--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/intervene_upset.xml	Wed Sep 12 13:22:43 2018 -0400
@@ -0,0 +1,84 @@
+<tool id="intervene_upset" name="UpSet diagram" version="@TOOL_VERSION@">
+    <description>of intersection of genomic regions or list sets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">intervene</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#set $labels = ",".join(["'%s'" % @ESCAPE_IDENTIFIER@ for file in $input])
+#set $type = 'genomic 'if $input[0].is_of_type('interval') else 'list'
+intervene upset
+--type $type
+--input #echo " ".join(["'%s'" % file for file in $input])
+--names $labels
+--output results
+--order $order
+--ninter $ninter
+$showzero
+$showsize
+--mbcolor '$mbcolor'
+--sbcolor '$sbcolor'
+--mblabel '$mblabel'
+--sxlabel '$sxlabel'
+--figtype $figtype
+--figsize $figsize_width $figsize_height
+--dpi $dpi &&
+mv results/Intervene_upset.${figtype} results/Intervene_upset.plot
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="txt" multiple="true" label="Select input files for which to produce intersections"/>
+        <param argument="--order" type="select" label="Select the order of intersections of sets">
+            <option value="freq">Frequency</option>
+            <option value="degree">Degree</option>
+        </param>
+        <param argument="--ninter" type="integer" value="30" min="1" label="Number of top intersections to show in plot"/>
+        <param argument="--showzero" type="boolean" truevalue="--showzero" falsevalue="" label="Show empty intersections in plot?"/>
+        <!-- the argparse action is wrong for showsize, check this when upgrading tool in future -->
+        <param argument="--showsize" type="boolean" truevalue="" falsevalue="--showsize" checked="true" label="Show intersection sizes above bars ?"/>
+        <param argument="--mbcolor" type="color" label="Color of the main bar plot" value="#ea5d4e">
+            <expand macro="color_sanitizer"/>
+        </param>
+        <param argument="--sbcolor" type="color" label="Color of the set size bar plot" value="#317eab">
+            <expand macro="color_sanitizer"/>
+        </param>
+        <param argument="--mblabel" type="text" label="The y-axis label of the intersection size bars" value="No. of Intersections">
+            <expand macro="quote_sanitizer"/>
+        </param>
+        <param argument="--sxlabel" type="text" label="The x-axis label of the set size bars" value="Set size">
+            <expand macro="quote_sanitizer"/>
+        </param>
+        <expand macro="figure_params"/>
+    </inputs>
+    <outputs>
+        <data name="plot" format="pdf" label="UpSet plot on ${on_string}" from_work_dir="results/Intervene_upset.plot">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="figtype"/>
+                </action>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="a.txt,b.txt,c.txt"/>
+            <output name="plot" value="upset.pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input" value="a.bed,b.bed,c.bed"/>
+            <output name="plot" value="bed_upset.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool produces an upset plot for the intersection of sets from different datasets. 
+These can be regular lists or BED/GFF/interval files which will be processed using bedtools intersect.
+
+.. image:: $PATH_TO_IMAGES/upset.png
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>