# HG changeset patch
# User iuc
# Date 1583867295 14400
# Node ID 0bc84d7d94d44bd02675a9ac2196a415848c7ea8
# Parent  5426f006d7edba508e368ba1ad438df10cd63ac7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

diff -r 5426f006d7ed -r 0bc84d7d94d4 macros.xml
--- a/macros.xml	Sat Jan 25 04:38:26 2020 -0500
+++ b/macros.xml	Tue Mar 10 15:08:15 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 5426f006d7ed -r 0bc84d7d94d4 scHicClusterCompartments.xml
--- 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_
diff -r 5426f006d7ed -r 0bc84d7d94d4 test-data/scHicConsensusMatrices/consensus_matrix.mcool
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diff -r 5426f006d7ed -r 0bc84d7d94d4 test-data/scHicQualityControl/coverage.png
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diff -r 5426f006d7ed -r 0bc84d7d94d4 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt	Sat Jan 25 04:38:26 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt	Tue Mar 10 15:08:15 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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