Add digestion and peak proportion configuration options

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

@@ -21,7 +21,7 @@ def extract_request(form):
 
     #Options et methodes:
     taxonomy = ["fillin", "homology"]
-    pconfig = ["fillin", "allpeptides"]
+    pconfig = ["fillin", "allpeptides", "homology"]
     spectre = ["allpeptides", "selection"]
 
     error_found = False
@@ -162,15 +162,25 @@ def extract_request(form):
         extract_taxonomy_selection(form, log, req, error_messages, resdir)
 
     if method in pconfig:
+        digestion = None
+        min_prop_peaks = None
+        if "digestion" in form:
             if form["digestion"].value != "" and form["digestion"].value != "trypsin":
                 digestion = form["digestion"].value
-        else:
-            digestion = None
 
-        if digestion:
+        if "minimum_prop_peaks" in form:
+            if form["minimum_prop_peaks"].value != "" and form["minimum_prop_peaks"].value != "0.7":
+                min_prop_peaks = float(form["minimum_prop_peaks"].value)
+
+        if not digestion and not min_prop_peaks:
+            pass
+        else:
             with open(f'{common.CONFIG_FILE}', 'r') as f:
                 data = json.load(f)
+                if digestion:
                     data['enzyme'] = digestion
+                if min_prop_peaks:
+                    data['min_proportion_of_peaks'] = min_prop_peaks
                 json.dump(data, open(f'{resdir}/config.json', 'w'))
                 log.write(f"Digestion set to {digestion}\n")
                 req['config_file'] = resdir + '/config.json'

www/html/pampa/craft-allpeptides.php

@@ -128,7 +128,7 @@
     </div>
 
     <div class="formulaire">
-      <h2>Digestion <span style="font-weight: normal">(optional) :</span></h2>
+      <h2>Configuration <span style="font-weight: normal">(optional) :</span></h2>
         <table class="vide">
            <tr>
             <td class="label">
@@ -152,6 +152,19 @@
            </td>
          </tr>
         </table>
+        <br>
+        <table>
+          <tr>
+            <td class="label">
+              <B>Enter</B> the minimal proportion of peaks.
+            </td>
+          </tr>
+          <tr>
+            <td>
+              <input type="number" name="minimum_prop_peaks" step="0.01" min="0" max="1" value="0.7" required>
+            </td>
+          </tr>
+        </table>
     </div>
 
     <div class="center">

www/html/pampa/craft-fillin.php

@@ -137,7 +137,7 @@
       </div>
 
     <div class="formulaire">
-      <h2>Digestion <span style="font-weight: normal">(optional) :</span></h2>
+      <h2>Configuration <span style="font-weight: normal">(optional) :</span></h2>
         <table class="vide">
            <tr>
             <td class="label">

www/html/pampa/craft-homology.php

@@ -120,6 +120,33 @@
       </table>
     </div>
 
+    <div class="formulaire">
+      <h2>Configuration <span style="font-weight: normal">(optional) :</span></h2>
+        <table class="vide">
+           <tr>
+            <td class="label">
+              <B>Choose</B> your digestion enzyme.
+            </td>
+          </tr>
+          <tr>
+           <td>
+             <select name="digestion">
+                <option value="arg-c">arg-c</option>
+                <option value="asp-n">asp-n</option>
+                <option value="chymotrypsin high specificity">chymotrypsin high specificity</option>
+                <option value="chymotrypsin low specificity">chymotrypsin low specificity</option>
+                <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+                <option value="pepsin ph1.3">pepsin ph1.3</option>
+                <option value="pepsin ph2.0">pepsin ph2.0</option>
+                <option value="proline endopeptidase">proline endopeptidase</option>
+                <option value="trypsin" selected>trypsin (Default)</option>
+                <option value="trypsin_exception">trypsin_exception</option>
+             </select>
+           </td>
+         </tr>
+        </table>
+    </div>
+
     <div class="center">
       <input type="button" id="example-homology" name="example-homology" value="Example">
       <input type="submit" id="reset-craft-h" name="reset" value="Reset" />

www/html/pampa/craft-selection.php

@@ -114,6 +114,22 @@
       </table>
     </div>
 
+    <div class="formulaire">
+      <h2>Configuration <span style="font-weight: normal">(optional) :</span></h2>
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Enter</B> the minimal proportion of peaks.
+            </td>
+          </tr>
+          <tr>
+            <td>
+              <input type="number" name="minimum_prop_peaks" step="0.01" min="0" max="1" value="0.7" required>
+            </td>
+          </tr>
+        </table>
+    </div>
+
     <div class="center">
       <input type="button" id="example-selection" name="example-selection" value="Example">
       <input type="submit" id="reset-craft-s" name="reset" value="Reset" />