Permalink
Browse files

no more default arguments

  • Loading branch information...
1 parent 78970e6 commit ac81c235dc14e96c66dd1d9d0a91334a313c49f6 @audy committed Apr 19, 2012
@@ -8,9 +8,9 @@ class CLI
desc "cluster fasta file",
"--input=sorted.fasta --identity=0.80 --output=clusters.uc"
- method_option :input, :type => :string, :default => 'sorted.fasta'
- method_option :output, :type => :string, :default => 'clusters.uc'
- method_option :identity, :type => :numeric, :default => 0.8
+ method_option :input, :type => :string, :required => true
+ method_option :output, :type => :string, :required => true
+ method_option :identity, :type => :numeric, :required => true
def cluster
identity = options[:identity]
@@ -7,8 +7,8 @@ class CLI
desc "join reads end-to-end",
"--trimmed=trimmed/*.fasta --output=joined.fasta"
- method_option :trimmed, :type => :string, :default => 'trimmed/*.fasta'
- method_option :output, :type => :string, :default => 'joined.fasta'
+ method_option :trimmed, :type => :string, :required => true
+ method_option :output, :type => :string, :required => true
def join
@@ -8,9 +8,9 @@ class CLI
desc "otu_tables generates otu tables & representative reads",
"--clusters=clusters.uc --output=otu_prefix --joined=joined.fasta"
- method_option :clusters, :type => :string, :default => 'clusters.uc'
- method_option :output, :type => :string, :default => 'otus'
- method_option :joined, :type => :string, :default => 'joined.fasta'
+ method_option :clusters, :type => :string, :required => true
+ method_option :output, :type => :string, :required => true
+ method_option :joined, :type => :string, :required => true
def otu_table
input = options[:clusters]
@@ -8,9 +8,8 @@ class CLI
desc "sort fasta file by length",
"--input=joined.fasta --output=sorted.fasta"
- method_options :input => :string, :output => :string
- method_option :input, :type => :string, :default => 'joined.fasta'
- method_option :output, :type => :string, :default => 'sorted.fasta'
+ method_option :input, :type => :string, :required => true
+ method_option :output, :type => :string, :required => true
def sort
input = options[:input]
@@ -8,9 +8,9 @@ class CLI
desc "output separate fasta file containing sequences belonging to each cluster",
"--clusters=clusters.uc --reads=joined.fasta --min-clst-size=100"
- method_option :clusters, :type => :string, :default => 'clusters.uc'
- method_option :reads, :type => :string, :default => 'joined.fasta'
- method_option :out_dir, :type => :string, :default => 'clusters_split'
+ method_option :clusters, :type => :string, :required => true
+ method_option :reads, :type => :string, :required => true
+ method_option :out_dir, :type => :string, :required => true
method_option :buffer_size, :type => :numeric, :default => 1000
method_option :min_clst_size, :type => :numeric, :default => 100
@@ -9,7 +9,7 @@ class CLI
"--reads_dir=reads/* --out_dir=trimmed.fasta"
method_option :reads_dir, :type => :string, :required => true
- method_option :out_dir, :type => :string, :default => 'trimmed/'
+ method_option :out_dir, :type => :string, :required => true
def trim

0 comments on commit ac81c23

Please sign in to comment.