class SearchTool

Public Class Methods

new(option_support=[]) click to toggle source

Initializes commandline options common to all search tools. Individual search tools can add their own options, but should use Capital letters to avoid conflicts

Calls superclass method Tool::new
# File lib/protk/search_tool.rb, line 20
def initialize(option_support=[])
  super(option_support)

  if ( option_support.include? :enzyme )
    add_value_option(:enzyme,"Trypsin",['--enzyme enz', 'Enzyme'])
  end

  if ( option_support.include? :modifications )
    add_value_option(:var_mods,"",['--var-mods vm','Variable modifications. These should be provided in a comma separated list'])
    add_value_option(:fix_mods,"",['--fix-mods fm','Fixed modifications. These should be provided in a comma separated list'])
  end

  if ( option_support.include? :instrument )
    add_value_option(:instrument,"ESI-QUAD-TOF",['--instrument instrument', 'Instrument'])
  end

  if ( option_support.include? :mass_tolerance_units )
    add_value_option(:fragment_tolu,"Da",['--fragment-ion-tol-units tolu', 'Fragment ion mass tolerance units (Da or mmu).'])      
    add_value_option(:precursor_tolu,"ppm",['--precursor-ion-tol-units tolu', 'Precursor ion mass tolerance units (ppm or Da).'])
  end

  if ( option_support.include? :mass_tolerance )
    add_value_option(:fragment_tol,0.65,['-f', '--fragment-ion-tol tol', 'Fragment ion mass tolerance (unit dependent).'])
    add_value_option(:precursor_tol,200,['-p','--precursor-ion-tol tol', 'Precursor ion mass tolerance.'])
  end
  
  if ( option_support.include? :precursor_search_type )
    add_value_option(:precursor_search_type,"monoisotopic",['-a', '--search-type type', 'Use monoisotopic or average precursor masses. (monoisotopic or average)'])
  end

  if ( option_support.include? :strict_monoisotopic_mass )
    add_boolean_option(:strict_monoisotopic_mass,false,['-s', '--strict-monoisotopic-mass', 'Dont allow for misassignment of monoisotopic mass to another isotopic peak'])
  end

  if ( option_support.include? :missed_cleavages )
    add_value_option(:missed_cleavages,2,['-v', '--num-missed-cleavages num', 'Number of missed cleavages allowed'])
  end

  if ( option_support.include? :cleavage_semi )
    add_boolean_option(:cleavage_semi,false,['--cleavage-semi', 'Search for peptides with up to 1 non-enzymatic cleavage site'])
  end

  if ( option_support.include? :respect_precursor_charges )
    add_boolean_option(:respect_precursor_charges,false,['-q', '--respect-charges','Dont respect charges in the input file. Instead impute them by trying various options'])
  end

  if ( option_support.include? :searched_ions )
    add_value_option(:searched_ions,"",['--searched-ions si', 'Ion series to search'])
  end

  if ( option_support.include? :multi_isotope_search )
    add_boolean_option(:multi_isotope_search,false,["--multi-isotope-search","Expand parent mass window to include windows around neighbouring isotopic peaks"])
  end

  if ( option_support.include? :num_peaks_for_multi_isotope_search )
    add_value_option(:num_peaks_for_multi_isotope_search,0,["--num-peaks-for-multi-isotope-search np","Number of peaks to include in multi-isotope search"])
  end

  if ( option_support.include? :glyco)
    add_boolean_option(:glyco,false,['-g','--glyco', 'Expect N-Glycosylation modifications as variable mod in a search or as a parameter when building statistical models'])
  end

  if ( option_support.include? :acetyl_nterm)
    add_boolean_option(:acetyl_nterm,false,['-y','--acetyl-nterm', 'Expect N-terminal acetylation as a variable mod in a search or as a parameter when building statistical models'])
  end

  if ( option_support.include? :methionine_oxidation)
    add_boolean_option(:methionine_oxidation,false,['-m', '--methionineo', 'Expect Oxidised Methionine modifications as variable mod in a search'])
  end

  if ( option_support.include? :carbamidomethyl)
    add_boolean_option(:carbamidomethyl,false,['-c', '--carbamidomethyl', 'Expect Carbamidomethyl C modifications as fixed mod in a search'])
  end
  
  if ( option_support.include? :maldi)
    add_boolean_option(:maldi,false,['-l', '--maldi', 'Run a search on MALDI data'])
  end

  @option_parser.summary_width=40

    
end