--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicPlotConsensusMatrices.xml	Thu Jan 23 16:02:12 2020 -0500
@@ -0,0 +1,84 @@
+<tool id="schicexplorer_schicplotconsensusmatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>plot single-cell Hi-C interaction matrices cluster consensus matrices</description>
+    <macros>
+        <token name="@BINARY@">scHicPlotConsensusMatrices</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+
+        --matrix $matrix_mcooler
+        #if $chromosomes:
+            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            --chromosomes $chromosome
+        #end if
+        
+        #if $colormap:
+            --colorMap $colormap
+        #end if
+        #if $dpi:
+            --dpi $dpi
+        #end if 
+        --outFileName plot.$image_file_format
+
+        --threads @THREADS@
+
+        && mv plot.$image_file_format plot
+
+    ]]></command>
+    <inputs>
+        <expand macro="matrix_mcooler_macro"/>
+        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+        <expand macro="colormap" />
+        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
+        
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+            <option value="pdf">pdf</option>
+        </param>
+        
+    </inputs>
+    <outputs>
+        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+            <change_format>
+                <when input="image_file_format" value="svg" format="svg" />
+                <when input="image_file_format" value="pdf" format="pdf" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
+            <param name="image_file_format" value="png" />
+            <param name="dpi" value="300" />
+            <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>        
+        </test>
+         <test>
+            <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
+            <param name="image_file_format" value="png" />
+            <param name="dpi" value="300" />
+            <param name="chromosomes" value="chr1 chr2" />
+
+            <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>        
+        </test>
+       
+    </tests>
+    <help><![CDATA[
+
+Plot consensus matrices
+=======================
+
+scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster.
+
+.. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png
+   :width: 50%
+
+For more information about scHiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://schicexplorer.readthedocs.io/
+]]></help>
+    <expand macro="citations" />
+
+</tool>
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