Added cit pipline tutorial and updated documentation

wilhelm-lab · Oct 10, 2024 · fcbea30 · fcbea30
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diff --git a/.gitignore b/.gitignore
@@ -144,9 +144,7 @@ hash.file
 
 
 # output files in tutorials folder
-tutorials/
-!tutorials/Oktoberfest Tutorial.ipynb
-!tutorials/Oktoberfest_workshop.ipynb
+!tutorials/*.ipynb
 
 # example data
 data/

diff --git a/docs/_static/custom_cookietemple.css b/docs/_static/custom_cookietemple.css
@@ -75,6 +75,10 @@ table.align-default {
     padding-left: 50px;
 }
 
+.ptm-config-table tbody tr:not(:first-child) td:nth-child(1) {
+    padding-left: 50px;
+}
+
 .lib-refinement-learning-config-table
     tbody
     tr:nth-child(n + 2):nth-child(-n + 5)

diff --git a/docs/config.rst b/docs/config.rst
@@ -147,17 +147,37 @@ Applicable to in-silico digestion
    |     db                     | Defines whether the digestion should contain only targets, only decoys or both (concatenated); can be "target", "decoy" or "concat"; default = "concat"            |
    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
+Applicable to PTM pipeline
+---------------------------------
+
+.. table::
+   :class: fixed-table ptm-config-table
+
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   | Parameter                  |                             Description                                                                                                                            |
+   +============================+====================================================================================================================================================================+
+   | ptm_localization           | Flag to indicate whether the user want to run the PTM localization pipeline or not.                                                                                |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   | ptmLocalizationOptions     | Contains specific settings for the ptm pipele (see following 2 nested parameters)                                                                                  |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   |     unimod_id              | unimod_id from unimod.org to indicate the target ptm. e.g (7 for citrullination/deamidation)                                                                       |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   |     possible_sites         | List of Possible sites where the PTM can happen. e.g (['R','N','Q'] for citrullination/deamidation)                                                                |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+   |     neutral_loss           | Flag to annotate neutral loss peaks or not.                                                                                                                        |
+   +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
 Applicable to local intensity prediction
 ----------------------------------------
 
 .. table::
    :class: fixed-table
 
-    +--------------------------+---------------------------------------------------+
-    | Parameter                | Description                                       |
-    +==========================+===================================================+
-    | dlomixInferenceBatchSize | Batch size to use for local inference with DLomix |
-    +--------------------------+---------------------------------------------------+
+    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+    | Parameter                  | Description                                                                                                                                                        |
+    +============================+====================================================================================================================================================================+
+    | dlomixInferenceBatchSize | Batch size to use for local inference with DLomix                                                                                                                    |
+    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 Applicable to transfer/refinement learning
 ------------------------------------------