# HG changeset patch
# User iuc
# Date 1632402531 0
# Node ID e88a7de55d6eabb3e5300af68bf6f139fbf97602
# Parent  78608ec02d629fa2179b187310aac162724de1e9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit fde1985c9d6860f9a03ddfd38378a5c3f5e31fcb"

diff -r 78608ec02d62 -r e88a7de55d6e roary.xml
--- a/roary.xml	Sat Feb 13 11:59:15 2021 +0000
+++ b/roary.xml	Thu Sep 23 13:08:51 2021 +0000
@@ -1,5 +1,8 @@
 <tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
+    <xrefs>
+        <xref type="bio.tools">roary</xref>
+    </xrefs>
     <macros>
         <token name="@TOOL_VERSION@">3.13.0</token>
         <token name="@VERSION_SUFFIX@">1</token>
@@ -9,10 +12,12 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
+        #import re
         #set $filenames = list()
         #for $gff in $gff_input.gffs
-            cp '$gff' '${gff.element_identifier}.gff' &&
-            #set $filename = str($gff.element_identifier) + '.gff'
+            #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($gff.element_identifier))
+            ln -s '$gff' '${escaped_element_identifier}.gff' &&
+            #set $filename = str($escaped_element_identifier) + '.gff'
             $filenames.append(str($filename))
         #end for