Mercurial > repos > iuc > schicexplorer_schicqualitycontrol

changeset 2:4a841ab67e3b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:22:47 +0000
parents 5f2eacae0bb8
children
files macros.xml scHicQualityControl.xml
diffstat 2 files changed, 8 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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