--- a/gemini_lof_sieve.xml	Tue Apr 28 22:55:56 2015 -0400
+++ b/gemini_lof_sieve.xml	Mon May 04 22:46:38 2015 -0400
@@ -1,11 +1,12 @@
 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
     <description>Filter LoF variants by transcript position and type</description>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">lof_sieve</token>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
 <![CDATA[
         gemini @BINARY@
@@ -13,7 +14,6 @@
             > "${ outfile }"
 ]]>
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="infile" />
     </inputs>
@@ -27,10 +27,10 @@
     <help>
 **What it does**
 
-Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far 
-more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool 
-reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. 
-In addition, it also reports the predicted function of the transcript so that one can segregate candidate 
+Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far
+more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool
+reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence.
+In addition, it also reports the predicted function of the transcript so that one can segregate candidate
 LoF variants that affect protein_coding transcripts from processed RNA, etc.
 
 @CITATION@