Fix initial errors

Start by fixing errors so we can run as
it currently is:
- Main function wasn't actually called
- Calc_band_ratio takes a single image
  array, not a list
Loop through all the images

Loop over all of the returned images in the
list, and create a list of masks rather than
just a single one for one image.
Refactor to use the standard interface

Refactor the run method to use the same
interface as the other tools - pass only
the name of a text file, which is then
read in the run method.
Allow ratio threshold to be passed in
Allow band indices to be passed through

Let user specify the band indices to use,
by passing through in the parameters key
in the json file.

The bands default to the 0th and last index
if they are not specified in the parameters.
Save mask to GeoTiff

After calculating all the cloud masks,
save them to geotiff files. The filename
is the same as the original reflectance
file, with with _cloudmask appended at the
end.

User can pass the parameter "nosave" (with
any value - we just check if the key is
present) in the parameters to turn off
geotiff creation.
Add cloudscreening tool to web docs
Add cloud screening tool to run_tool.sh