--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicCluster.xml	Thu Jan 23 15:57:55 2020 -0500
@@ -0,0 +1,98 @@
+<tool id="schicexplorer_schiccluster" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>clusters single-cell Hi-C interaction matrices on the raw data</description>
+    <macros>
+        <token name="@BINARY@">scHicCluster</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+
+        --matrix '$matrix_mcooler'
+
+        --numberOfClusters $numberOfClusters
+
+        --clusterMethod $clusterMethod_selector
+
+        #if $chromosomes:
+            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            --chromosomes $chromosome
+        #end if
+
+        --dimensionReductionMethod $dimensionReductionMethod_selector
+
+        --outFileName cluster_list.txt
+
+        --threads @THREADS@
+
+
+
+    ]]></command>
+    <inputs>
+        
+        <expand macro="matrix_mcooler_macro"/>
+        <param name="clusterMethod_selector" type="select" label="Cluster method:">
+                <option value="kmeans" selected="True">K-means</option>
+                <option value="spectral" >Spectral clustering</option>
+        </param>
+        <param name="dimensionReductionMethod_selector" type="select" label="Apply dimension reduction:">
+                <option value="none" selected="True">No dimension reduction</option>
+                <option value="knn" >Exact k-nearest neighbors</option>
+                <option value="pca" >Principal components</option>
+        </param>
+        <param name="numberOfClusters" type="integer" value="7"  label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />   
+
+        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${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='dimensionReductionMethod_selector' value='none' />
+            <param name='numberOfClusters' value='7' />
+            <output name="outFileName" file="scHicCluster/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='kmeans' />
+            <param name='dimensionReductionMethod_selector' value='none' />
+            <param name='numberOfClusters' value='7' />
+            <param name='chromosomes' value='chr1 chr2' />
+
+            <output name="outFileName" file="scHicCluster/cluster_kmeans_chromosomes.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='dimensionReductionMethod_selector' value='knn' />
+            <param name='numberOfClusters' value='7' />
+            <output name="outFileName" file="scHicCluster/cluster_spectral_knn.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='dimensionReductionMethod_selector' value='pca' />
+            <param name='numberOfClusters' value='7' />
+            <output name="outFileName" file="scHicCluster/cluster_spectral_pca.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Clustering on raw data
+======================
+
+scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
+The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. 
+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>