ffc 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 35c8b3d8fb277ab78a5be75866307c6f2e25305e
+  data.tar.gz: 578acf312a8d7768ce31d831b4d28db67b784a3f
+SHA512:
+  metadata.gz: 5268f2197e7880929760fba4d546f0d1014b62cd9d3cde03699c3cdf92c82a220be5466a4086bb81411a2f05a3f1a9546a3af23a1bc99f6292ced69595a3e3d7
+  data.tar.gz: fcc18b031f5b8b73ff400fcfd6670dab4dfa73cb08d319ccc019fe903f74f24619e909ec3bbc87672fe5575091c4e1e26d271950004a8892c9848144768b53de

data/.gitignore

@@ -0,0 +1,16 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status
+
+/vendor/bundle
+.DS_Store
+

data/.rspec

@@ -0,0 +1,2 @@
+--format documentation
+--color

data/.travis.yml

@@ -0,0 +1,5 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.4.0
+before_install: gem install bundler -v 1.14.4

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in conv.gemspec
+gemspec

data/README.md

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+# FFC
+
+File Formats Conversion Tool
+
+Especially, this tool may be useful for bioinformatics.
+
+## Installation
+
+Install it yourself as:
+
+    $ gem install ffc
+
+## Examples
+
+To convert markdown file to HTML file:
+
+    $ ffc convert a.md a.html
+    $ ffc c a.md a.html
+
+To convert "sam" format file to "bam" format file (It converts automatically if you do not know appreciate commands and parameters.):
+
+    $ ffc convert a.sam a.bam
+    $ ffc c a.sam a.bam
+    
+To show the whole list of available convert commands:
+
+    $ ffc list a.png
+    $ ffc l a.png
+    
+To show help:
+
+    $ ffc help [COMMAND]
+    $ ffc h [COMMAND]
+
+When there are alternative tools, you can select one of them.
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Notice
+
+If there are no package to run a suggested command, this tool will install the package with `brew install` in default.
+
+If you use another package manager such as `apt`, `yum` or `conda`, you can configure the default command. But there is no interface or guide yet. 
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/6br/ffc.
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "ffc"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/ffc

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+#!/usr/bin/env ruby
+
+require 'ffc'
+Conv::CLI.start

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/ffc

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+#!/usr/bin/env ruby
+
+require "ffc"
+Conv::CLI.start

data/ffc.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ffc/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "ffc"
+  spec.version       = Conv::VERSION
+  spec.authors       = ["6br"]
+  spec.email         = ["git_hub-ruby@yahoo.co.jp"]
+
+  spec.summary       = %q{Support to convert file formats by preset UNIX commands}
+  spec.description   = %q{Support to convert file formats choosing from a preset UNIX command list}
+  spec.homepage      = "https://github.com/6br/ffc"
+
+  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
+  # to allow pushing to a single host or delete this section to allow pushing to any host.
+  if spec.respond_to?(:metadata)
+    #spec.metadata['allowed_push_host'] = "http://mygemserver.com"
+  else
+    raise "RubyGems 2.0 or newer is required to protect against " \
+      "public gem pushes."
+  end
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.14"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_runtime_dependency "thor"
+  spec.add_runtime_dependency "tty-prompt"
+  spec.add_runtime_dependency "config"
+  spec.add_runtime_dependency "systemu"
+end

data/lib/.#cvt.rb

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+lib/tate@Toshiyuki-no-MacBook-Pro.local.96971

data/lib/ffc.rb

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+# -*- coding: utf-8 -*-
+require "ffc/version"
+require "ffc/cli"
+
+require 'mkmf'
+require 'systemu'
+require "open3"
+require "config"
+
+module Conv
+
+  class Conv
+    attr_accessor :conv_items, :package_manager
+
+    def initialize
+      path_name = Pathname.new( File.expand_path(File.join(File.dirname(__FILE__), 'db.bin')))
+      if !path_name.exist?
+        self.save!
+      end
+      path_name.open('rb') do |f|
+        @conv_items = Marshal.load(f)
+        @conv_items.default_proc = ->(h, k) { h[k] = [] }
+      end
+    end
+
+    def self.save!
+      @conv_items = Hash.new{ |h,k| h[k] = [] }
+      #items.each{ |item| item.input.each { |t| @conv_items[t] << item }}
+      self.rehash.each{ |item| @conv_items[item.input] << item }
+      @conv_items.default_proc = nil
+      File.open(File.expand_path(File.join(File.dirname(__FILE__), 'db.bin')), 'w') {|f| f.write(Marshal.dump(@conv_items)) }
+    end
+
+    def self.update!(new_item)
+      #TODO(NOT IMPLEMENTED)
+      #new_item.last_access = Time.now
+      #p new_item
+      #p @conv_items.select{ |item| item.command == new_item.command }#[0] = new_item
+      #@conv_items.default_proc = nil
+      #File.open(File.expand_path(File.join(File.dirname(__FILE__), 'db.bin')), 'w') {|f| f.write(Marshal.dump(@conv_items)) }
+    end
+
+    def find_item(inputs, output, input_format=nil, output_format=nil, package_manager=nil)
+      inputs = inputs.map{ |input| Pathname(input) }
+      output = Pathname(output)
+      inputs_ext = inputs.map{ |input| input.extname.slice(1..-1) }
+      output_ext = output.extname.slice(1..-1)
+      inputs_ext = input_format if input_format
+      output_ext = output_format if output_format
+      return @conv_items[inputs_ext].select{ |t| t.output == [output_ext] }.sort_by{ |item| item.last_access }.map{ |t| t.input_path=inputs;t.output_path=output;t }
+      #@prompt.select
+    end
+
+    def list(inputs, input_format=nil, package_manager=nil)
+      inputs_path = inputs.map{ |input| Pathname(input) }
+      inputs_ext = inputs_path.map{ |input| input.extname.slice(1..-1) }
+      inputs_ext = input_format if input_format
+      #input = Pathname(input)
+      #input_ext = input.extname
+      return @conv_items[inputs_ext].sort_by{ |item| item.last_access }.sort_by{ |item| item.last_access }.map{ |t| t.input_path=inputs;t.output_path=t.generate_output_filename(inputs[0]);t }
+    end
+
+    private
+    def self.rehash
+      items = []
+      items << ConvItem.new(input: ["bam"], output: ["sam"], command: "samtools view -h {input} > {output}", substitute: "{}", package: "samtools", output_buffer: :stdout)
+      items << ConvItem.new(input: ["sam"], output: ["bam"], command: "samtools view -bS {input} > {output}", substitute: "{}", package: "samtools", output_buffer: :stdout)
+      items << ConvItem.new(input: ["bam"], output: ["bai"], command: "samtools index {input}", substitute: "{}", package: "samtools")
+      items << ConvItem.new(input: ["fa"], output: ["fai"], command: "samtools faidx {input}", substitute: "{}", package: "samtools")
+      items << ConvItem.new(input: ["bam"], output: ["fasta"], command: "samtools fasta {input} > {output}", substitute: "{}", package: "samtools")
+      items << ConvItem.new(input: ["bam"], output: ["fastq"], command: "samtools fastq {input} > {output}", substitute: "{}", package: "samtools")
+      items << ConvItem.new(input: ["sam"], output: ["gtf"], command: "cufflinks {input}", substitute: "{}", package: "cufflinks")
+      items << ConvItem.new(input: ["bam"], output: ["gtf"], command: "cufflinks {input}", substitute: "{}", package: "cufflinks")
+      items << ConvItem.new(input: ["vcf"], output: ["vcf.gz"], command: "bgzip -c {input} > {output}", substitute: "{}", package: "samtools")
+      items << ConvItem.new(input: ["mid"], output: ["wav"], command: "timidity {input} -Ow -o {output}", substitute: "{}", package: "tmidity")
+      items << ConvItem.new(input: ["sam", "gtf"], output: ["txt"], command: "htseq-count {input} {input} > {output}", substitute: "{}", package: "htseq", pacman: "pip install")
+      items << ConvItem.new(input: ["bam", "gtf"], output: ["txt"], command: "htseq-count -f bam {input} {input} > {output}", substitute: "{}", package: "htseq", pacman: "pip install")
+      ["png", "pdf", "ps", "jpg"].each do |i|
+        items << ConvItem.new(input: ["dot"], output: [i], command: "dot -T#{i} {input} > {output}", substitute: "{}", package: "graphviz")
+      end
+      ["png", "jpg", "tif", "bmp", "gif"].permutation(2).each do |i, j|
+        items << ConvItem.new(input: [i], output: [j], command: "convert {input} {output}", substitute: "{}", package: "imagemagick")
+      end
+      items << ConvItem.new(input: ["wav"], output: ["mp3"], command: "lame {input} {output}", substitute: "{}", package: "lame")
+      items << ConvItem.new(input: ["wav"], output: ["mp3"], command: "avconv -i {input} {output}", substitute: "{}", package: "libav")
+      items << ConvItem.new(input: ["md"], output: ["html"], command: "python -m markdown {input} > {output}", substitute: "{}", package: "markdown", pacman: "pip install")
+      items << ConvItem.new(input: ["md"], output: ["html"], command: "pandoc -f markdown_github {input} > {output}", substitute: "{}", package: "pandoc")
+      items
+    end
+  end
+
+  class ConvItem
+    attr_accessor :input, :output, :command, :package, :substitute, :last_access, :pacman, :output_buffer, :input_path, :output_path
+
+    def initialize **params
+      Config.load_and_set_settings(Dir.home + ".conv")
+      @package_manager = Settings.package_manager
+      params.each{|k,v| self.send("#{k}=", v) if self.methods.include?(k)}
+    end
+
+    def generate_command(options, input, output)
+      return [self.cmd, self.brew]
+    end
+
+    def generate_output_filename(input, option=:exchange)
+      extensions = self.output
+      case option
+      when :exchange
+        extensions = extensions.map{ |ext| Pathname(input).sub_ext("."+ext).to_s }
+      when :prefix
+        extensions = extensions.map{ |ext| input + "." + ext }
+      #when :withtime
+      #  extensions = extensions.map{ |ext| Pathname(input + "." + ext) }
+      end
+      extensions[0]
+    end
+
+    def cmd(inputs, output)
+      cmd = self.command
+
+      inputs.each{ |input| cmd.sub!("{input}", input)}
+      cmd.sub!("{output}", output)
+      return cmd
+    end
+
+    def to_s
+      return self.output.to_s + " " + self.cmd(@input_path, @output_path) + "  (" + self.package + ")"
+    end
+
+    def run!(inputs, output)
+      raise "Error -- no input file" unless inputs.all?{ |t| Pathname(t).exist?}
+      status, stdout, stderr = systemu self.cmd(inputs, output)
+
+      return status, stdout, stderr
+    end
+
+    def brew!
+      status, stdout, stderr= systemu self.brew_command
+      #status, stdout = Open3.capture2(self.brew_command)
+      return status, stdout, stderr
+    end
+
+    def brew_command
+      if self.pacman
+        return pacman + " " + package
+      else
+        if !@package_manager
+          return "brew install " + package
+        else
+          return @package_manager + package
+        end
+      end
+    end
+  end
+
+end

data/lib/ffc/cli.rb

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+# -*- coding: utf-8 -*-
+require 'ffc'
+require 'thor'
+require 'tty-prompt'
+
+module Conv
+  class CLI < Thor
+    package_name "ffc"
+    #default_command :convert
+
+    desc "convert INPUTS OUTPUT", "convert file formats from input to output."
+    option :confirm, type: :boolean, aliases: '-c', desc: "Confirm or choice from alternative tools."
+    #option :onetime, type: :boolean, aliases: '-1', desc: "Do not save in the internal command history."
+    option :overwrite, type: :boolean, aliases: '-w', desc: "Overwrite output file without confirm."
+    option :autobrew, type: :boolean, aliases: '-b', desc: "Install without confirmation if there is no candidate binary."
+    option :input_format, type: :array, aliases: '-i', desc: "Specify input file formats regardless of extensions."
+    option :output_format, type: :string, aliases: '-o', desc: "Specify the output file format regardless of the extension."
+    option :hidelist, type: :boolean, aliases: '-h', desc: "Do not show lists related to inputs when no candidates"
+    option :quiet, type: :boolean, aliases: '-q', desc: "Run quietly."
+    option :dryrun, type: :boolean, aliases: '-d', desc: "Do not execute command."
+    option :package_manager, type: :array, aliases: '-p', desc: "Set Package manager prefix such as 'brew install'"
+    def convert(*inputs, output) # Define commands as a method.
+      prompt = TTY::Prompt.new(interrupt: :exit)
+      items = Conv.new.find_item(inputs, output, input_format=input_format, output_format=output_format, package_manager: options[:package_manager])
+      candidate = items[0]
+      if items.empty?
+        prompt.error "No candidates."
+        inputs << output
+        list(*inputs) if !options[:hidelist]
+      else
+          if options[:confirm]#interactive]
+            candidate = prompt.select("Choose commands (To cancel, press CTRL+C)", items) #do |item|
+          end
+          prompt.ok candidate.cmd(inputs, output) unless options[:quiet]
+          return if !options[:overwrite] && !ask_overwrite(output) || options[:dryrun]
+          status, stdout, stderr = candidate.run!(inputs, output)
+          prompt.ok stdout
+          prompt.error stderr
+          if status != 0
+            if options[:autobrew] || !prompt.no?("Install " + candidate.package + " with package manager? (" + candidate.brew_command + ")")
+              status, stdout, stderr = candidate.brew!
+              prompt.say stdout
+              prompt.error stderr
+              if status == 0
+                status, stdout, stderr = candidate.run!(inputs, output)
+                prompt.ok stdout
+                prompt.error stderr
+              end
+            end
+          else
+            Conv.update!(candidate) unless options[:onetime]
+          end
+      end
+    end
+
+    desc "list INPUTS", "show aveilable convert formats."
+    #option :interactive, type: :boolean, aliases: '-i', desc: "Only show lists"
+    option :showonly, type: :boolean, aliases: '-s', desc: "Only show lists"
+    option :add_prefix, type: :boolean, aliases: '-p', desc: "Add prefix to input's filename"
+    option :overwrite, type: :boolean, aliases: '-w', desc: "Overwrite output without confirm"
+    option :autobrew, type: :boolean, aliases: '-b', desc: "Install without confirmation if there is no candidate binary."
+    option :input_format, type: :array, aliases: '-i', desc: "Specify input file formats regardless of extensions."
+    option :quiet, type: :boolean, aliases: '-q', desc: "Run quietly."
+    option :dryrun, type: :boolean, aliases: '-d', desc: "Do not execute command."
+    option :package_manager, type: :array, aliases: '-p', desc: "Set Package manager prefix such as 'brew install'"
+    def list(*inputs)
+      prompt = TTY::Prompt.new(interrupt: :exit)
+      items = Conv.new.list(inputs, input_format=input_format, package_manager: options[:package_manager])
+      #p inputs,items
+      if items.empty?
+        prompt.error "No candidates."
+        return
+      end
+      if !options[:showonly]
+        candidate = prompt.select("Choose commands (To cancel: CTRL+C)", items) #do |item|
+        option = options[:add_prefix] ? :prefix : :exchange
+        output = candidate.generate_output_filename(inputs[0], option)
+
+        return if !options[:overwrite] && !ask_overwrite(output) || options[:dryrun]
+        prompt.ok candidate.cmd(inputs, output) unless options[:quiet]
+        status, stdout, stderr = candidate.run!(inputs, output)#(options[:autobrew])
+        prompt.say stdout
+        prompt.error stderr
+        if status != 0
+          if options[:autobrew] || !prompt.no?("Install " + candidate.package + " with package manager? (" + candidate.brew_command + ")")
+              status, stdout, stderr = candidate.brew!
+              prompt.say stdout
+              prompt.error stderr
+              if status == 0
+                status, stdout, stderr = candidate.run!(inputs, output)
+                prompt.say stdout
+                prompt.error stderr
+              end
+          end
+        else
+          Conv.update!(candidate) unless options[:onetime]
+        end
+      else
+        prompt.say items.join("")
+
+      end
+    end
+
+    desc "sort INPUT", "Sort the file. (Not Implemented)"
+    option :overwrite, type: :boolean, aliases: '-w', desc: "Overwrite existing file"
+    def sort(input)
+#
+    end
+
+    desc "index INPUT", "Index the file. (Not Implemented)"
+    option :overwrite, type: :boolean, aliases: '-w', desc: "Overwrite existing file"
+    def index(input)
+#
+    end
+
+    desc "rehash", "Rehash index and clean command history. (For debugging)"
+    def rehash
+      Conv.save!
+    end
+
+    private
+    def ask_overwrite(output)
+      if Pathname(output).exist?
+        return TTY::Prompt.new.yes?("Overwrite existing file " + output + "?")
+      end
+      true
+    end
+
+  end
+end
+

data/lib/ffc/version.rb

@@ -0,0 +1,3 @@
+module Conv
+  VERSION = "0.1.0"
+end

metadata

@@ -0,0 +1,158 @@
+--- !ruby/object:Gem::Specification
+name: ffc
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- 6br
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-03-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: tty-prompt
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: config
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: systemu
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Support to convert file formats choosing from a preset UNIX command list
+email:
+- git_hub-ruby@yahoo.co.jp
+executables:
+- ffc
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- README.md
+- Rakefile
+- bin/console
+- bin/ffc
+- bin/setup
+- exe/ffc
+- ffc.gemspec
+- lib/.#cvt.rb
+- lib/db.bin
+- lib/ffc.rb
+- lib/ffc/cli.rb
+- lib/ffc/version.rb
+homepage: https://github.com/6br/ffc
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.8
+signing_key: 
+specification_version: 4
+summary: Support to convert file formats by preset UNIX commands
+test_files: []