Update the pVACvector params descriptions

[susannasiebert]

This PR updates the appropriate pVACvector parameter descriptions to be tailored to pVACvector and reference junctional epitopes:

  -e1 CLASS_I_EPITOPE_LENGTH, --class-i-epitope-length CLASS_I_EPITOPE_LENGTH
                        Length of MHC Class I junctional epitopes to predict. Multiple epitope lengths can be specified using a comma-separated list. Typical epitope lengths vary between 8-15. Required for
                        Class I prediction algorithms. (default: [8, 9, 10, 11])
  -e2 CLASS_II_EPITOPE_LENGTH, --class-ii-epitope-length CLASS_II_EPITOPE_LENGTH
                        Length of MHC Class II junctional epitopes to predict. Multiple epitope lengths can be specified using a comma-separated list. Typical epitope lengths vary between 11-30. Required for
                        Class II prediction algorithms. (default: [12, 13, 14, 15, 16, 17, 18])
  -b BINDING_THRESHOLD, --binding-threshold BINDING_THRESHOLD
                        Fail junctions where any junctional epitope has ic50 binding scores below this value. (default: 500)
  --percentile-threshold PERCENTILE_THRESHOLD
                        Fail junctions where any junctional epitope has a percentile rank below this value. (default: None)
  --percentile-threshold-strategy {conservative,exploratory}
                        Specify the how to evaluate junctional epitopes if a percentile threshold is set. The 'conservative' option fails a junction if a junctional epitope fails EITHER the binding threshold
                        OR the percentile threshold (default). The 'exploratory' option fails a junction only if a junctional epitope fails BOTH the binding threshold AND the percentile threshold. (default:
                        conservative)
  --allele-specific-binding-thresholds
                        Use allele-specific binding thresholds when evaluating junctional epitopes. To print the allele-specific binding thresholds run `pvacvector allele_specific_cutoffs`. If an allele does
                        not have a special threshold value, the `--binding-threshold` value will be used. (default: False)
  -m {lowest,median}, --top-score-metric {lowest,median}
                        The ic50 scoring metric to use when evaluating junctional epitopes by binding-threshold. lowest: Use the best MT Score (i.e. the lowest MT ic50 binding score of all chosen prediction
                        methods). median: Use the median MT Score (i.e. the median MT ic50 binding score of all chosen prediction methods). (default: median)

It also adds a paragraph to the pVACvector usage docs about the --percentile-threshold-strategy parameter.

Closes #1190

[chrisamiller]

one minor comment, but generally all looks to be good

[chrisamiller]

+1