--- a/seqsero2.xml	Wed Mar 01 13:21:51 2023 -0500
+++ b/seqsero2.xml	Tue Mar 25 23:22:38 2025 -0400
@@ -1,13 +1,12 @@
-<tool id="seqsero_v2" name="SeqSero2 v1.2.1" version="8">
+<tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="8">
     <description>Salmonella serotype prediction</description>
     <macros>
-        <token name="@VERSION@">1.2.1</token>
+        <token name="@VERSION@">1.3.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">seqsero2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      echo "SeqSero2 v1.2.1";
       mkdir ./output;
 
       #if $reads.reads_select == 'history'
@@ -49,6 +48,8 @@
       echo $name ;
       echo "-=-=-=-=-" ;
       touch output/SeqSero_log.txt ;
+      SeqSero2_package.py --version ;
+      echo "-=-=-=-=-" ;
       SeqSero2_package.py
         -p \${GALAXY_SLOTS:-1}
         -t $tval 
@@ -106,7 +107,7 @@
 
     </inputs>
     <outputs>
-      <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/>
+      <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv" />
     </outputs>
     <tests>
        <!-- <test>
@@ -149,7 +150,7 @@
          <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
          <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
          <assert_stdout>
-          <has_text text="predicted antigenic profile does not exist" />
+          <has_text text="input genome cannot be identified as Salmonella" />
          </assert_stdout>
        </test>
        <!-- <test>