bio-fastqc 0.10.4 → 0.10.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ee05612afd7abcb08e1a6df37c16e23af1d1dff69212356b8fee08868130db8a
-  data.tar.gz: c97b10724023afe960ae41af729276300f103d1ccd6d6bf8f3eac57fc9caf847
+  metadata.gz: ddd77c8a1af5b9dfc191fa536cfca801ca4103ff63a9e2479a5cbdc1efed9de7
+  data.tar.gz: 04a615591af4c0c5afe5897bb1cccc67be6eaddb191b05592ed669ee91b89a35
 SHA512:
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-  data.tar.gz: ca9ce91aca5779567369c21d9c531f157f4c9637af606669595fd308955533b564d7769f0afea24f8eab268d78897f3b27d0f3e82ae437feaef7288b9300d7b2
+  metadata.gz: b81e1fb00428cc991e53271817c49521415352424725e74e465e19d10cd2126f4b7358f5ad6c1e8d5c4ee938b825f18e3201eeb4d93864c0b596b9a94dd3ebe5
+  data.tar.gz: ae27039df3c89bbd92c7c894fe7f017b27a1fb2a340e8f8b948c5bc149a4e2a139abaa02bf99c124098875377d870b4d8289b915fd04323cdec74fb0c7d66101

data/VERSION

@@ -1 +1 @@
-0.10.4
+0.10.6

data/dockerfile/Dockerfile

@@ -0,0 +1,2 @@
+FROM ruby:2.5.0-slim
+RUN gem install bio-fastqc -v 0.10.4

data/lib/bio/fastqc/cli.rb

@@ -6,14 +6,14 @@ require 'json'
 module Bio
   module FastQC
     class CLI < Thor
-      desc "parse [--format format] [filename]", "parse fastqc data in fastqc directory or zipfile. output format: json (--json), json-ld (--jsonld), rdf-turtle (--ttl), or one-line tsv format (--tsv)."
+      desc "parse [--format format] [filename]", "parse fastqc data in directory or zipfile. output format should be json, json-ld, turtle, or tsv"
       option :format, :default => "json"
-      def parse(file)
-        data = Data.read(file)
-        summary = Parser.new(data).summary
-        puts Converter.new(summary).convert_to(options[:format])
-      # rescue
-      #   puts "Wrong input file type: specify fastqc result data, directory or zipfile"
+      def parse(*files)
+        files.each do |file|
+          data = Data.read(file)
+          summary = Parser.new(data).summary
+          puts Converter.new(summary).convert_to(options[:format])
+        end
       end
     end
   end

data/lib/bio/fastqc/converter.rb

@@ -13,9 +13,9 @@ module Bio
         case format
         when "json"
           to_json
-        when "json-ld"
+        when "json-ld", "jsonld"
           to_jsonld
-        when "turtle"
+        when "turtle", "ttl"
           to_turtle
         when "tsv"
           to_tsv

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-fastqc
 version: !ruby/object:Gem::Version
-  version: 0.10.4
+  version: 0.10.6
 platform: ruby
 authors:
 - Tazro Inutano Ohta
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-07-21 00:00:00.000000000 Z
+date: 2018-07-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
@@ -219,6 +219,7 @@ files:
 - Rakefile
 - VERSION
 - bin/fastqc-util
+- dockerfile/Dockerfile
 - lib/bio-fastqc.rb
 - lib/bio/fastqc.rb
 - lib/bio/fastqc/cli.rb