# HG changeset patch
# User iuc
# Date 1583867182 14400
# Node ID 36e26166034d413d6cf242fa14545329d39e6611
# Parent  a532cbac217aec3eed8b95073d994ca326b54c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

diff -r a532cbac217a -r 36e26166034d macros.xml
--- a/macros.xml	Thu Jan 23 15:57:55 2020 -0500
+++ b/macros.xml	Tue Mar 10 15:06:22 2020 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">4</token>
 
      <xml name="requirements">
         <requirements>
@@ -9,8 +9,8 @@
         </requirements>
         <version_command>@BINARY@ --version</version_command>
     </xml>
-    <xml name='matrix_mcooler_macro'>
-        <param name='matrix_mcooler' type="data" format="mcool"
+    <xml name='matrix_scooler_macro'>
+        <param name='matrix_scooler' type="data" format="scool"
             label="Matrix to compute on"/>
     </xml>
     <xml name='matrix_cooler_multiple_macro'>
@@ -18,7 +18,7 @@
             label="Matricies to compute on" multiple="true"/>
     </xml>
     <token name="@ESCAPE_IDENTIFIER_FASTQ@"><![CDATA[re.sub('[^\s\w\.]', '_', str($fastq.element_identifier))]]></token>
-    <token name="@ESCAPE_IDENTIFIER_MCOOL@"><![CDATA[re.sub('[^\s\w\.]', '_', str($matrix_mcooler.element_identifier))]]></token>
+    <token name="@ESCAPE_IDENTIFIER_SCOOL@"><![CDATA[re.sub('[^\s\w\.]', '_', str($matrix_scooler.element_identifier))]]></token>
     <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
 
     <xml name="citations">
diff -r a532cbac217a -r 36e26166034d scHicCluster.xml
--- a/scHicCluster.xml	Thu Jan 23 15:57:55 2020 -0500
+++ b/scHicCluster.xml	Tue Mar 10 15:06:22 2020 -0400
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
 
         --numberOfClusters $numberOfClusters
 
@@ -20,7 +20,7 @@
         #end if
 
         --dimensionReductionMethod $dimensionReductionMethod_selector
-
+        --numberOfNearestNeighbors $numberOfNearestNeighbors
         --outFileName cluster_list.txt
 
         --threads @THREADS@
@@ -30,7 +30,7 @@
     ]]></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>
@@ -41,6 +41,7 @@
                 <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="numberOfNearestNeighbors" type="integer" value="100"  label="Number of nearest neighbors" help='How many nearest neighbors should be computed for the k-nn graph?' />   
 
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
     </inputs>
@@ -49,14 +50,14 @@
     </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='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='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='dimensionReductionMethod_selector' value='none' />
             <param name='numberOfClusters' value='7' />
@@ -65,14 +66,14 @@
             <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='matrix_scooler' value='test_matrix.scool' />
             <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='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='spectral' />
             <param name='dimensionReductionMethod_selector' value='pca' />
             <param name='numberOfClusters' value='7' />
@@ -86,8 +87,8 @@
 
 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.
+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_
 
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diff -r a532cbac217a -r 36e26166034d test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt	Thu Jan 23 15:57:55 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt	Tue Mar 10 15:06:22 2020 -0400
@@ -1,6 +1,6 @@
-# QC report for single-cell Hi-C data generated by scHiCExplorer 1-dev
+# QC report for single-cell Hi-C data generated by scHiCExplorer 4
 scHi-C sample contained 20 cells:
 Number of removed matrices containing bad chromosomes 0
-Number of removed matrices due to low read coverage (< 100000): 8
+Number of removed matrices due to low read coverage (< 100000): 10
 Number of removed matrices due to too many zero bins (< 0.001 density, within 30000000 relative genomic distance): 0
-12 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.
\ No newline at end of file
+10 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.
\ No newline at end of file
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