Implement command-line interface for QC of files

1 files changed, 29 insertions, 0 deletions

diff --git a/README.org b/README.org
index aef1a08..53ac63c 100644
--- a/README.org
+++ b/README.org
@@ -53,3 +53,32 @@ To check for correct type usage in the application, run:
 #+BEGIN_SRC shell
   mypy --show-error-codes .
 #+END_SRC
+
+** Running QC
+
+*** Command-Line Version
+
+To run qc against a file, the syntax is:
+#+BEGIN_SRC shell
+  python3 -m qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>
+#+END_SRC
+where
+- ~<filetype>~ is one of "*average*" or "*standard-error*"
+- ~<filepath>~ is either an absolute path to the file, or a path relative to the
+  current working directory
+- if the ~--strainsfile~ option is not provided, it will default to the one in
+  the root directory of this repository
+- the ~--verbose~ option is a flag, defaulting to ~False~ that controls the
+  display of optional progress messages
+
+To view the usage information for the application, run
+#+BEGIN_SRC shell
+  python3 -m qc --help
+#+END_SRC
+
+**** TODO Figure out how to put qc.py in a /bin or /scripts directory and still be able to import the modules in the repo
+**** TODO Reduce the command to simply ~qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>~
+
+*** Web Version
+
+Coming soon...