updated README.md

README.md

@@ -1,10 +1,18 @@
 # Staging module for Miltenyi - MACSIMA to MCMICRO
 
+The macsima2mc.py script stages MACSima data sets for being registerd with ASHLAR in MCMICRO.
 
-## Docker implementation
+The script takes as main input the path to the cycle folder that cointains the raw tiles generated by the Miltenyi-MACSima platform.  macsima2mc.py reads these tiles and distributes them into acquisition groups. i.e tiles with common rack, well, ROI and exposure levels will be written into an ome.tiff file with the necessary metadata for registration.  To be more precise two such ome.tiff files will be generated per cycle, one corresponds to the background signal and the other to the markers signal.
 
-TODO: Add instructions on how to run the tool from Docker
-
 ## CLI
 
-TODO: Add instructions on how to run the CLI
+| Argument| Type| Description | Default value |
+|----|----|----|---|
+
+- Required arguments:
+    - -i [string/path]: absolute path to the the parent folder of the raw tiles, i.e. the cycle folder whose name follows the pattern X_Cycle_N, where N represents the cycle number.  
+
+    - -o [string/path]: absolute path to the 
+
+- Optional arguments:
+    - rm [string][default 'DAPI']: name of the reference marker for registration