# HG changeset patch
# User iuc
# Date 1583867640 14400
# Node ID 7c2387e72aac8cf0d5c84617841dfe0c22450415
# Parent  6eda3d3b562de135d29f7b081cced4505736b0b4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

diff -r 6eda3d3b562d -r 7c2387e72aac macros.xml
--- a/macros.xml	Thu Jan 23 16:09:58 2020 -0500
+++ b/macros.xml	Tue Mar 10 15:14:00 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 6eda3d3b562d -r 7c2387e72aac scHicNormalize.xml
--- a/scHicNormalize.xml	Thu Jan 23 16:09:58 2020 -0500
+++ b/scHicNormalize.xml	Tue Mar 10 15:14:00 2020 -0400
@@ -8,9 +8,9 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
 
-        --outFileName normalized_matrix.mcool
+        --outFileName normalized_matrix.scool
 
         --threads @THREADS@
 
@@ -19,15 +19,15 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="normalized_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: normalized matrix"/>
+        <data name="outFileName" from_work_dir="normalized_matrix.scool" format="scool" label="${tool.name} on ${on_string}: normalized matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
-            <output name="outFileName" ftype="mcool">
+            <param name='matrix_scooler' value='test_matrix.scool' />
+            <output name="outFileName" ftype="scool">
                 <assert_contents>
                     <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                     Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
@@ -188,7 +188,9 @@
 Normalize matrices
 ==================
 
-scHicNOrmalize normalizes all read coverages to the lowest read coverage found in a mcool file.
+scHicNormalize scales the read coverage of all matrices stored in the provided scool file to the matrix displaying the lowest read coverage in the said file.
+This is a highly parallelized version of HiCExplorer's ̀ hicNormalize`, for more information, you can refer to this page:
+https://hicexplorer.readthedocs.io/en/latest/content/tools/hicNormalize.html
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
 
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diff -r 6eda3d3b562d -r 7c2387e72aac test-data/scHicQualityControl/coverage.png
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diff -r 6eda3d3b562d -r 7c2387e72aac test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt	Thu Jan 23 16:09:58 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt	Tue Mar 10 15:14:00 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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