lederhosen 0.1.8 → 0.1.9
Sign up to get free protection for your applications and to get access to all the features.
- data/lib/lederhosen/tasks/cluster.rb +18 -6
- data/lib/version.rb +1 -1
- metadata +3 -3
@@ -8,20 +8,32 @@ module Lederhosen
|
|
8
8
|
desc "cluster",
|
9
9
|
"cluster a fasta file using UCLUST"
|
10
10
|
|
11
|
-
method_option :input,
|
12
|
-
method_option :output,
|
13
|
-
method_option :identity,
|
11
|
+
method_option :input, :type => :string, :required => true
|
12
|
+
method_option :output, :type => :string, :required => true
|
13
|
+
method_option :identity, :type => :numeric, :required => true
|
14
|
+
method_option :stepwords, :type => :numeric, :default => 8
|
15
|
+
method_option :wordlen, :type => :numeric, :default => 8
|
16
|
+
method_option :maxaccepts, :type => :numeric, :default => 1
|
17
|
+
method_option :maxrejects, :type => :numeric, :default => 8
|
14
18
|
|
15
19
|
def cluster
|
16
|
-
identity
|
17
|
-
output
|
18
|
-
input
|
20
|
+
identity = options[:identity]
|
21
|
+
output = options[:output]
|
22
|
+
input = options[:input]
|
23
|
+
stepwords = options[:stepwords]
|
24
|
+
maxaccepts = options[:maxaccepts]
|
25
|
+
maxrejects = options[:maxrejects]
|
26
|
+
wordlen = options[:wordlen]
|
19
27
|
|
20
28
|
cmd = [
|
21
29
|
'uclust',
|
22
30
|
"--input #{input}",
|
23
31
|
"--uc #{output}",
|
24
32
|
"--id #{identity}",
|
33
|
+
"--stepwords #{stepwords}",
|
34
|
+
"--maxaccepts #{maxaccepts}",
|
35
|
+
"--maxrejects #{maxrejects}",
|
36
|
+
"--w #{wordlen}"
|
25
37
|
].join(' ')
|
26
38
|
|
27
39
|
@shell.mute { run cmd }
|
data/lib/version.rb
CHANGED
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: lederhosen
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 9
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 1
|
9
|
-
-
|
10
|
-
version: 0.1.
|
9
|
+
- 9
|
10
|
+
version: 0.1.9
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Austin G. Davis-Richardson
|