update the tool page

docs/46_tools.md

@@ -1,5 +1,85 @@
-# Converting between ReproSchema and REDCap
+# Toolkit
 
-In the world of research data management, flexibility and compatibility are key. Understanding this, we provide specialized tools designed to seamlessly convert data between ReproSchema format and REDCap CSV format. Whether you're transitioning from REDCap to ReproSchema or vice versa, these tools ensure a smooth and efficient conversion process, preserving the integrity and structure of your data.
+In the world of research data management, flexibility and compatibility are key. Understanding this, we provide specialized tools designed to create, validata schemas, and convert data between ReproSchema format and REDCap CSV format. Whether you're transitioning from REDCap to ReproSchema or vice versa, these tools ensure a smooth and efficient conversion process, preserving the integrity and structure of your data.
 
-For detailed instructions on how to use these conversion tools, please visit [reproschema-py](https://github.com/ReproNim/reproschema-py). This link provides comprehensive guidance on usage, ensuring you can easily adapt your data to the format best suited for your research needs.
+## Install reproschema-py
+
+```
+pip install reproschema
+```
+
+## CLI usage
+
+`reproschema-py` can be used as a Commend-Line Interface.
+
+```
+$ reproschema
+Usage: reproschema [OPTIONS] COMMAND [ARGS]...
+
+  A client to support interactions with ReproSchema
+
+  To see help for a specific command, run
+
+  reproschema COMMAND --help     e.g. reproschema validate --help
+
+Options:
+  --version
+  -l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
+                                  Log level name  [default: INFO]
+  --help                          Show this message and exit.
+
+Commands:
+  convert
+  create
+  redcap2reproschema  Convert REDCap CSV files to Reproschema format.
+  reproschema2redcap  Convert reproschema protocol to REDCap CSV format.
+  serve
+  validate
+```
+
+## `reproschema2redcap` Usage
+
+To convert ReproSchema protocol to REDCap CSV format, use the following command
+
+```
+reproschema reproschema2redcap <input_dir_path> <output_csv_filename>
+```
+
+- `<input_dir_path>`: The path to the root folder of a protocol. For example, to convert the reproschema-demo-protocol provided by ReproNim, you can use the following commands:
+  ```bash
+  git clone https://github.com/ReproNim/reproschema-demo-protocol.git
+  cd reproschema-demo-protocol
+  pwd
+  ```
+  In this case,  the output from `pwd` (which shows your current directory path)should be your `<input_dir_path>`.
+- `<output_csv_filename>`: The name of the output CSV file where the converted data will be saved.
+
+## `redcap2reproschema` Usage
+The `redcap2reproschema` function is designed to process a given REDCap CSV file and YAML configuration to generate the output in the reproschema format.
+
+### Prerequisites
+Before the conversion, ensure you have the following:
+
+**YAML Configuration File**:
+   - Download [templates/redcap2rs.yaml](templates/redcap2rs.yaml) and fill it out with your protocol details.
+
+### YAML File Configuration
+In the `templates/redcap2rs.yaml` file, provide the following information:
+
+- **protocol_name**: This is a unique identifier for your protocol. Use underscores for spaces and avoid special characters.
+- **protocol_display_name**: The name that will appear in the application.
+- **protocol_description**: A brief description of your protocol.
+
+Example:
+```yaml
+protocol_name: "My_Protocol"
+protocol_display_name: "Assessment Protocol"
+protocol_description: "This protocol is for assessing cognitive skills."
+```
+
+The `redcap2reproschema`` function has been integrated into a CLI tool, use the following command:
+```bash
+reproschema redcap2reproschema path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml
+```
+
+Those tools can also be used as Python functions. For detailed instructions, please visit [reproschema-py](https://github.com/ReproNim/reproschema-py). 

mkdocs.yml

@@ -25,7 +25,7 @@ nav:
       - Create new assessments for a protocol: "43_create_new_assess.md"
       - Add a feedback section: "44_setup_feedback.md"
       - Finalize the protocol: "45_finalize_protocol.md"
-      - Additional tools: "46_tools.md"
+      - Toolkit: "46_tools.md"
 
   # - Creating a new activity and protocol: "create_new_activity_protocol.md"
   # - Testing your schema and collecting data: "testing_using_schema.md"