docs: Include config-gui in docs

docs/source/command-line-interface.md

@@ -3,6 +3,7 @@
 
 `metaDMG` has the following commands:
 - [`config`](command_line_interface_config)
+- [`config-gui`](command_line_interface_config_gui)
 - [`compute`](command_line_interface_compute)
 - [`dashboard`](command_line_interface_dashboard)
 - [`get-data`](command_line_interface_get_data)
@@ -89,6 +90,35 @@ $ metaDMG config raw_data/alignment.sorted.bam --damage-mode local --max-positio
 
 ---
 
+
+(command_line_interface_config_gui)=
+## Config GUI
+
+`metaDMG config-gui` is a simple graphical user interface (GUI) to help with the config creation.
+The command itself does not take any parameters, everything is done by clicking and dragging.
+For more information about what the different buttons and sliders mean, see the normal [`config`](command_line_interface_config) command.
+
+### Examples
+
+```console
+$ metaDMG config-gui
+```
+
+The GUI presented looks like this:
+
+```{figure} images/config-gui.png
+:class: bg-primary mb-1
+:width: 700px
+:align: center
+```
+
+Mandatory fields that need to be filled are coloured red.
+Note that if you change the damage mode to `LOCAL` or `GLOBAL`, the bottom left
+square becomes disabled, since these parameters are only relevant for `LCA`.
+
+---
+
+
 (command_line_interface_compute)=
 ## Compute
 

docs/source/getting-started.md

@@ -38,15 +38,19 @@ The fit related (`[fit]`) dependencies are:
 - `joblib`
 - `psutil`
 
-And the visualization related (`[viz]`) dependencies are:
+The visualization related (`[viz]`) dependencies are:
 - `matplotlib`
 - `plotly`
 - `dash`
 - `dash-bootstrap-components`
 - `orjson`
 - `tqdm`
 
-In general, we allow for the custom installion of only the core packages `pip install metaDMG`, core + fit related packages: `pip install "metaDMG[fit]"`, core + visualization related packages: `pip install "metaDMG[viz]"` or core + fit + viz: `pip install "metaDMG[all]"`.
+
+And the GUI related (`[gui]`) dependencies are:
+- `customtkinter`
+
+In general, we allow for the custom installion of only the core packages `pip install metaDMG`, core + fit related packages: `pip install "metaDMG[fit]"`, core + visualization related packages: `pip install "metaDMG[viz]"` or core + fit + viz + gui: `pip install "metaDMG[all]"`.
 
 ```{warning} metaDMG is not tested on Windows.
 ```
@@ -110,15 +114,22 @@ Here we sketch how a typical workflow works in `metaDMG`. In short:
 $ metaDMG config raw_data/alignment.sorted.bam \
     --names raw_data/names-mdmg.dmp \
     --nodes raw_data/nodes-mdmg.dmp \
-    --acc2tax raw_data/acc2taxid.map.gz
+    --acc2tax raw_data/acc2taxid.map.gz \
+    --custom-database
+```
+
+If you prefer a more visual approach, the same can also be done using the `config-gui` command:
+
+```console
+$ metaDMG config-gui
 ```
 
 ### Run the computation
 
 After the config has been created, we run the actual program using the `compute` command. This can take a while depending on the number (and size) of the files.
 
 ```console
-$ metaDMG compute
+$ metaDMG compute config.yaml
 ```
 
 ### Dashboard

docs/source/tutorial.md

@@ -45,6 +45,14 @@ Most of the options should be quite self-explanatory. `--bayesian` indicates tha
 
 After running this command, you should notice a new file in your directory: `config.yaml`. This is a normal `.yaml` file which can be opened and edited with your favorite text editor. In case you wanted to call the config file something different, you can add `--config-file config_simple.yaml`.
 
+The same as above can also be done more visually by using the `config-gui` command:
+
+```console
+$ metaDMG config-gui
+```
+Just remember to check the relevant boxes off and save a config file.
+In case you are missing any mandatory fields, it should pop up and warn you automatically.
+
 ### Compute
 
 Now that we have generated a config file with all of the necessary parameters, we can start the actual computation. This is done by running: