# HG changeset patch
# User iuc
# Date 1583867603 14400
# Node ID 799a9fe1265cdf4c12e5691f9ba117f664a74f99
# Parent  fad89d56674ac70a141080f39c24728536921b73
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

diff -r fad89d56674a -r 799a9fe1265c macros.xml
--- a/macros.xml	Thu Jan 23 16:09:03 2020 -0500
+++ b/macros.xml	Tue Mar 10 15:13:23 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 fad89d56674a -r 799a9fe1265c scHicAdjustMatrix.xml
--- a/scHicAdjustMatrix.xml	Thu Jan 23 16:09:03 2020 -0500
+++ b/scHicAdjustMatrix.xml	Tue Mar 10 15:13:23 2020 -0400
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
         --action $action_selector
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
@@ -16,7 +16,7 @@
         #end if
 
 
-        --outFileName adjusted_matrix.mcool
+        --outFileName adjusted_matrix.scool
 
         --threads @THREADS@
 
@@ -25,7 +25,7 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="action_selector" type="select" label="Action to take apply on matrices:">
                 <option value="keep" selected="True">Keep the listed chromosomes</option>
                 <option value="remove" >Remove the listed chromosomes</option>
@@ -33,14 +33,14 @@
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="adjusted_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: merged matrix"/>
+        <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='keep' />
             <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' />
-            <output name="outFileName" ftype="mcool">
+            <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, 
@@ -201,7 +201,7 @@
 Adjust all matrices
 ===================
 
-scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the mcool file.
+scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the scool file.
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
 
diff -r fad89d56674a -r 799a9fe1265c test-data/scHicConsensusMatrices/consensus_matrix.mcool
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diff -r fad89d56674a -r 799a9fe1265c test-data/scHicQualityControl/coverage.png
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diff -r fad89d56674a -r 799a9fe1265c test-data/scHicQualityControl/density.png
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diff -r fad89d56674a -r 799a9fe1265c test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt	Thu Jan 23 16:09:03 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt	Tue Mar 10 15:13:23 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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