lederhosen 0.1.4 → 0.1.5

data/lib/lederhosen/tasks/add_names.rb

@@ -6,7 +6,7 @@ module Lederhosen
 	class CLI
 
 		desc "add_names",
-			"--blat=blat_output.txt --table=cluster_table.csv --level=taxonomic level (i.e 6 genus)"
+			"add names to otu abundance matrix using blat output and the out file"
 
 		method_option :blat,   :type => :string, :required => true
 		method_option :table,  :type => :string, :required => true

data/lib/lederhosen/tasks/cluster.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "cluster",
-         "--input=sorted.fasta --identity=0.80 --output=clusters.uc"
+         "cluster a fasta file using UCLUST"
 
     method_option :input,    :type => :string,  :required => true
     method_option :output,   :type => :string,  :required => true
@@ -27,4 +27,4 @@ module Lederhosen
     end
 
   end
-end
+end

data/lib/lederhosen/tasks/join.rb

@@ -5,7 +5,7 @@ module Lederhosen
     # PAIRED-END READ WORK-AROUND (JOIN THEM)
     #
     desc "join",
-         "--trimmed=trimmed/*.fasta --output=joined.fasta"
+         "join trimmed reads into a single file"
 
     method_option :trimmed, :type => :string, :required => true
     method_option :output,  :type => :string, :required => true
@@ -39,4 +39,4 @@ module Lederhosen
     end
 
   end
-end
+end

data/lib/lederhosen/tasks/k_filter.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "k_filter",
-         "--input=joined.fasta --output=filtered.fasta --k=10 --cutoff=50"
+         "filter novel reads likely to form small/singleton clusters (experimental)"
 
     method_option :input,    :type => :string,  :required => true
     method_option :output,   :type => :string,  :required => true
@@ -76,4 +76,4 @@ module Lederhosen
     end
   end
 
-end
+end

data/lib/lederhosen/tasks/name.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "name",
-         "--reps --reps=representative_reads.fasta --database taxcollector.fa --output blast_like_output.txt"
+         "identify representative reads in a TaxCollector database using BLAT"
 
     method_option :reps,     :type => :string, :required => true
     method_option :database, :type => :string, :required => true
@@ -33,4 +33,4 @@ module Lederhosen
     end
 
   end
-end
+end

data/lib/lederhosen/tasks/otu_table.rb

@@ -8,7 +8,7 @@ module Lederhosen
   class CLI
 
     desc "otu_table",
-         "--clusters=clusters.uc --output=otu_prefix"
+         "create an OTU abundance matrix from UCLUST output"
 
     method_option :clusters, :type => :string, :required => true
     method_option :output,   :type => :string, :required => true
@@ -48,4 +48,4 @@ module Lederhosen
     end
 
   end
-end
+end

data/lib/lederhosen/tasks/rep_reads.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "rep_reads",
-         "--clusters=clusters.uc --joined=joined.fasta --output=representative_reads.fasta"
+         "output a fasta file containing representative reads for each cluster given a UCLUST output file and the joined reads file"
 
     method_option :clusters, :type => :string, :required => true
     method_option :output,   :type => :string, :required => true
@@ -41,4 +41,4 @@ module Lederhosen
     end
 
   end
-end
+end

data/lib/lederhosen/tasks/sort.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "sort",
-         "--input=joined.fasta --output=sorted.fasta"
+         "sort reads by length in descending order (pre-requisite for UCLUST)"
 
     method_option :input,  :type => :string, :required => true
     method_option :output, :type => :string, :required => true
@@ -18,4 +18,4 @@ module Lederhosen
     end
 
   end
-end
+end

data/lib/lederhosen/tasks/split.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "split",
-         "--clusters=clusters.uc --reads=joined.fasta --min-clst-size=1 --out-dir=output_directory"
+         "create fasta files containing reads from each cluster"
 
     method_option :clusters,      :type => :string, :required => true
     method_option :reads,         :type => :string, :required => true
@@ -78,4 +78,4 @@ module Lederhosen
       puts "done"
     end
   end
-end
+end

data/lib/lederhosen/tasks/trim.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "trim",
-         "--reads_dir=reads/* --out_dir=trimmed.fasta"
+         "trim reads based on quality scores"
 
     method_option :reads_dir, :type => :string, :required => true
     method_option :out_dir,   :type => :string, :required => true
@@ -33,4 +33,4 @@ module Lederhosen
       pbar.finish
     end
   end
-end
+end

data/lib/lederhosen/tasks/uc_filter.rb

@@ -6,7 +6,7 @@ module Lederhosen
   class CLI
 
     desc "uc_filter",
-         "--input=clusters.uc --output=clusters.uc.filtered --reads=50 --samples=10"
+         "filter UCLUST output to remove small, infrequent clusters"
 
     method_option :input,    :type => :string,  :required => true
     method_option :output,   :type => :string,  :required => true
@@ -55,4 +55,4 @@ module Lederhosen
     end
   end
 
-end
+end

data/lib/version.rb

@@ -1,3 +1,3 @@
 module Lederhosen
-  VERSION = '0.1.4'
+  VERSION = '0.1.5'
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 17
   prerelease: 
   segments: 
   - 0
   - 1
-  - 4
-  version: 0.1.4
+  - 5
+  version: 0.1.5
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson