docs: add percolator install instructions and example of qc report

compomics · Nov 30, 2023 · cfe41ad · cfe41ad
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diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
 
-> ⚠️ Note: This is the documentation for the fully redeveloped version 3.0 of MS²Rescore, While
+> ⚠️ Note: This is the documentation for the fully redeveloped version 3.0 of MS²Rescore. While
 > MS²Rescore 3.0 has been drastically improved over the previous version, you might run into some
 > unforeseen issues. Please report any issues you encounter on the [issue tracker][issues] or post
 > your questions on the [GitHub Discussions][discussions] forum.
@@ -50,7 +50,7 @@ MS²Rescore is available as a [desktop application][desktop], a [command line to
 
 > **MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0.**
 > Louise Marie Buur*, Arthur Declercq*, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer*, and Ralf Gabriels*.
-> _ChemRxiv_ (2023) [doi:10.26434/chemrxiv-2023-rvr9n](https://doi.org/10.26434/chemrxiv-2023-rvr9n) <br/> > \*contributed equally <span class="__dimensions_badge_embed__" data-doi="10.26434/chemrxiv-2023-rvr9n" data-hide-zero-citations="true" data-style="small_rectangle"></span>
+> _ChemRxiv_ (2023) [doi:10.26434/chemrxiv-2023-rvr9n](https://doi.org/10.26434/chemrxiv-2023-rvr9n) <br/> \*contributed equally <span class="__dimensions_badge_embed__" data-doi="10.26434/chemrxiv-2023-rvr9n" data-hide-zero-citations="true" data-style="small_rectangle"></span>
 
 **MS²Rescore for immunopeptidomics:**
 

diff --git a/docs/source/_static/img/percolator-install-path.png b/docs/source/_static/img/percolator-install-path.png
diff --git a/docs/source/_static/img/qc-reports.png b/docs/source/_static/img/qc-reports.png
diff --git a/docs/source/gui.rst b/docs/source/gui.rst
@@ -193,3 +193,11 @@ contains interactive charts that visualize the results and various quality contr
    :alt: Output files
 
    Overview of the output files after rescoring the X!Tandem example.
+
+Double click the ``*.ms2rescore.report.html`` file to open it in the default web browser:
+
+.. figure:: ../_static/img/qc-reports.png
+   :width: 100%
+   :alt: Rescoring report
+
+   Rescoring QC report with interactive charts.
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -48,7 +48,7 @@ Docker container
     :target: https://quay.io/repository/biocontainers/ms2rescore
 
 First check the latest version tag on
-`biocontainers/ms2rescore/tags <https://quay.io/repository/biocontainers/ms2rescore?tab=tags>`__.
+`biocontainers/ms2rescore/tags <https://quay.io/repository/biocontainers/ms2rescore?tab=tags>`_.
 Then pull and run the container with:
 
 .. code-block:: bash
@@ -60,6 +60,23 @@ files, ``<tag>`` is the container version tag, and ``<ms2rescore-arguments>`` ar
 command line options (see :ref:`Command line interface`).
 
 
+Installing Percolator
+=====================
+
+To use :ref:`percolator` as rescoring engine, it must be installed separately. Percolator is
+available for most platforms and can be downloaded from the
+`GitHub releases page <https://github.com/percolator/percolator/releases/latest>`_. Ensure that
+the ``percolator`` executable is in your ``PATH``. On Windows, this can be done by checking the
+``Add percolator to the system PATH for current user`` option during installation:
+
+.. figure:: ../_static/img/percolator-install-path.png
+   :width: 60%
+   :alt: Percolator installation on Windows
+
+.. note::
+   Alternatively, :ref:`mokapot` can be used as rescoring engine, which does not require a separate
+   installation.
+
 For development
 ===============