diff scHicClusterCompartments.xml @ 1:0bc84d7d94d4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

--- a/scHicClusterCompartments.xml	Sat Jan 25 04:38:26 2020 -0500
+++ b/scHicClusterCompartments.xml	Tue Mar 10 15:08:15 2020 -0400
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
 
         --numberOfClusters $numberOfClusters
 
@@ -41,7 +41,7 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="clusterMethod_selector" type="select" label="Cluster method:">
                 <option value="kmeans" selected="True">K-means</option>
                 <option value="spectral" >Spectral clustering</option>
@@ -73,19 +73,19 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='numberOfClusters' value='3' />
             <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='spectral' />
             <param name='numberOfClusters' value='3' />
             <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='numberOfClusters' value='3' />
             <param name='binarization' value='True'/>
@@ -97,7 +97,7 @@
             <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
        <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='numberOfClusters' value='3' />
             <param name='binarization' value='True'/>
@@ -116,7 +116,7 @@
 
 scHicClusterCompartments 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 A/B compartments track. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * (number of bins). 
-Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, 
+Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. 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_