# HG changeset patch
# User iuc
# Date 1637787991 0
# Node ID 91887494eb977bd35de91df7b39205474476476d
# Parent  e88a7de55d6eabb3e5300af68bf6f139fbf97602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 40335305f3461201b017380c60c4c96c7e07322f"

diff -r e88a7de55d6e -r 91887494eb97 roary.xml
--- a/roary.xml	Thu Sep 23 13:08:51 2021 +0000
+++ b/roary.xml	Wed Nov 24 21:06:31 2021 +0000
@@ -1,12 +1,12 @@
 <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>
+    <macros>
+        <token name="@TOOL_VERSION@">3.13.0</token>
+        <token name="@VERSION_SUFFIX@">2</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">roary</xref>
     </xrefs>
-    <macros>
-        <token name="@TOOL_VERSION@">3.13.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
-    </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">roary</requirement>
     </requirements>
@@ -14,10 +14,11 @@
     <command detect_errors="exit_code"><![CDATA[
         #import re
         #set $filenames = list()
+        ## Roary resolves symbolic links and breaks if there is whitespace in the path.
+        ## Copying and renaming the files resolves that issue.
         #for $gff in $gff_input.gffs
-            #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($gff.element_identifier))
-            ln -s '$gff' '${escaped_element_identifier}.gff' &&
-            #set $filename = str($escaped_element_identifier) + '.gff'
+            #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
+            cp '$gff' $filename &&
             $filenames.append(str($filename))
         #end for