--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lissero.xml	Fri Mar 13 12:01:17 2026 +0000
@@ -0,0 +1,53 @@
+<tool id="lissero" name="lissero" version="1.0.1+galaxy2" python_template_version="3.5" profile="21.05">
+<requirements>
+    <requirement type="package" version="0.4.9">lissero</requirement>
+    
+</requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        lissero 
+        #if $settings.advanced == "advanced"
+          --min_id $settings.min_id
+          --min_cov $settings.min_cov
+        #end if
+        '$input1' > output1;
+        python $__tool_directory__/variant4b.py output1 output2.txt ${input1.element_identifier};   
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fasta" />
+        <conditional name="settings">
+            <param name="advanced" type="select" label="Specify advanced parameters">
+                <option value="simple" selected="true">No, use program defaults.</option>
+                <option value="advanced">Yes, see full parameter list.</option>
+            </param>
+            <when value="simple">
+            </when>
+            <when value="advanced">
+                <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" /> 
+                <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" /> 
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="lissero.tsv" label="${tool.name} on ${on_string}: LisSero" from_work_dir="*.txt"/>
+    </outputs>
+    <help><![CDATA[
+        Usage: lissero [OPTIONS] FASTA...
+
+  In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
+  lmo0737, ORF2819, ORF2110, Prs
+
+  References:
+
+  Doumith et al. Differentiation of the major Listeria monocytogenes
+  serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
+
+Options:
+  -h, --help              Show this message and exit.
+  --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]
+
+    ]]></help>
+    <citations>
+      <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation> 
+    </citations>
+</tool>