# HG changeset patch
# User iuc
# Date 1583866685 0
# Node ID fa08edee5a7926a579b68041005549b982261e7f
# Parent  aafd4ef10b1343e56c06fadd51b3b9eeb3b9e0de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

diff -r aafd4ef10b13 -r fa08edee5a79 macros.xml
--- a/macros.xml	Thu Jan 23 20:54:33 2020 +0000
+++ b/macros.xml	Tue Mar 10 18:58:05 2020 +0000
@@ -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 aafd4ef10b13 -r fa08edee5a79 scHicPlotClusterProfiles.xml
--- a/scHicPlotClusterProfiles.xml	Thu Jan 23 20:54:33 2020 +0000
+++ b/scHicPlotClusterProfiles.xml	Tue Mar 10 18:58:05 2020 +0000
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix $matrix_mcooler
+        --matrix $matrix_scooler
         --clusters $clusters
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
@@ -33,7 +33,7 @@
 
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
         <param name="maximalDistance" type="integer" value="2000000"  label="Maximal distance" help='Maximal distance to consider for plotting' />   
         <conditional name="order_by_conditional">
@@ -59,7 +59,7 @@
         
     </inputs>
     <outputs>
-        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+        <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '>
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
                 <when input="image_file_format" value="pdf" format="pdf" />
@@ -68,7 +68,7 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' />
             <conditional name="order_by_conditional">
                 <param name="order_by_selection" value="svl"/>
@@ -88,7 +88,8 @@
 Plot cluster profiles
 =====================
 
-scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix assoziated to a cluster, within the cluster the matrices can be order either via their short vs long range ratio or by the order of the file.
+scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix associated to a cluster, within the cluster the matrices can be ordered either via their short vs long range ratio or by the order of the file.
+This tool is useful as a quality control of a cluster to check if all matrices assigned to that cluster are displaying similar contacts distribution.
 
 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png
    :width: 50%
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diff -r aafd4ef10b13 -r fa08edee5a79 test-data/scHicQualityControl/coverage.png
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diff -r aafd4ef10b13 -r fa08edee5a79 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt	Thu Jan 23 20:54:33 2020 +0000
+++ b/test-data/scHicQualityControl/qc_report.txt	Tue Mar 10 18:58:05 2020 +0000
@@ -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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