Refactor msgfplus wdl based on new version of plexedpiper

[biodavidjm]

Summary of the main changes:

proteomics_msgfplus.wdl

The user must specify new options

VARIABLE NAME MODIFICATION

• ptm_type is now called proteomics_experiment and is required for all proteomic experiments, i.e., not only for PTMs. The values currently accepted are: pr, ph, ub, ac.

Suggestion for OmicsPipeline: dropdown menu with these 4 options.

NEW REQUIRED VARIABLES

• refine_prior: Peptides are allowed to match multiple proteins in the prior. However, if refine_prior = true, the greedy set cover algorithm is applied to the prior and non-prior sets separately before combining ids. Default: TRUE.
  This means that any redundancy would be removed. Suggestion for OmicsPipeline: add the default value by default in the form.
• unique_only: Whether to discard peptides that match multiple proteins (not recommended). If TRUE, it will ignore arguments pr_ratio and refine_prior. Default: FALSE. Suggestion for OmicsPipeline: add the default value in the form (and let the user choose TRUE in a drop-down menu

Other changes: the wrapper_pp* tasks are now simplified to a one task wrapper_pp.

NEW SCRIPT: pp.R

This script is copied to the plexedpiper docker container.

Other updates

• Scripts
• Templates with new wdl input arguments
• PlexedPiper docker file