--- a/lexicmap.xml	Tue Sep 16 14:27:32 2025 +0000
+++ b/lexicmap.xml	Thu Sep 18 11:27:35 2025 +0000
@@ -21,7 +21,11 @@
         --index '${db_opts.lexicmap_index.fields.path}'
     #end if
 
-    '$query' --out-file '$out_file'
+    #for $q in $query
+        '$q'
+    #end for
+
+    --out-file '$out_file'
 
     --top-n-genomes '$top_n_genomes'
 
@@ -96,6 +100,7 @@
         </data>
     </outputs>
     <tests>
+        <!-- Test 1 - query a local index with one query -->
         <test expect_num_outputs="1">
             <conditional name="db_opts">
                 <param name="db_opts_selector" value="db"/>
@@ -107,6 +112,19 @@
             </section>
             <output name="out_file" value="lexicmap_query_result.tsv" />
         </test>
+        <!-- Test 2 - query a local index with multiple query files -->
+        <test expect_num_outputs="1">
+            <conditional name="db_opts">
+                <param name="db_opts_selector" value="db"/>
+                <param name="lexicmap_index" value="LexicMapIndex1" />
+            </conditional>
+            <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz" />
+            <section name="advanced_settings">
+                <param name="load_whole_seeds" value="true" />
+            </section>
+            <output name="out_file" value="lexicmap_query_result2.tsv" />
+        </test>
+        <!-- Test 3 - query a  index found in the history with one query -->
         <test expect_num_outputs="1">
             <conditional name="db_opts">
                 <param name="db_opts_selector" value="histdb"/>