bio-fastqc 0.10.6 → 0.10.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ddd77c8a1af5b9dfc191fa536cfca801ca4103ff63a9e2479a5cbdc1efed9de7
-  data.tar.gz: 04a615591af4c0c5afe5897bb1cccc67be6eaddb191b05592ed669ee91b89a35
+  metadata.gz: 3aa1e38f87a09d7211972e5ef8bde5717423b659346beca5eaea315918b64f6c
+  data.tar.gz: f601d5b3826e32eaf6a60f528ceac58f77745201a5856d9afdc41741b8659d1f
 SHA512:
-  metadata.gz: b81e1fb00428cc991e53271817c49521415352424725e74e465e19d10cd2126f4b7358f5ad6c1e8d5c4ee938b825f18e3201eeb4d93864c0b596b9a94dd3ebe5
-  data.tar.gz: ae27039df3c89bbd92c7c894fe7f017b27a1fb2a340e8f8b948c5bc149a4e2a139abaa02bf99c124098875377d870b4d8289b915fd04323cdec74fb0c7d66101
+  metadata.gz: c96d2295b2d1628232411749be52a90dc461619b47e2b0f43458dd8b3149071883dbd7f9c95e5c5b783708f70d31c8b3d94bd1940e1e1207365823def32ad581
+  data.tar.gz: 5e0ba4dc8138e89819e0bb612a1ac3d5381e3a54e3b882176cc60b35043c0842e612fed929524d0177b61f4e25a7ad4c9010abd4a1f2b50fd4184eca203cc08c

data/VERSION

@@ -1 +1 @@
-0.10.6
+0.10.7

data/dockerfile/Dockerfile

@@ -1,2 +1,2 @@
 FROM ruby:2.5.0-slim
-RUN gem install bio-fastqc -v 0.10.4
+RUN gem install bio-fastqc -v 0.10.7

data/lib/bio/fastqc/cli.rb

@@ -6,13 +6,23 @@ require 'json'
 module Bio
   module FastQC
     class CLI < Thor
-      desc "parse [--format format] [filename]", "parse fastqc data in directory or zipfile. output format should be json, json-ld, turtle, or tsv"
+      desc "parse [--format format] [--outdir output directory] [filepath, ..]", "parse fastqc data in directory or zipfile. output format: json, json-ld, turtle, or tsv"
       option :format, :default => "json"
+      option :output, :default => nil
       def parse(*files)
         files.each do |file|
           data = Data.read(file)
           summary = Parser.new(data).summary
-          puts Converter.new(summary).convert_to(options[:format])
+          out = Converter.new(summary).convert_to(options[:format])
+
+          outdir_path = options[:outdir]
+          if outdir_path && File.directory?(outdir_path)
+            filename_org = File.basename(summary[:filename])
+            fpath = File.join(outdir_path, filename_org + "." + options[:format])
+            open(fpath, "w"){|f| f.puts(out) }
+          else
+            puts out
+          end
         end
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-fastqc
 version: !ruby/object:Gem::Version
-  version: 0.10.6
+  version: 0.10.7
 platform: ruby
 authors:
 - Tazro Inutano Ohta