Merge pull request #142 from maxibor/viewer_doc

Viewer doc

Author: maxibor

docs/source/how_to/images/amdirt-filter-download-buttons.png

@@ -13,6 +13,7 @@ The purpose of the `viewer` command is to provide a easy-to-use graphical-user i
 > ⚠️ _The `viewer` tool was previously named `filter`, and might still be referred as such in some parts of the documentation._
 
 For video based walkthroughs please see [Tutorials](/tutorials/viewer.md).
+
 ## When
 
 You should use this tool when you wish to find particular types of ancient metagenomic data, but wish to explore the dataset manually and interactively (i.e., don't know exactly what you're looking for yet), and/or if you do not wish to download the AncientMetagenomeDir full tables yourself and filter them within languages such as R or Python (with pandas).
@@ -87,7 +88,15 @@ Now validate your selection! Press the 'Validate selection' button at the bottom
 
 > ⚠️ _If you wish to download the data, make sure you have already selected your 'Data download method' in the sidebar before pressing 'Validate selection'!_
 
-Once the select is validated, more buttons will appear allowing you to download different files
+Once the selection is validated, the library filtering table will appear below
+
+![AMDirT libraries filtering table](images/amdirt-filter-libraries-table.png)
+
+You can proceed to select your libraries of choice (or all of them) in the same way as the samples table. Once happy, you can then click on 'Validate library selection'
+
+Your different download options will finally appear:
+
+![AMDirT output download options](images/amdirt-filter-download-buttons.png)
 
 In this case we suggest you press:
 
@@ -97,8 +106,6 @@ In this case we suggest you press:
 
 See [Output](#output) for descriptions of all output possible files.
 
-![AMDirT buttons after selection validation](images/amdirt-filter-validate-buttons.png)
-
 To use the **download** script, you can simply run:
 
 ```bash

docs/source/how_to/images/amdirt-filter-libraries-table.png

@@ -1,52 +1,8 @@
 # viewer
 
-On this page we provide step-by-step video tutorials on how to use the AMDirT graphical-user-interface (GUI) of the `viewer` command.
-
-> ℹ️ _The `viewer` subcommand was previously known as `filter`._
-
-The [full walkthrough](#full-walkthrough) of all steps in a single video can be seen at the end of this page.
-
-## Loading AMDirT viewer
-
-This tutorial shows how to activate a [pre-created](README#install) conda environment from a command-line interface, and load the graphical-user interface (GUI) in your browser.
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/EANpFh__6V8" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
-
-## Selecting Table
-
-This tutorial shows you how to select which release of AncientMetagenomeDir you wish to explore, as well as how to select the given research-area specific AncientMetagenomeDir table of interest.
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/dUzeJfSTQCU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
-
-## Row Selection
-
-This tutorial shows how to increase the number of rows in the tabular view of the GUI.
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/DFHlGQcREy0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
-
-## Column Options
-
-This tutorial shows you how to reorder columns, hide/display columns, and filter columns by the particular specifications of the user.
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/uRPkvGum19A" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
-
-## Selecting Rows
-
-This tutorial shows how to select different rows of interest.
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/-EnIIMEIGgA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
-
-## Exporting Information
-
-This tutorial shows how to export the selected data for downstream use, in this case, download scripts and a input table for the [nf-core/eager](https://nf-co.re/eager) ancient DNA pipeline.
+On this page we provide a step-by-step video tutorial on how to use the AMDirT graphical-user-interface (GUI) of the `viewer` command.
 
 For more detail about all possible output files, please see the corresponding pages on [How To](/how_to/index).
 
-<iframe width="560" height="315" src="https://www.youtube.com/embed/Re6YAdGmm7w" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; 
-clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
-
-## Full walkthrough
-
-This tutorial has all the above steps in a single video to show the full procedure from beginning to end.
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/iWrHJFG7Ky0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+<iframe width="560" height="315" src="https://www.youtube.com/embed/7qcGXIEt9As" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; 
+clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>