Merge pull request #54 from plantinformatics/kenny/misc/add-index-pages

Kenny/misc/add index pages
plantinformatics · Jan 8, 2025 · 904d4eb · 904d4eb
2 parents 7f1d9e2 + abca396
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diff --git a/docs/Basic-Functions/index.md b/docs/Basic-Functions/index.md
@@ -0,0 +1,2 @@
+# Basic Functions
+
diff --git a/docs/Use-Cases/VCF-genotype-search.md b/docs/Use-Cases/VCF-genotype-search.md
@@ -3,13 +3,6 @@
 In this Use Case, a summary of genotypes for AGG Plant Genetic Resources can be simply and rapidly visualised. For example, a user may wish to view the genotypes for a set of accessions of interest at a small subset of trait linked markers, to make a decision on which accessions to use in an experiment. In this example we will use Pretzel to display a summary of a set of AGG barley Plant Genetic Resources at two markers
 AVRIG00246  and AVRIG00484.
 
-!!! note
-
-    The following feature is currently being developed. Please access it at [https://dev.plantinformatics.io/login](https://dev.plantinformatics.io/login) using the following login credentials.
-    Username: test@test
-    Password: test
-
-
 ![vcf-feature-search](https://github.com/user-attachments/assets/f29743ac-29ff-4660-a384-5991cc48028c)
 
 ## Loading a VCF and selecting samples 
@@ -31,9 +24,10 @@ To select a range of samples, hold down the CRTL key and select another sample i
 ## Adding features to be searched
 Within the Features input text box, paste your feature IDs.
 The one used in this example is:
-
-    AVRIG00246
-    AVRIG00484
+``` text title="Feature names"
+AVRIG00246
+AVRIG00484
+```
 ![vcf-feature-search-05](https://github.com/user-attachments/assets/a914dd99-83eb-421e-b5cf-c6a17d36abb9)
 ## End output
 ![vcf-feature-search-06](https://github.com/user-attachments/assets/44b9ca10-cb88-4342-b5ef-06ac47faf054)

diff --git a/docs/Use-Cases/Visualise-the-location-of-a-subset-of-markers.md b/docs/Use-Cases/Visualise-the-location-of-a-subset-of-markers.md
@@ -5,9 +5,10 @@ Click on the "Search" button the left hand search panel
 ![enter image description here](https://pretzel-images-public.s3.ap-southeast-2.amazonaws.com/use-case/visualise-subset-of-markers%E2%80%8B/sm-1.png)
 
 Enter the a list of feature names into the search text box input and press the search button
-
-    AVRIG00246
-    AVRIG00484
+``` text title="Feature names"
+AVRIG00246
+AVRIG00484
+```
 
 ![enter image description here](https://pretzel-images-public.s3.ap-southeast-2.amazonaws.com/use-case/visualise-subset-of-markers%E2%80%8B/sm-2.png)
 

diff --git a/docs/Use-Cases/index.md b/docs/Use-Cases/index.md
@@ -0,0 +1 @@
+# Use Cases
diff --git a/docs/User-Stories/index.md b/docs/User-Stories/index.md
@@ -0,0 +1 @@
+# User Stories
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -30,15 +30,18 @@ nav:
   - About Pretzel:
     - index.md
   - User Stories:
+    - User-Stories/index.md
     - User-Stories/User-story-1.md
     - User-Stories/User-story-2.md
     - User-Stories/User-story-3.md
   - Use Cases:
+    - Use-Cases/index.md
     - Use-Cases/Finding-a-marker-or-gene-on-a-genome.md
     - Use-Cases/Visualise-genotype-data-for-a-subset-of-accessions-around-specific-genomic-regions.md
     - Use-Cases/Visualise-the-location-of-a-subset-of-markers.md
     - Use-Cases/VCF-genotype-search.md
   - Basic Functions:
+    - Basic-Functions/index.md
     - Basic-Functions/Search-tab.md
     - Basic-Functions/Features-tab.md
     - Basic-Functions/Adding-and-removing-datasets-from-the-view.md