# HG changeset patch
# User iuc
# Date 1583867258 14400
# Node ID 649c86cedcb442ed41cb5330c8f7ad77d17a7664
# Parent  e59d83af97a19689c3a37538575f49f0c3713ad1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

diff -r e59d83af97a1 -r 649c86cedcb4 macros.xml
--- a/macros.xml	Thu Jan 23 15:59:42 2020 -0500
+++ b/macros.xml	Tue Mar 10 15:07:38 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 e59d83af97a1 -r 649c86cedcb4 scHicDemultiplex.xml
--- a/scHicDemultiplex.xml	Thu Jan 23 15:59:42 2020 -0500
+++ b/scHicDemultiplex.xml	Tue Mar 10 15:07:38 2020 -0400
@@ -19,6 +19,12 @@
         --bufferSize $bufferSize
         --threads @THREADS@
 
+        && cd outputFiles
+        && mkdir forward
+        && mkdir reverse
+        && mv *R1.fastq.gz forward
+        && mv *R2.fastq.gz reverse
+
     ]]></command>
     <inputs>
         
@@ -29,8 +35,11 @@
 
     </inputs>
     <outputs>
-        <collection name="outputFastqs" type="list" label="Demultiplexed fastq files">
-            <discover_datasets pattern="__name__" format="fastq.gz" directory="outputFiles" />
+        <collection name="outputFastqsForward" type="list" label="Demultiplexed fastq files: Forward">
+            <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/forward" />
+        </collection>
+        <collection name="outputFastqsReverse" type="list" label="Demultiplexed fastq files: Reverse">
+            <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/reverse" />
         </collection>
     </outputs>
     <tests>
@@ -39,57 +48,60 @@
             <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' />
             <param name='srrToSample' value='scHicDemultiplex/samples.txt' />
             <param name='bufferSize' value='1000' />
+            <output_collection name="outputFastqsForward" type="list" count="24">
+                <!-- <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> -->
+                <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <!-- <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> -->
+                <element name="Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+            </output_collection>
 
-            
-            <output_collection name="outputFastqs" type="list" count="48">
-                <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
-                <element name="Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz"  ftype="fastq.gz" compare='sim_size' delta='40000'/>
+            <output_collection name="outputFastqsReverse" type="list" count="24">
+                <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
+                <element name="Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz"  ftype="fastqsanger.gz" compare='sim_size' delta='40000'/>
             </output_collection>
         </test>
     </tests>
@@ -99,7 +111,9 @@
 =================================
 
 scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to
-a seperated forward and reverse strand fastq files per cell.
+a seperated forward and reverse strand fastq files per cell. For other datasets, a third-party demultiplexing strategy must be used.
+
+Afterwards, the demultiplexed mapped data can be used with HiCExplorer `hicBuildMatrix` to create single cell .cool matrices that must be stored in a .scool file using `scHicMergeToSCool`, in order to be used for downstream analyses in the scHiCExplorer suite.
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
 
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diff -r e59d83af97a1 -r 649c86cedcb4 test-data/scHicQualityControl/coverage.png
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diff -r e59d83af97a1 -r 649c86cedcb4 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt	Thu Jan 23 15:59:42 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt	Tue Mar 10 15:07:38 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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