--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicCompareMatrices.xml	Wed Mar 07 03:37:57 2018 -0500
@@ -0,0 +1,75 @@
+<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>normalize and compare two HiC matricies</description>
+    <macros>
+        <token name="@BINARY@">hicCompareMatrices</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+    @BINARY@
+    --matrices '$matrix1' '$matrix2'
+    --operation $operation
+    --outFileName matrix.$outputFormat
+
+    && mv matrix.$outputFormat matrix
+]]>
+    </command>
+    <inputs>
+        <param name='matrix1' type="data" format="h5,cool"
+            label="First matrix"/>
+        <param name='matrix2' type="data" format="h5,cool"
+            label="Second matrix to compare against the first"/>
+
+        <param name='operation' type='select' label="Operation to be used for the comparison">
+            <option value='diff'>diff</option>
+            <option value="ratio">ratio</option>
+            <option value="log2ratio">log2ratio</option>
+        </param>
+        <param name='outputFormat' type='select' label="Output file format">
+            <option value='h5'>HiCExplorer format</option>
+            <option value="cool">cool</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
+            <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix1" value="small_test_matrix.h5"/>
+            <param name="matrix2" value="small_test_matrix.h5"/>
+            <param name="operation" value='log2ratio' />
+            <param name="outputFormat" value="h5" />
+            <output name="outFileName" file="compare_matrices_log2ratio.h5" ftype="h5" compare="sim_size" delta='2000'/>
+        </test>
+        <test>
+            <param name="matrix1" value="pearson_small_50kb.cool"/>
+            <param name="matrix2" value="pearson_small_50kb.cool"/>
+            <param name="operation" value='ratio' />
+            <param name="outputFormat" value="cool" />
+            <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+Comparison of HiC matrices
+==========================
+`hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To
+normalize the matrices each element is divided by sum of the matrix.
+
+Input
+-----
+- the matricies to be compared
+
+
+
+| 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>