class GalaxyUtil

Public Class Methods

decode_galaxy_string!(mstring) click to toggle source

Galaxy changes things like @ to __at__ we need to change it back

# File lib/protk/galaxy_util.rb, line 28
def self.decode_galaxy_string!(mstring)
    mstring.gsub!("__at__","@")
    mstring.gsub!("__oc__","{")
    mstring.gsub!("__cc__","}")
    mstring.gsub!("__ob__","[")
    mstring.gsub!("__cb__","]")
    mstring.gsub!("__gt__",">")
    mstring.gsub!("__lt__","<")
    mstring.gsub!("__sq__","'")
    mstring.gsub!("__dq__","\"")
    mstring.gsub!("__cn__","\n")
    mstring.gsub!("__cr__","\r")
    mstring.gsub!("__tc__","\t")
    mstring.gsub!("__pd__","#")

    # For characters not allowed at all by galaxy
    mstring.gsub!("__pc__","|")

    mstring
end
for_galaxy?() click to toggle source
# File lib/protk/galaxy_util.rb, line 9
def self.for_galaxy?    
  fg = ARGV[0]=="--galaxy"
  ARGV.shift if fg
  fg
end
stage_fasta(input_path,options={}) click to toggle source
# File lib/protk/galaxy_util.rb, line 20
def self.stage_fasta(input_path,options={})
  options = { :extension => '.fasta', :force_copy => false }.merge(options)
  GalaxyStager.new(input_path, options )
end
stage_pepxml(input_pepxml_path,options={}) click to toggle source
# File lib/protk/galaxy_util.rb, line 15
def self.stage_pepxml(input_pepxml_path,options={})
  options = { :extension => '.pep.xml', :force_copy => false }.merge(options)
  GalaxyStager.new(input_pepxml_path, options )
end