# HG changeset patch
# User iuc
# Date 1681482167 0
# Node ID 4a841ab67e3b2d284696347f5f07628054edcc98
# Parent  5f2eacae0bb889380a77828809d32d3ef2e491e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d

diff -r 5f2eacae0bb8 -r 4a841ab67e3b macros.xml
--- a/macros.xml	Tue Mar 10 15:15:17 2020 -0400
+++ b/macros.xml	Fri Apr 14 14:22:47 2023 +0000
@@ -1,10 +1,11 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">4</token>
+    <token name="@TOOL_VERSION@">4</token>
+    <token name="@PROFILE@">22.05</token>
 
      <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">schicexplorer</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">schicexplorer</requirement>
             <yield />
         </requirements>
         <version_command>@BINARY@ --version</version_command>
diff -r 5f2eacae0bb8 -r 4a841ab67e3b scHicQualityControl.xml
--- a/scHicQualityControl.xml	Tue Mar 10 15:15:17 2020 -0400
+++ b/scHicQualityControl.xml	Fri Apr 14 14:22:47 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="schicexplorer_schicqualitycontrol" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="schicexplorer_schicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
     <description>quality control for single-cell Hi-C interaction matrices</description>
     <macros>
         <token name="@BINARY@">scHicQualityControl</token>
@@ -6,9 +6,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        ## https://github.com/open2c/cooler/issues/299
+        cp '$matrix_scooler' matrix.scooler &&
+
         @BINARY@
 
-        --matrix '$matrix_scooler'
+        --matrix matrix.scooler
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
             --chromosomes $chromosome