update readmes and remove examples (#25)

Author: iblacksand

.gitignore

@@ -20,3 +20,5 @@ ref.txt
 target_symbols.txt
 /*.gmt
 /*.rnk
+test.json
+test.txt

README.md

@@ -10,6 +10,8 @@ This CLI is focused purely on computation. **It does not provide GMT files or HT
 
 ## Install
 
+Requires the [rust toolchain](https://rustup.rs/). Then run the following command in your terminal:
+
 ```shell
 cargo install webgestalt
 ```
@@ -25,5 +27,5 @@ webgestalt --help
 Example of running over-representation analysis using `kegg.gmt`, with an interesting list at `int.txt` and a reference of `ref.txt`. Outputs JSON file at `output.json`
 
 ```shell
-ora -g kegg.gmt -i int.txt -r ref.txt -o output.json
+webgestalt ora -g kegg.gmt -i int.txt -r ref.txt -o output.json
 ```

src/main.rs

@@ -10,10 +10,6 @@ use webgestalt_lib::methods::nta::NTAConfig;
 use webgestalt_lib::methods::ora::ORAConfig;
 use webgestalt_lib::readers::utils::Item;
 use webgestalt_lib::readers::{read_gmt_file, read_rank_file};
-
-/// WebGestalt CLI.
-/// ORA and GSEA enrichment tool.
-/// Created by John Elizarraras from the Bing Zhang Lab.
 #[derive(Parser)]
 #[command(author, version, about, long_about = None)]
 struct CliArgs {

test.json

@@ -8,13 +8,14 @@ Supported methods include:
 
 - Over-Representation Analysis (ORA)
 - Gene Set Enrichment Analysis (GSEA)
+- Network topology-based analysis (NTA)
 
 ## Installation
 
 To use webgestalt_lib in your Rust project, add the following line to your `Cargo.toml`.
 
 ```toml
-webgestalt_lib = "0.2.0" # change to wanted version
+webgestalt_lib = "0.3.0" # change to wanted version
 ```
 
 If you are just interested in running an analysis, rather than develop new tools, please use one of the packages mentioned at the beginning of the README.