class GalaxyUtil
Public Class Methods
decode_galaxy_string!(mstring)
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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?()
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# 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={})
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# 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={})
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# 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