--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/intervene_pairwise.xml	Wed Sep 12 13:22:43 2018 -0400
@@ -0,0 +1,96 @@
+<tool id="intervene_pairwise" name="Pairwise intersection" version="@TOOL_VERSION@">
+    <description>and heatmap for genomic intervals</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 pairwise
+--type $type
+--input #echo " ".join(["'%s'" % file for file in $input])
+--names $labels
+--compute $compute
+#if str($corrtype) != 'None'
+    --corr
+    --corrtype $corrtype
+#end if
+--htype $htype
+$diagonal
+--output results
+--barcolor '$barcolor'
+--fontsize '$fontsize'
+--title '$title'
+--figtype $figtype
+--figsize $figsize_width $figsize_height
+--dpi $dpi &&
+mv results/Intervene_pairwise_*.${figtype} results/Intervene_pairwise.plot
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="interval" multiple="true" label="Select input files for which to produce intersections"/>
+        <param argument="--compute" type="select" label="Use this metric for the heatmap">
+            <option value="count">count: calculates the number of overlaps</option>
+            <option value="frac" selected="true">frac: calculates the fraction of overlap</option>
+            <option value="jaccard">jaccard: calculate the Jaccard statistic</option>
+            <option value="reldist">reldist: calculate the distribution of relative distances</option>
+            <!-- fisher option needs additional genome assembly, probably triggers on demand download
+            <option value="fisher">fisher: calculate Fisher`s statistic</option>
+            -->
+        </param>
+        <param argument="--corrtype" type="select" label="Select the type of correlation">
+            <option value="None">Don't calculate correlation</option>
+            <option value="pearson">Pearson correlation</option>
+            <option value="kendall">Kendall correlation</option>
+            <option value="spearman">Spearman correlation</option>
+        </param>
+        <param argument="--htype" type="select" label="Heatmap plot type">
+            <option value="tribar">tribar</option>
+            <option value="dendrogram">dendrogram</option>
+            <option value="color">color</option>
+            <option value="pie">pie</option>
+            <option value="circle">circle</option>
+            <option value="square">square</option>
+            <option value="ellipse">ellipse</option>
+            <option value="number">number</option>
+            <option value="shade">shade</option>
+        </param>
+        <param argument="--diagonal" type="boolean" truevalue="--diagonal" falsevalue="" label="Show the diagonal values in the heatmap ?"/>
+        <!-- the argparse action is wrong for showsize, check this when upgrading tool in future -->
+        <param argument="--barcolor" type="color" label="Boxplot color" value="#53cfff">
+            <expand macro="color_sanitizer"/>
+        </param>
+        <param argument="--fontsize" type="integer" value="8" label="Label font size"/>
+        <param argument="--title" type="text" label="Heatmap main title" value="Pairwise intersection">
+            <expand macro="quote_sanitizer"/>
+        </param>
+        <expand macro="figure_params"/>
+    </inputs>
+    <outputs>
+        <data name="plot" format="pdf" label="Pairwise plot on ${on_string}" from_work_dir="results/Intervene_pairwise.plot">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="figtype"/>
+                </action>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="a.bed,b.bed,c.bed"/>
+            <output name="plot" value="bed_pairwise.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Plots the pairwise intersections of multiple interval files.
+
+.. image:: $PATH_TO_IMAGES/pairwise.png
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>