# HG changeset patch
# User iuc
# Date 1646858991 0
# Node ID 579f1cabfe79095c0bb4857c10626077a6de7233
# Parent  b469f6d53d0692626aba5e2b0a06a97305c1e57f
"planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"

diff -r b469f6d53d06 -r 579f1cabfe79 legsta.xml
--- a/legsta.xml	Mon Feb 21 20:23:38 2022 +0000
+++ b/legsta.xml	Wed Mar 09 20:49:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="legsta" name="legsta" version="@TOOL_VERSION@" profile="20.01">
+<tool id="legsta" name="legsta" version="@TOOL_VERSION@+galaxy1" profile="20.01">
     <description>Legionella pneumophila sequence based typing</description>
 
     <macros>
@@ -7,13 +7,22 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
+        #import re
+        #set safe_names=[]
+
+        #for $i in $contigs
+            #set safe_name=re.sub('[^\s\w\-.]', '_', str($i.element_identifier))
+            $safe_names.append($safe_name)
+            ln -s '$i' '$safe_name';
+        #end for
+
         legsta
 
         $noheader
         $csv
 
-        #for $i in $contigs
-            '$i'
+        #for $safe_name in $safe_names
+            '$safe_name'
         #end for
 
         > '$output'
@@ -41,7 +50,7 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
-                    <has_text text="1,1,4,3,1,1,1,1" />
+                    <has_text text="NC_006368.fna.bz2,1,1,4,3,1,1,1,1" />
                 </assert_contents>
             </output>
         </test>