--- a/macs2_bdgpeakcall.xml	Thu Feb 12 10:40:25 2015 -0500
+++ b/macs2_bdgpeakcall.xml	Mon Oct 12 11:24:39 2015 -0400
@@ -1,12 +1,13 @@
 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0">
     <description>Call peaks from bedGraph output</description>
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
     <expand macro="requirements">
         <requirement type="package" version="4.1.0">gnu_awk</requirement>
     </expand>
+    <expand macro="stdio" />
     <expand macro="version_command" />
-    <macros>
-        <import>macs2_macros.xml</import>
-    </macros>
     <command>
         macs2 bdgpeakcall
         --ifile "${ infile }"
@@ -19,19 +20,18 @@
         &amp;&amp;
         awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
 
-        <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" 
+        <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
             help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. DEFAULT: 5.0 (--cutoff)"/>
         <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/>
         <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/>
 
-        <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" 
+        <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
             label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region."
             help="(-call-summits)"/>
-        <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" 
+        <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False"
             label="Include trackline into bedGraph output"
             help="required by USCS (--no-trackline)"/>
     </inputs>