--- a/lexicmap.xml	Thu Nov 20 19:38:51 2025 +0000
+++ b/lexicmap.xml	Thu Jan 22 09:42:53 2026 +0000
@@ -13,27 +13,10 @@
     #set INDICES = $db_opts.lexicmap_index.fields.path.split(",")
 #end if
 
-extract_query_ids() {
-    local input_files="\$1";
-    local query_ids="";
-    IFS=',' read -ra files <<< "\$input_files";
-    query_ids="";
-    for query_file in "\${files[@]}"; do
-        if file --mime-type "\$query_file" | grep -q "gzip"; then
-            query_ids+=\$(zcat "\$query_file" | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
-        else
-            query_ids+=\$(cat "\$query_file" | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
-        fi
-    done;
-    declare -g -a query_array=();
-    IFS='>' read -r -a query_array <<< "\$query_ids";
-}
-&&
 #for $counter, $index in enumerate($INDICES):
+    set -eu;
     lexicmap search
-
         --threads "\${GALAXY_SLOTS:-1}"
-
         ${load_whole_seeds}
         ${all}
 
@@ -70,8 +53,16 @@
 #end for
 
 #if len($INDICES) > 1
+    query_ids="";
+    #for $query_file in $query
+        #if $query_file.is_of_type("fasta.gz")
+            query_ids+=\$(zcat '$query_file' | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
+        #else
+            query_ids+=\$(cat '$query_file' | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
+        #end if
+    #end for
+    IFS='>' read -r -a query_array <<< "\$query_ids";
     counter=0 &&
-    extract_query_ids '$query' &&
     for ((i=0; i<\${#query_array[@]}; i++)); do
         counter=\$((counter + 1));
         lexicmap utils merge-search-results
@@ -85,7 +76,7 @@
 #end if
     ]]></command>
     <inputs>
-        <param name="query" type="data" format="fasta.gz" label="LexicMap query file" multiple="true"  help=""/>
+        <param name="query" type="data" format="@FASTA_TYPES@" label="LexicMap query file" multiple="true" help=""/>
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="LexiMap index source">
               <option value="histdb">From your history</option>