Docs: moved extensions into files by category and filled in information.

docs/extensions.rst

@@ -18,96 +18,10 @@ The below modules are Tripal 3 compatible and grouped roughly by category.
 ..
 .. https://tripal-hq.readthedocs.io/en/latest/index.html
 
-Annotation Modules
--------------------
+.. toctree::
+   :maxdepth: 2
+   :caption: Categories
 
-Tripal Analysis Expression
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-A module for loading, annotating, and visualizing NCBI Biosamples and expression data.
-
-
-https://github.com/tripal/tripal_analysis_expression
-
-Tripal Analysis Blast
-~~~~~~~~~~~~~~~~~~~~~~
-
-https://github.com/tripal/tripal_analysis_blast
-
-
-Tripal Analysis KEGG
-~~~~~~~~~~~~~~~~~~~~~
-
-https://github.com/tripal/tripal_analysis_kegg
-
-
-Tripal Analysis Interpro
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-https://github.com/tripal/tripal_analysis_interpro
-
-Tripal JBrowse
-~~~~~~~~~~~~~~
-
-https://github.com/tripal/tripal_jbrowse
-
-Tripal CV-Xray
-~~~~~~~~~~~~~~~
-
-Tripal CV-Xray maps content annotations onto controlled vocabulary trees.  The end result is a browseable CV field that lets users explore ontologies and find associated content.
-
-https://github.com/statonlab/tripal_cv_xray
-
-Administrative Modules
-------------------------
-
-
-Tripal Alchemist
-~~~~~~~~~~~~~~~~~~~~
-Tripal Alchemist allows you to transform entities from one type to another.  Define multiple bundles with the same base table and easily convert existing entities to the new type.
-
-https://github.com/statonlab/tripal_alchemist
-
-
-
-Tripal Apollo
-~~~~~~~~~~~~~~~~~~~~
-
-
-Tripal Curator
-~~~~~~~~~~~~~~~~~~~~
-
-https://github.com/statonlab/tripal_curator
-
-
-Tripal ElasticSearch
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-
-https://github.com/tripal/tripal_elasticsearch
-
-
-Tripal HeadQuarters
-~~~~~~~~~~~~~~~~~~~~
-
-Tripal HeadQuarters (HQ) provides an administrative layer for Tripal, giving users limited access to content creation forms which must be approved by an admin before they are inserted into the database.
-Admins can use Chado-specific permissions to define organism or project-specific administrative rights.
-
-https://tripal-hq.readthedocs.io/en/latest/index.html
-
-Developer Tools
-----------------
-
-Tripal Fields Generator
-~~~~~~~~~~~~~~~~~~~~~~~~
-
-This is a CLI tool to help automate the generation of Tripal fields.
-
-https://github.com/tripal/fields_generator
-
-Tripal Test Suite
-~~~~~~~~~~~~~~~~~~
-
-Tripal Test Suite is a composer package that handles common test practices such as bootstrapping Drupal before running the tests, creating test file, creating and managing database seeders (files that seed the database with data for use in testing) and much more.
-
-https://github.com/tripal/TripalTestSuite
+   extensions/administrative
+   extensions/annotation
+   extensions/developer

docs/extensions/administrative.rst

@@ -0,0 +1,37 @@
+Administrative
+==============
+
+Tripal Alchemist
+-----------------
+
+Tripal Alchemist allows you to transform entities from one type to another.  Define multiple bundles with the same base table and easily convert existing entities to the new type.
+
+`Documentation <https://github.com/statonlab/tripal_alchemist/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripal_alchemist>`__
+
+
+Tripal Property Curations
+-------------------------
+
+Tripal Property Curations is a Toolbox for curating Chado Properties. It is under development and not suitable for use yet.
+
+`Documentation <https://github.com/statonlab/tripal_curator/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripal_curator>`__
+
+
+Tripal ElasticSearch
+--------------------
+
+The Tripal Elasticsearch module allows you to easily manage the indexing and display of Elasticsearch on your Tripal website. It also easily enables Cross-Site Querying, allowing you to connect to other Tripal sites and provide additional search results to your users.
+
+`Documentation <https://github.com/tripal/tripal_elasticsearch/blob/master/docs/README.md>`__
+`Repository <https://github.com/tripal/tripal_elasticsearch>`__
+
+
+Tripal HeadQuarters
+-------------------
+
+Tripal HeadQuarters (HQ) provides an administrative layer for Tripal, giving users limited access to content creation forms which must be approved by an admin before they are inserted into the database. Admins can use Chado-specific permissions to define organism or project-specific administrative rights.
+
+`Documentation <https://tripal-hq.readthedocs.io/en/latest/index.html>`__
+`Repository <https://github.com/statonlab/tripal_hq>`__

docs/extensions/annotation.rst

@@ -0,0 +1,57 @@
+Analysis/Annotation
+===================
+
+Tripal Analysis Expression
+--------------------------
+
+A module for loading, annotating, and visualizing NCBI Biosamples and expression data.
+
+`Documentation <https://github.com/tripal/tripal_analysis_expression/blob/master/README.md>`__
+`Repository <https://github.com/tripal/tripal_analysis_expression>`__
+
+Tripal Analysis Blast
+---------------------
+
+This module extends the Tripal Analysis Module and provides a method for loading XML results from the NCBI blast program. Blast results appear on each feature page.
+
+`Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/blast.html>`__
+`Repository <https://github.com/tripal/tripal_analysis_blast>`__
+
+Tripal Analysis KEGG
+--------------------
+
+This module provides a method for loading of KEGG ortholog assignments derived from the KEGG Automated Annotation Server (KAAS). KEGG assignments appear on each feature page, and a full KEGG report is available for browsing results once uploaded.
+
+`Repository <https://github.com/tripal/tripal_analysis_kegg>`__
+
+Tripal Analysis Interpro
+------------------------
+
+This module provides a method for loading XML results from the InterProScan program. The module can load InterProScan XML v4 or InterProScan XML v5 generated from the command-line or web-based versions of InterProScan. Additionally, GO terms mapped by InterProScan can optionally be assigned to features.
+
+`Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/interpro.html>`__
+`Repository <https://github.com/tripal/tripal_analysis_interpro>`__
+
+Tripal JBrowse
+--------------
+
+This module provides integration between Tripal sites and pre-existing GMOD JBrowse instances. It allows you to create pages on your Tripal site with an embedded JBrowse instance by filling out a simple form.
+
+`Documentation <https://github.com/tripal/tripal_jbrowse/blob/7.x-2.1.x/README.md>`__
+`Repository <https://github.com/tripal/tripal_jbrowse>`__
+
+Tripal CV-Xray
+--------------
+
+Tripal CV-Xray maps content annotations onto controlled vocabulary trees.  The end result is a browseable CV field that lets users explore ontologies and find associated content.
+
+`Documentation <https://github.com/statonlab/tripal_cv_xray/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripal_cv_xray>`__
+
+Tripal Galaxy
+-------------
+
+This module is for integration of Tripal and the Galaxy Project. It facillitates the creation of forms on your Tripal site that submit jobs to a galaxy instance.
+
+`Documentation <https://github.com/tripal/tripal_galaxy/blob/7.x-1.x/README.md>`__
+`Repository <https://github.com/tripal/tripal_galaxy>`__

docs/extensions/developer.rst

@@ -0,0 +1,19 @@
+
+Developer Tools
+===============
+
+Tripal Fields Generator
+-----------------------
+
+This is a CLI tool to help automate the generation of Tripal fields.
+
+`Documentation <https://github.com/tripal/fields_generator/blob/master/README.md>`__
+`Repository <https://github.com/tripal/fields_generator>`__
+
+Tripal Test Suite
+-----------------
+
+Tripal Test Suite is a composer package that handles common test practices such as bootstrapping Drupal before running the tests, creating test file, creating and managing database seeders (files that seed the database with data for use in testing) and much more.
+
+`Documentation <https://tripaltestsuite.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/tripal/TripalTestSuite>`__