--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicAverageRegions.xml	Mon Dec 16 15:21:06 2019 -0500
@@ -0,0 +1,90 @@
+<tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>sums Hi-C contacts around given reference points and computes their average.</description>
+    <macros>
+        <token name="@BINARY@">hicAverageRegions</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+       
+
+        ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
+        @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext'
+
+        --regions '$regions'
+        #if $rangeFormat_conditional.rangeFormat_selector == 'optionGenomicUnits':
+            --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
+        #else:
+            --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
+        #end if
+        --outFileName output_matrix.npz
+
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+        <param argument="--regions" type="data" format='bed'
+                        label="Regions to average"
+                        help="BED file which stores a list of regions that are summed and averaged."/>
+       
+         <conditional name="rangeFormat_conditional">
+            <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
+                <option value="optionGenomicUnits">Range in genomic units</option>
+                <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option>
+            </param>
+            <when value="optionGenomicUnits">
+                 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
+                 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
+            </when>
+            <when value="optionBinUnits">
+                 <param name="upstreamRange" type="integer" value="" label="Upstream range"/>
+                 <param name="downstreamRange" type="integer" value="" label="Downstream range"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+            <param name="regions" value="hicAverageRegions/regions.bed" />
+            <conditional name="rangeFormat_conditional">
+                <param name="rangeFormat_selector" value='optionGenomicUnits'/>
+                <param name="upstreamRange" value='100000'/>
+                <param name="downstreamRange" value='100000'/>
+            </conditional>
+
+            <output name='outFileName' file='hicAverageRegions/result_range_100000.npz'  ftype="zip" compare="sim_size" delta="20000" />
+        </test>
+       <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+            <param name="regions" value="hicAverageRegions/regions.bed" />
+            <conditional name="rangeFormat_conditional">
+                <param name="rangeFormat_selector" value='optionBinUnits'/>
+                <param name="upstreamRange" value='100'/>
+                <param name="downstreamRange" value='100'/>
+            </conditional>
+
+            <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz'  ftype="zip" compare="sim_size" delta="20000" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Average regions
+===============
+
+This tool sums Hi-C contacts around given reference points and computes their average. This tool is useful to detect differences at certain reference points as for example TAD boundaries between samples.
+
+WARNING: This tool can only be used with fixed bin size Hi-C matrices. No guarantees how and if it works on restriction site interaction matrices.
+
+Use the output to plot the average with hicPlotAverageRegions.
+
+_________________
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>