fix more E2E tests

[sroet]

This will become a continuation of #123

[sroet]

@McHaillet I have encountered a test which differged so much from the script that I don't know what the option mapping is anymore:

outfile = 'OutputCCC/ellipse.mrc'
func = 'create_mask.py'
cmd = f"{func} -e {128} -m {40} -n {30} -l {20} -o {outfile} -s {5} -c {3}"

errors out with:

Some exception(s) while parsing the command line arguments:
Could not match argument -e to any option
Could not match argument 128 to any option
Could not match argument -l to any option
Could not match argument 20 to any option
Option -b requires arguments but none are given
Option -r requires arguments but none are given

Use '--help' to get information on how this script can be called.

Do you know what the current correct flags are for that script?

[McHaillet]

Should have used git mv when I renamed that file :0

These are the changed parameters: -e should be -b or --boxSize -m should be -r or --radius -n should be -m or --minor1 -l should be -n or --minor2

So the command should be like this: f"{func} --boxSize {128} --radius {40} --minor1 {30} --minor2 {20} --outputFileName {outfile} --sigma {5} --cutoff {3}"

[sroet]

Should have used git mv when I renamed that file :0

These are the changed parameters: -e should be -b or --boxSize -m should be -r or --radius -n should be -m or --minor1 -l should be -n or --minor2

So the command should be like this: f"{func} --boxSize {128} --radius {40} --minor1 {30} --minor2 {20} --outputFileName {outfile} --sigma {5} --cutoff {3}"

--minor1 was not a recognized keyword (it was --minor) and neither was --cutoff (it was --cuttoff 🤦‍♂️ ) so I updated the keywords in the script (not the test) so that your command would work

[sroet]

@McHaillet please review this PR, I think it is best to merge this in (now that test_BinScripts works) and continue on a separate branch/PR to keep review manageable