--- a/config.yml	Fri Mar 03 14:10:24 2023 +0000
+++ b/config.yml	Wed Aug 30 14:21:18 2023 +0000
@@ -42,13 +42,14 @@
     spectrum_type: "default is {{ defaults.spectrum_type }}"
     sample_type: "default is {{ defaults.sample_type }}"
     resolution: "default is {{ defaults.resolution }}"
-    resolution: "default is {{ defaults.resolution }}"
     name: The precursor name
     peakforest.url: "default={{ defaults.peakforest.url }}"
     peakforest.token: The token to comunicate with peakforest api
     polarity: positive|negative
     raw_metadata: example - 1-1__INCHIKEY__=QNAYBMKLOCPYGJ-REOHCLBHSA-N_L-Alanine_MS_POS_plasma_RT__=0.84_filtree.csv
     scan_type: ms|msms|rmn
+    rt_min: Min retention time
+    rt_max: Max retention time
     run_dry_html: when "--run-dry", provides the output directory for {{ generated.html }}
     run_dry_js: when "--run-dry", provides the output directory for {{ generated.js }}
     raw_metadata_sep: "raw metadata separator"
@@ -56,10 +57,13 @@
     logging.file.path: "The file path to output logs to"
     validation: "Set the default validation to the provided value, TRUE or FALSE."
     output_json: "Provide a path to output a JSON file."
+    pid: "Path to the pid file"
+    ip: "the net intf to link to"
+    port: "the net port to bind on"
   meta:
     ## meta info about the tool itself
     author: Lain Pavot
-    version: 1.1.0
+    version: 1.2.1
   shortcuts:
     ## to define things like: "we can use -p instead of --polarity"
     peakforest.token: t
@@ -81,6 +85,8 @@
 ## if append is true, outputs are appended to the file.
 ## otherwise, the file is emptied each time the app runs.
 defaults:
+  ip: 0.0.0.0
+  port: 8000
   peakforest:
     url: https://nightly.peakforest.org
     token: ''
@@ -109,6 +115,9 @@
       path:
       append: False
   output_json: ''
+  rt_min: 0.9
+  rt_max: 1.9
+  pid:
 
 ## token related info
 token:
@@ -119,10 +128,6 @@
   ## if not, you can provide you token here
   value:
 
-network:
-  ip: 0.0.0.0
-  port: 8000
-
 workdir:
   ## create a tmp directory
   create_tmp: true
@@ -134,19 +139,19 @@
 ## the templates paths
 templates:
   ## meta is what wrapps the whole page.
-  main: meta.html
-  main_mix: meta-compound-mix.html
-  main_ref: meta-compound-ref.html
+  main: src/meta.html
+  main_mix: src/meta-compound-mix.html
+  main_ref: src/meta-compound-ref.html
   ## form is one instance of a pf form
-  # form: form.html
-  # form: compound-ref.html
-  form: form.html
-  form_mix: compound-mix.html
-  form_ref: compound-ref.html
+  # form: src/form.html
+  # form: src/compound-ref.html
+  form: src/form.html
+  form_mix: src/compound-mix.html
+  form_ref: src/compound-ref.html
   ## one item of the tab list
-  tab_list: tab_list.html
+  tab_list: src/tab_list.html
   ## the js for one form
-  js: add-one-spectrum-index.js
+  js: src/add-one-spectrum-index.js
   ## placeholders for the html templates.
   ## this will not change the placeholders syntax for this file.
   placeholders: