clarify install confirmation

README.md

@@ -24,7 +24,24 @@ $ git clone https://github.com/StaPH-B/staphb_toolkit.git
 $ ./staphb_toolkit/setup.py
 ```
 
-Test the pipeline with the following command:  
+Test the pipeline with the following command and ensure you see the same usage output:  
 ```
-$ staphb-tk test
+$ staphb-tk
+usage: staphb-tk [optional arguments] <application> [application arguments]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --docker_config <path>, -c <path>
+                        Configuration file for container images and tags; if
+                        none provided, default container versions will be
+                        used.
+  --get_docker_config   Get the default docker container configureation file.
+  --list, -l            List all of the software available in the toolkit.
+  --update              Check for and install a ToolKit update.
+  --auto_update         Toggle automatic ToolKit updates. Default is off.
+
+custom program execution:
+
+    mash_species        MASH Species uses a custom database to identify the
+                        isolate species.
 ```