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# File 'bin/gfastqc', line 45
def self.parse(args)
options = OpenStruct.new
options.config = 'config.yml'
options.step = ''
opt_parser = OptionParser.new do |opts|
opts.banner = 'Usage: qc_overview.rb '
opts.on('-c', '--config [config]',
'choose the config from get info about the samples') do |config|
options.config = config
end
opts.on('-p', '--pipengine',
'if you used pipengine to produce the fastqc result is better to use this option. gfastqc will look into the output directory specified in the sample.yml') do
options.pipengine = true
end
opts.on('-g', '--groups',
'if you specified groups in your configuration file, select this option') do
options.groups = true
end
opts.on('-s', '--step [STEP]',
'choose the step from which extract the fastqc data') do |step|
options.step = step
end
opts.on('-a', '--first [FIRST]',
'forward strand reads') do |first|
options.first = first
end
opts.on('-b', '--second [SECOND]',
'reverse strand reads') do |second|
options.second = second
end
opts.on('-n', '--usename',
'use sample name to build the path (maybe later implement placeholding like pipengine') do
options.usename = true
end
opts.on_tail("-h", "--help", "Show this message") do
puts opts
exit
end
end
opt_parser.parse!(args)
options
end
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