--- a/macs2_bdgpeakcall.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_bdgpeakcall.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -3,58 +3,67 @@
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="4.1.0">gnu_awk</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command>
+        <![CDATA[
+
         macs2 bdgpeakcall
-        --ifile "${ infile }"
-        --cutoff "${ cutoff }"
-        --min-length "${ minlen }"
-        --max-gap "${ maxgap }"
-        ${ callsummits }
+        --ifile '${ infile }'
+        --cutoff '${ cutoff }'
+        --min-length '${ minlen }'
+        --max-gap '${ maxgap }'
+        ${ cutoff_analysis } 
         ${ notrackline }
-        --ofile "macs2_bdgpeakcall.bdg"
-        &amp;&amp;
-        awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
+        --ofile '${ outfile }'
+
+        ]]>
     </command>
     <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"
-            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"
-            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"
-            label="Include trackline into bedGraph output"
-            help="required by USCS (--no-trackline)"/>
+            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. Default=200 (--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="cutoff_analysis" type="boolean" truevalue="--cutoff-analysis" falsevalue="" checked="False" label="Perform cutoff analysis" help="While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, --min-len and --max-gap may affect the results. Default=False (--cutoff-analysis)"/>
+        <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" label="Include trackline into bedGraph output" help="required by UCSC Genome Browser (--no-trackline)"/>
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" />
+            <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
             <param name="cutoff" value="5.0"/>
             <param name="minlen" value="200"/>
             <param name="maxgap" value="30"/>
-            <output name="outfile" file="bdgpeakcall_on_callpeak_treatment.tabular"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="chrV" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" />
+            <param name="cutoff" value="5.0"/>
+            <param name="minlen" value="200"/>
+            <param name="maxgap" value="30"/>
+            <param name="cutoff_analysis" value="true" />
+            <output name="outfile" file="bdgpeakcall_output_cutoff.bdg"/>
         </test>
     </tests>
     <help>
+    <![CDATA[
 **What it does**
 
-Call peaks from bedGraph output.
-bdgpeakcall from macs2
+This is **bdgpeakcall** utility from the MACS2_ Package. It calls peaks from bedGraph output.
+
+.. _MACS2: https://github.com/taoliu/MACS
 
 
 @citation@
+    ]]>
     </help>
     <expand macro="citations" />
 </tool>