        <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
             label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
-        <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" 
+        <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
             label="Run the C-alpha association test" help="(--calpha)"/>
-        <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included" 
+        <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included"
             help="(--min-aaf)">
             <!--validator type="in_range" min="0.0"/-->
         </param>
-        <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included" 
+        <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included"
             help="(--max-aaf)">
             <!--validator type="in_range" min="0.0"/-->
         </param>
 
-        <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test" 
+        <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test"
             help="(--permutations)">
             <validator type="in_range" min="0"/>
         </param>
@@ -65,7 +65,7 @@
     <help>
 **What it does**
 
-The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. 
+The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis.
 By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.
 
 $ gemini burden test.burden.db