Mercurial > repos > iuc > abricate

diff abricate.xml @ 5:f9bf6a8d8547 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"
author iuc
date Wed, 11 Sep 2019 23:57:17 -0400
parents 78c75f134c16
children 1bb2ba6d3d96
line wrap: on
line diff
--- a/abricate.xml	Mon Mar 19 10:42:19 2018 -0400
+++ b/abricate.xml	Wed Sep 11 23:57:17 2019 -0400
@@ -9,7 +9,12 @@
     <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate '$file_input'
+        #import re
+        #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
+
+        ln -sf '${file_input}' ${sample_name} &&
+        
+        abricate ${sample_name}
         $adv.no_header
         #if $adv.min_dna_id
             --minid=$adv.min_dna_id