update example autofill, method choice working

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

@@ -51,6 +51,11 @@ def extract_request(form):
     else:
         log.write("Job name: None\n")
 
+    if 'method' in form:
+        req["method"] = form['method'].value
+    else:
+        error_messages.append(f"Method is required")
+
     if 'craft-example' in form:
         FormTools.extract_files_from_list([common.CRAFT_PEPTIDE], resdir)
         req["peptides_path"] = resdir + '/' + "craft_peptides.tsv"
@@ -130,7 +135,9 @@ def launch_software(run_id, req):
 
     sequences_arg = req["sequences_dir"]
 
-    command = "python pampa_craft.py --homology -p " + peptides_arg + " -d " + sequences_arg + " -o " + common.RESULT_DIR + run_id + "/" + output_arg
+    method = req['method']
+
+    command = "python pampa_craft.py --" + method + " -p " + peptides_arg + " -d " + sequences_arg + " -o " + common.RESULT_DIR + run_id + "/" + output_arg
     if 'limit_path' in req:
         limit_arg = req["limit_path"]
         command += " -l " + limit_arg

www/html/pampa/craft-form.php

@@ -31,36 +31,37 @@
       </table>
     </div>
 
+    <h2>Method</h2>
     <table class="vide table-center pampa-choice">
 
     <tr>
       <td>
         <div>
-          <input type="radio" id="allpeptides" name="drone" value="allpeptides" checked/>
+          <input type="radio" id="allpeptides" name="method" value="allpeptides"/>
           <label for="allpeptides">Allpeptides</label>
         </div>
       </td>
       <td>
         <div>
-          <input type="radio" id="deamidation" name="drone" value="deamidation"/>
+          <input type="radio" id="deamidation" name="method" value="deamidation"/>
           <label for="deamidation">Deamidation</label>
         </div>
       </td>
       <td>
         <div>
-          <input type="radio" id="fillin" name="drone" value="fillin"/>
+          <input type="radio" id="fillin" name="method" value="fillin"/>
           <label for="fillin">Fillin</label>
         </div>
       </td>
       <td>
         <div>
-          <input type="radio" id="homology" name="drone" value="homology"/>
+          <input type="radio" id="homology" name="method" value="homology" checked/>
           <label for="homology">Homology</label>
         </div>
       </td>
       <td>
         <div>
-          <input type="radio" id="selection" name="drone" value="selection"/>
+          <input type="radio" id="selection" name="method" value="selection"/>
           <label for="selection">Selection</label>
         </div>
       </td>

www/html/pampa/js/pampa.js

@@ -107,6 +107,7 @@ $(document).on("click", "#example-craft", function() {
         $("#sequences_input input").attr("required", false);
         $("#sequences_example").show();
         $("input[name='craft-example']").attr("checked", true);
+        $("#homology").prop("checked", true);
     });
 });