--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicClusterSVL.xml	Thu Jan 23 16:01:20 2020 -0500
@@ -0,0 +1,83 @@
+<tool id="schicexplorer_schicclustersvl" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>clusters single-cell Hi-C interaction matrices with svl dimension reduction</description>
+    <macros>
+        <token name="@BINARY@">scHicClusterSVL</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+
+        --matrix '$matrix_mcooler'
+
+        --numberOfClusters $numberOfClusters
+        --distanceShortRange $distanceShortRange
+        --distanceLongRange $distanceLongRange
+
+        --clusterMethod $clusterMethod_selector
+
+        #if $chromosomes:
+            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            --chromosomes $chromosome
+        #end if
+
+        --outFileName cluster_list.txt
+
+        --threads @THREADS@
+    ]]></command>
+    <inputs>
+        
+        <expand macro="matrix_mcooler_macro"/>
+        <param name="clusterMethod_selector" type="select" label="Cluster method:">
+                <option value="kmeans" selected="True">K-means</option>
+                <option value="spectral" >Spectral clustering</option>
+        </param>
+
+        <param name="numberOfClusters" type="integer" value="7"  label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />   
+        <param name="distanceShortRange" type="integer" value="2000000"  label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />   
+        <param name="distanceLongRange" type="integer" value="12000000"  label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />   
+
+        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='kmeans' />
+            <param name='numberOfClusters' value='3' />
+            <param name='distanceShortRange' value='2000000' />
+            <param name='distanceLongRange' value='12000000' />
+
+            <output name="outFileName" file="scHicClusterSVL/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='spectral' />
+            <param name='numberOfClusters' value='3' />
+            <param name='distanceShortRange' value='2000000' />
+            <param name='distanceLongRange' value='12000000' />
+
+            <output name="outFileName" file="scHicClusterSVL/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+   
+    </tests>
+    <help><![CDATA[
+
+Clustering with dimension reduction via short vs long range ratio
+=================================================================
+
+scHicClusterSVL uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
+The clustering is applied on dimension reduced data based on the ratio of short vs long range contacts per chromosome. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * (number of chromosomes). 
+Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, 
+can be faster or less memory demanding.
+
+For more information about scHiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://schicexplorer.readthedocs.io/
+]]></help>
+    <expand macro="citations" />
+
+</tool>