correction of minor details in CLI help

v1.2.1

Update CLI.py

Added qc metrics functionality

*Added qc.py
*Rename subdirectory argument in CLI (currently is -osd = --output_subdir)
*Added the option to save all cycle info and qc as a csv table.
*Multiprocessing is used in qc.py to accelerate calculation on images.
*Added functionality to the CLI flag -rr = --remove_reference_marker

Corrected error in catching markers pattern

Update mc_tools.py

modify the markers pattern to catch cases in which the marker has an hyphen in the name

Added handling of missing channels in a tile

The script exceptions.py was added to better handle and manage exceptions in the data set, such as: 1) missing tiles for a given channels and 2) missing reference marker for a whole acquisition, e.g. DAPI.

Illumination correction option

1. Installation of basicpy via RUN pip install in the Dockerfile
2. Added the -ic flag in the CLI to call the illumination correction on the tiles
3. If the -ic flag is used, the output images will have the prefix "corr" in the name.
4. Added the -od argument to specify the name of the deepest output directory. Default value is "raw" to make it compatible with MCMICRO.

First release

Python scripts to stage MACSima data for ASHLAR/MCMICRO