--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rm_spurious_events.xml	Tue Nov 14 05:54:14 2017 -0500
@@ -0,0 +1,48 @@
+<tool id="bctools_remove_spurious_events" name="Remove spurious" version="@VERSION@">
+    <description>crosslinking events</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        rm_spurious_events.py
+        '$events'
+        --threshold '$threshold'
+        --outfile '$events_filtered'
+    ]]></command>
+    <inputs>
+        <param name="events" type="data" format="bed" label="BED6 file containing alignments"/>
+        <param name="threshold" argument="--threshold" type="float" value="0.1" optional="true" label="Threshold for spurious event removal" help="Remove all crosslinking events that combine less reads than this fraction of the maximum number of reads at this position."/>
+    </inputs>
+    <outputs>
+        <data name="events_filtered" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="events" value="merged_pcr_dupes_spurious.bed"/>
+            <param name="threshold" value="0.5"/>
+            <output name="events_filtered" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+bctools - Remove spurious events originating from errors in unique molecular identifiers (UMIs)
+===============================================================================================
+
+This tool compares all events sharing the same coordinates. Among each group
+of events the maximum number of PCR duplicates is determined. By default, all events that
+are supported by less than 10 percent of this maximum count are removed.
+
+Input
+-----
+
+* BED6 containing crosslinking events with score field set to number of PCR duplicates
+
+Output
+------
+
+* BED6 with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>