--- a/lissero.xml	Sun Nov 20 23:30:00 2022 +0000
+++ b/lissero.xml	Sun Dec 11 15:46:49 2022 +0000
@@ -1,13 +1,13 @@
-<tool id="lissero" name="lissero" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="lissero" name="Serogrouping typing prediction for Listeria monocytogenes" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <requirements>
         <requirement type="package">lissero</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         lissero 
-        #if $settings.advanced=="advanced"
-          --min_id $settings.min_id
-          --min_cov $settings.min_cov
-        #end if
+        #if $advanced
+          --min_id $advanced.min_id
+          --min_cov $advanced.min_cov
+        #end_if_
         '$input1' > '$output1'
     ]]></command>
     <inputs>
@@ -41,24 +41,11 @@
 
 Options:
   -h, --help              Show this message and exit.
-  -s, --serotype_db TEXT  [default:
-                          /home/user/miniconda3/lib/python3.9/site-
-                          packages/lissero/db]
   --min_id FLOAT          Minimum percent identity to accept a match. [0-100][default=95.0]
   --min_cov FLOAT         Minimum coverage of the gene to accept a match. [0-100][default=95.0]
-  --logfile TEXT          Save log to a file instead of printing to stderr
-  --version               Show Version Information
 
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@misc{githublissero,
-  author = {LastTODO, FirstTODO},
-  year = {TODO},
-  title = {lissero},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/MDU-PHL/lissero},
-}</citation>
+      <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation> 
     </citations>
 </tool>