# HG changeset patch
# User jpayne
# Date 1776786411 0
# Node ID 5ca386f1720d17b93cd6e055cb18339710393524
# Parent  7a2bd16bd8d98ad3d5c52396c743b7bde32b6ed8
planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty

diff -r 7a2bd16bd8d9 -r 5ca386f1720d seqsero2S.xml
--- a/seqsero2S.xml	Wed Jan 21 20:40:57 2026 +0000
+++ b/seqsero2S.xml	Tue Apr 21 15:46:51 2026 +0000
@@ -1,8 +1,8 @@
-<tool id="seqsero2s" name="SeqSero2S" version="1">
+<tool id="seqsero2s" name="SeqSero2S" version="1.1.4">
     <description>Simplified Salmonella serotype prediction</description>
     <requirements>
         <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> -->
-        <container type="docker">quay.io/biocontainers/seqsero2s:1.1.3--pyhdfd78af_0</container>
+        <container type="docker">quay.io/biocontainers/seqsero2s:1.1.4--pyhdfd78af_1</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       mkdir ./output;
@@ -33,8 +33,8 @@
           gunzip -c $forward > forward.fastq;
           #set $forward = './forward.fastq'
         #end if
-        ln -s $forward ${name}_1.fastq;
-        ln -s $reverse ${name}_2.fastq;
+        ln -s $forward "${name}_1.fastq";
+        ln -s $reverse "${name}_2.fastq";
       #else 
         #set $name = $reads.assembly.name.replace(' ', '_')
         #set $infile = $name + ".fasta" 
@@ -44,7 +44,7 @@
       #end if
       echo "$name" ;
       echo "-=-=-=-=-" ;
-      touch output/SeqSero_log.txt ;
+      touch output/data_log.txt ;
       /usr/local/bin/SeqSero2S.py --version ;
       echo "-=-=-=-=-" ;
       /usr/local/bin/SeqSero2S.py
@@ -55,9 +55,9 @@
       #if $mode == 'a':
         -b $maptype 
       #end if
-        -i "$infile" &&
-        echo "-=-=-=-=-" &&
-        cat output/SeqSero_log.txt &&
+        -i $infile &&
+        echo "-=-=-=-=-" ;
+        cat output/data_log.txt &&
         echo "-=-=-=-=-" &&
         ls -lah ./output
     ]]></command>