moved full usage to docs as we now have an example

README.md

@@ -153,8 +153,6 @@ Expected output:
 [INFO] - OMOP installation completed
 ```
 
----
-
 ## **Example Usage**
 
 Follow these steps to initialize and manage a phenotype using `acmc`. In this example, we use a source concept code list for the Concept Set `Abdominal Pain` created from [ClinicalCodes.org](ClinicalCodes.org). The source concept codes are is read2. We genereate versioned phenotypes for read2 and then translate to snomed with a another version.  
@@ -329,141 +327,6 @@ Expected Output:
 [INFO] - New version: v1.0.4
 [INFO] - Phenotype published successfully
 ```
-## Usage
-
-The `acmc` command-line tool provides various commands to interact with TRUD, OMOP, and Phenotype data. Below are the usage details for each command.
-
-### General Syntax
-
-```bash
-acmc [OPTIONS] COMMAND [SUBCOMMAND] [ARGUMENTS]
-```
-
-Where:
-- `[OPTIONS]` are global options that apply to all commands (e.g., `--debug`, `--version`).
-- `[COMMAND]` is the top-level command (e.g., `trud`, `omop`, `phen`).
-- `[SUBCOMMAND]` refers to the specific operation within the command (e.g., `install`, `validate`).
-
-### Global Options
-
-- `--version`: Display the acmc tool version number
-- `--debug`: Enable debug mode for more verbose logging.
-
-### Commands
-
-#### TRUD Command
-
-The `trud` command is used for installing NHS TRUD vocabularies.
-
-- **Install TRUD**
-
-  Install clinically assurred TRUD medical code mappings:
-
-  ```bash
-  acmc trud install
-  ```
-
-#### OMOP Command
-
-The `omop` command is used for installing OMOP vocabularies.
-
-- **Install OMOP**
-
-  Install vocabularies in a local OMOP database:
-
-  ```bash
-  acmc omop install -d <OMOP_DIRECTORY_PATH> -v <OMOP_VERSION>
-  ```
-
-  - `-d`, `--omop-dir`: (Optional) Directory path to extracted OMOP downloads, default is `./build/omop`
-  - `-v`, `--version`: OMOP vocabularies release version.
-
-- **Clear OMOP**
-
-  Clear data from the local OMOP database:
-
-  ```bash
-  acmc omop clear
-  ```
-
-- **Delete OMOP**
-
-  Delete the local OMOP database:
-
-  ```bash
-  acmc omop delete
-  ```
-
-#### PHEN Command
-
-The `phen` command is used phenotype-related operations.
-
-- **Initialize Phenotype**
-
-  Initialize a phenotype directory locally or from a remote git repository:
-
-  ```bash
-  acmc phen init -d <PHENOTYPE_DIRECTORY> -r <REMOTE_URL>
-  ```
-
-  - `-d`, `--phen-dir`: (Optional) Directory to write phenotype configuration (the default is ./build/phen).
-  - `-r`, `--remote_url`: (Optional) URL to a remote git repository.
-
-- **Validate Phenotype**
-
-  Validate the phenotype configuration:
-
-  ```bash
-  acmc phen validate -d <PHENOTYPE_DIRECTORY>
-  ```
-
-  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
-
-- **Map Phenotype**
-
-  Process phenotype mapping and specify the target coding and output format:
-
-  ```bash
-  acmc phen map -d <PHENOTYPE_DIRECTORY> -t <TARGET_CODING> -o <OUTPUT_FORMAT>
-  ```
-
-  - `-t`, `--target-coding`: Specify the target coding (e.g., `read2`, `read3`, `icd10`, `snomed`, `opcs4`).
-  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
-  - `-o`, `--output`: Output format(s) (`csv`, `omop`, or both), default is 'csv'.
-
-- **Publish Phenotype Configuration**
-
-  Publish a phenotype configuration, committing all changes and tagging with a new version number. If the phenotype has been initialised from a remote git URL, then the commit and new version tag will be pushed to the remote repo:
-
-  ```bash
-  acmc phen publish -d <PHENOTYPE_DIRECTORY>
-  ```
-
-  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
-
-- **Copy Phenotype Configuration**
-
-  Copy a phenotype configuration from a source directory to a target directory at a specific version. This is used when wanting to compare versions of phenotypes using the `acmc phen diff` command: 
-
-  ```bash
-  acmc phen copy -d <PHENOTYPE_DIRECTORY> -td <TARGET_DIRECTORY> -v <PHENOTYPE_VERSION>
-  ```
-
-  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
-  - `-td`, `--target-dir`: (Optional) Directory to copy the phenotype configuration to, (the default is ./build).
-  - `-v`, `--version`: The phenotype version to copy.
-
-- **Compare Phenotype Configurations**
-
-  Compare a a new phenotype version with pervious version of a phenotype:
-
-  ```bash
-  acmc phen diff -d <NEW_PHENOTYPE_DIRECTORY> -old <OLD_PHENOTYPE_DIRECTORY>
-  ```
-
-  - `-d`, `--phen-dir`: (Optional) Directory of current phenotype configuration (the default is ./build/phen).
-  - `-old`, `--phen-dir-old`: (Required) Directory of old phenotype version)
-
 
 ## License
 

docs/index.md

@@ -34,4 +34,141 @@ The tool supports verification and mapping across diagnostic coding formats belo
 
    Processed resources will be saved in the `build/maps/processed/` directory.
 
-*Note: NHS TRUD provides one-way mappings. To reverse mappings, duplicate the `.parquet` file and reverse the filename (e.g., `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`).*
\ No newline at end of file
+*Note: NHS TRUD provides one-way mappings. To reverse mappings, duplicate the `.parquet` file and reverse the filename (e.g., `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`).*
+
+
+
+## Usage
+
+The `acmc` command-line tool provides various commands to interact with TRUD, OMOP, and Phenotype data. Below are the usage details for each command.
+
+### General Syntax
+
+```bash
+acmc [OPTIONS] COMMAND [SUBCOMMAND] [ARGUMENTS]
+```
+
+Where:
+- `[OPTIONS]` are global options that apply to all commands (e.g., `--debug`, `--version`).
+- `[COMMAND]` is the top-level command (e.g., `trud`, `omop`, `phen`).
+- `[SUBCOMMAND]` refers to the specific operation within the command (e.g., `install`, `validate`).
+
+### Global Options
+
+- `--version`: Display the acmc tool version number
+- `--debug`: Enable debug mode for more verbose logging.
+
+### Commands
+
+#### TRUD Command
+
+The `trud` command is used for installing NHS TRUD vocabularies.
+
+- **Install TRUD**
+
+  Install clinically assurred TRUD medical code mappings:
+
+  ```bash
+  acmc trud install
+  ```
+
+#### OMOP Command
+
+The `omop` command is used for installing OMOP vocabularies.
+
+- **Install OMOP**
+
+  Install vocabularies in a local OMOP database:
+
+  ```bash
+  acmc omop install -d <OMOP_DIRECTORY_PATH> -v <OMOP_VERSION>
+  ```
+
+  - `-d`, `--omop-dir`: (Optional) Directory path to extracted OMOP downloads, default is `./build/omop`
+  - `-v`, `--version`: OMOP vocabularies release version.
+
+- **Clear OMOP**
+
+  Clear data from the local OMOP database:
+
+  ```bash
+  acmc omop clear
+  ```
+
+- **Delete OMOP**
+
+  Delete the local OMOP database:
+
+  ```bash
+  acmc omop delete
+  ```
+
+#### PHEN Command
+
+The `phen` command is used phenotype-related operations.
+
+- **Initialize Phenotype**
+
+  Initialize a phenotype directory locally or from a remote git repository:
+
+  ```bash
+  acmc phen init -d <PHENOTYPE_DIRECTORY> -r <REMOTE_URL>
+  ```
+
+  - `-d`, `--phen-dir`: (Optional) Directory to write phenotype configuration (the default is ./build/phen).
+  - `-r`, `--remote_url`: (Optional) URL to a remote git repository.
+
+- **Validate Phenotype**
+
+  Validate the phenotype configuration:
+
+  ```bash
+  acmc phen validate -d <PHENOTYPE_DIRECTORY>
+  ```
+
+  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+
+- **Map Phenotype**
+
+  Process phenotype mapping and specify the target coding and output format:
+
+  ```bash
+  acmc phen map -d <PHENOTYPE_DIRECTORY> -t <TARGET_CODING> -o <OUTPUT_FORMAT>
+  ```
+
+  - `-t`, `--target-coding`: Specify the target coding (e.g., `read2`, `read3`, `icd10`, `snomed`, `opcs4`).
+  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+  - `-o`, `--output`: Output format(s) (`csv`, `omop`, or both), default is 'csv'.
+
+- **Publish Phenotype Configuration**
+
+  Publish a phenotype configuration, committing all changes and tagging with a new version number. If the phenotype has been initialised from a remote git URL, then the commit and new version tag will be pushed to the remote repo:
+
+  ```bash
+  acmc phen publish -d <PHENOTYPE_DIRECTORY>
+  ```
+
+  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+
+- **Copy Phenotype Configuration**
+
+  Copy a phenotype configuration from a source directory to a target directory at a specific version. This is used when wanting to compare versions of phenotypes using the `acmc phen diff` command: 
+
+  ```bash
+  acmc phen copy -d <PHENOTYPE_DIRECTORY> -td <TARGET_DIRECTORY> -v <PHENOTYPE_VERSION>
+  ```
+
+  - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+  - `-td`, `--target-dir`: (Optional) Directory to copy the phenotype configuration to, (the default is ./build).
+  - `-v`, `--version`: The phenotype version to copy.
+
+- **Compare Phenotype Configurations**
+
+  Compare a a new phenotype version with pervious version of a phenotype:
+
+  ```bash
+  acmc phen diff -d <NEW_PHENOTYPE_DIRECTORY> -old <OLD_PHENOTYPE_DIRECTORY>
+  ```
+
+  - `-d`, `--phen-dir`: (Optional) Directory of current phenotype configuration (the default is ./build/phen).
+  - `-old`, `--phen-dir-old`: (Required) Directory of old phenotype version)
\ No newline at end of file