Refine error_margin handling based on method type.

www/cgi-bin/pampa/pampa-craft.py

@@ -207,7 +207,11 @@ def launch_software(run_id, req):
     if 'limit_path' in req:
         limit_arg = req["limit_path"]
         command += " -l " + limit_arg
-    if 'error_margin' in req:
+    if 'error_margin' in req and method != "allpeptides":
+        error_arg = req["error_margin"]
+        command += " -e " + str(error_arg)
+    elif method == "allpeptides" and 'error_margin' in req:
+        if 'spectra_dir' in req:
             error_arg = req["error_margin"]
             command += " -e " + str(error_arg)
     if 'taxo_file' in req: