diff circos.xml @ 11:31a35811dda6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"

--- a/circos.xml	Mon Oct 11 10:09:51 2021 +0000
+++ b/circos.xml	Tue Nov 16 09:20:08 2021 +0000
@@ -11,7 +11,6 @@
         <import>macros_conffiles.xml</import>
         <import>macros_tests.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0797</edam_topic>
         <edam_topic>topic_0092</edam_topic>
@@ -19,7 +18,7 @@
     <edam_operations>
         <edam_operation>operation_0337</edam_operation>
     </edam_operations>
-    <version_command>circos --version</version_command>
+    <expand macro="requirements"/>
     <stdio>
       <!-- Anything other than zero is an error -->
       <exit_code range="1:"/>
@@ -27,6 +26,7 @@
       <!-- In case the return code has not been set propery check stderr too -->
       <regex match="Circos::Error::fatal_error.* called at"/>
     </stdio>
+    <version_command>circos --version</version_command>
     <command><![CDATA[
 ## Directory structure
 mkdir -p circos/conf/ circos/data/ &&
@@ -58,7 +58,7 @@
         genomeref.fa
         > circos/conf/karyotype.txt &&
 #else if $reference_genome.ref.ref_source == 'preset':
-    cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt &&
+    cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt &&
 #end if
 
 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`