--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_bdgpeakcall.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,60 @@
+<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0">
+    <description>Call peaks from bedGraph output</description>
+    <expand macro="requirements">
+        <requirement type="package" version="4.1.0">gnu_awk</requirement>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 bdgpeakcall
+        --ifile "${ infile }"
+        --cutoff "${ cutoff }"
+        --min-length "${ minlen }"
+        --max-gap "${ maxgap }"
+        ${ callsummits }
+        ${ notrackline }
+        --ofile "macs2_bdgpeakcall.bdg"
+        &amp;&amp;
+        awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ 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" 
+            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)"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="callpeak_treatment_part.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"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Call peaks from bedGraph output.
+bdgpeakcall from macs2
+
+
+@citation@
+    </help>
+    <expand macro="citations" />
+</tool>