Add dynamic minimum peaks configuration to form and backend

Dockerfile

@@ -83,6 +83,7 @@ RUN chown -R www-data:www-data /var/www
 # RUN git clone https://github.com/touzet/pampa.git /var/www/cgi-bin/pampa/pampa/
 # ajustement pour version web : pas de print sur sdtout mais envoie d'une réponse CGI de type content-type/html
 COPY ./pampa /var/www/cgi-bin/pampa/pampa
+RUN cp /var/www/cgi-bin/pampa/pampa/config.json /var/www/html/pampa/data_pampa/config.json
 COPY ./main_taxonomy_filtering.py /var/www/cgi-bin/pampa/pampa/
 COPY ./table_maker.py /var/www/cgi-bin/pampa/pampa
 

www/cgi-bin/pampa/pampa.py

@@ -236,6 +236,19 @@ def extract_request(form):
                 fOut.write(f"PTM={req['limit_PTM']} ")
             fOut.write("\n")
 
+    if form["minimum_peaks"].value != "" and form["minimum_peaks"].value != "5":
+        minimum = form["minimum_peaks"].value
+    else:
+        minimum = None
+
+    if minimum:
+        with open(f'{common.CONFIG_FILE}', 'r') as f:
+            data = json.load(f)
+            data['min_number_of_peaks'] = minimum
+            json.dump(data, open(f'{resdir}/config.json', 'w'))
+            log.write(f"Digestion set to {minimum}\n")
+            req['config_file'] = resdir + '/config.json'
+    
     log.write("Recap downloads :\n")
     for fn in req['files_uploaded']:
         log.write(f"dwl {fn}\n")
@@ -273,6 +286,8 @@ def launch_software(run_id, req):
         command += ' -n ' + req["nearoptimal_margin"]
         if "nearoptimal_all" in req:
             command += ' -a '
+    if "config_file" in req:
+        command += ' -c ' + req['config_file']
     command += " --web"  # Web version with log file and no console output
     open("acommand.txt", "w").write(f"{command}")  # log
     

www/html/pampa/data_pampa/config.json

-{
-    "taxonomy_ranks": ["subspecies", "Subspecies","species", "Species", "genus", "Genus", "subfamily", "Subfamily","family","Family", "suborder", "Suborder", "order", "Order", "class", "Class", "phylum", "Phylum"],
-    "peptide_table_order":["Rank", "TaxID", "OX", "OS", "Taxon Name", "Taxon name", "Taxon", "Sequence", "PTM", "Mass", "Marker", "GN", "Gene", "Hel", "Length", "SeqID", "SeqId", "Begin", "End", "Status", "Comment"],
-    "enzyme": "trypsin",
-    "number_of_missed_cleavages": 1,
-    "min_peptide_length":12,
-    "max_peptide_length":33,
-    "minimum_number_of_peaks": 5, 
-    "marker_order": ["P1", "COL1A1-508/P1",  "COL1A1-508", "A", "COL1A2-978/A",  "COL1A2-978", "B", "COL1A2-484/B", "COL1A2-484", "C",  "COL1A2-502/C","COL1A2-502", "P2","COL1A2-292/P2", "COL1A2-292", "D","COL1A2-793/D", "COL1A2-793", "E", "COL1A2-454/E",  "COL1A2-454", "F",   "COL1A1-586/F",  "COL1A1-586","F'", "G",  "COL1A2-757/G",  "COL1A2-757", "G'"] 
-}

www/html/pampa/form.php

@@ -56,6 +56,16 @@
       </table>
       <br>
 
+      <b>Minimum peaks configuration</b>
+      <table class="vide pampa_choice">
+        <tr>
+          <td>
+            <input type="number" name="minimum_peaks" step="1" min="1" max="100" value="5" required>
+          </td>
+        </tr>
+      </table>
+      <br>
+
       <b>Mass error tolerance</b>
       <table class="vide pampa_choice">
         <tr>