--- a/lissero/lissero.xml	Thu Feb 08 18:18:47 2024 +0000
+++ b/lissero/lissero.xml	Thu Feb 08 20:40:49 2024 +0000
@@ -9,7 +9,7 @@
           --min_cov $settings.min_cov
         #end if
         '$input1' > output1;
-        python $__tool_directory__/variant4b.py output1 output2.txt;   
+        python $__tool_directory__/variant4b.py output1 output2.txt ${input1.name};   
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="fasta" />

--- a/lissero/variant4b.py	Thu Feb 08 18:18:47 2024 +0000
+++ b/lissero/variant4b.py	Thu Feb 08 20:40:49 2024 +0000
@@ -1,6 +1,6 @@
 import sys
 
-def identify_variants_with_genes(input_file_path, output_file_path):
+def identify_variants_with_genes(input_file_path, output_file_path, simple_name):
     # Define the genes of interest
     genes_of_interest = ['LMO0737', 'ORF2110', 'ORF2819']
 
@@ -18,8 +18,11 @@
     gene_indices = [headers.index(gene) for gene in genes_of_interest]
     serotype_index = headers.index('SEROTYPE')
 
-    # Initialize a list to hold the modified lines
-    modified_lines = [lines[0]]  # Start with the header
+    # Modify the header to include the new first column
+    modified_header = f"FileName\t{lines[0]}"
+    
+    # Initialize a list to hold the modified lines, starting with the modified header
+    modified_lines = [modified_header]
 
     # Process each data line in the input file
     for line in lines[1:]:
@@ -28,8 +31,10 @@
         if all(data[index] == 'FULL' for index in gene_indices):
             # Modify the SEROTYPE column to "4b variant"
             data[serotype_index] = "4b variant"
-        # Rejoin the modified data into a single string and add it to the list
-        modified_lines.append('\t'.join(data) + '\n')
+        # Prepend the simple name to the line
+        modified_line = f"{simple_name}\t" + '\t'.join(data) + '\n'
+        # Add the modified line to the list
+        modified_lines.append(modified_line)
 
     # Write the modified lines to the output file
     with open(output_file_path, 'w') as file:
@@ -38,11 +43,12 @@
     print(f'Results written to {output_file_path}')
 
 if __name__ == "__main__":
-    if len(sys.argv) != 3:
-        print("Usage: python script.py <input_file_path> <output_file_path>")
+    if len(sys.argv) != 4:
+        print("Usage: python script.py <input_file_path> <output_file_path> <simple_name>")
         sys.exit(1)
 
     input_file_path = sys.argv[1]
     output_file_path = sys.argv[2]
-    identify_variants_with_genes(input_file_path, output_file_path)
+    simple_name = sys.argv[3]
+    identify_variants_with_genes(input_file_path, output_file_path, simple_name)