Merge pull request #415 from tristan-f-r/docs-yaml-highlight

update text blocks to yaml blocks

Author: ntalluri

docs/tutorial/beginner.rst

@@ -79,7 +79,7 @@ Algorithms
 -----------
 
 
-.. code-block:: text
+.. code-block:: yaml
     
     algorithms:
     - name: omicsintegrator1
@@ -107,7 +107,7 @@ Invalid or missing parameter keys will cause SPRAS to fail.
 Datasets
 --------
 
-.. code-block:: text
+.. code-block:: yaml
 
     datasets:
     - 
@@ -131,7 +131,7 @@ The dataset must include the following types of keys and files:
 Reconstruction Settings
 -----------------------
 
-.. code-block:: text
+.. code-block:: yaml
 
     reconstruction_settings:
     locations:
@@ -145,7 +145,7 @@ If you are running multiple configuration files, you can set unique paths to kee
 Analysis
 --------
 
-.. code-block:: text
+.. code-block:: yaml
 
     analysis:
     summary:
@@ -287,7 +287,7 @@ SPRAS has additional files and directories to use during runs. However, for most
 
 In the beginner.yaml configuration file, uncomment the run2 section under pathlinker so it looks like:
 
-.. code-block:: text
+.. code-block:: yaml
     
     run2:   
         k: [10, 100] 
@@ -406,7 +406,7 @@ Step 3: Running Post-Analyses within SPRAS
 ==========================================
 To enable downstream analyses, update the analysis section in your configuration file by setting both summary and cytoscape to true. Your analysis section in the configuration file should look like this:
 
-.. code-block:: text
+.. code-block:: yaml
 
     analysis:
         summary:

docs/tutorial/intermediate.rst

@@ -441,7 +441,7 @@ Step 3: Use ML Post-Analysis
 
 To enable downstream analyses, update the analysis section in your configuration file by setting both summary, cytoscape, and ml, to true. Your analysis section in the configuration file should look like this:
 
-.. code-block:: text
+.. code-block:: yaml
 
     analysis:
         ml: