Combine miga get params with --file

Close #154

lib/miga/cli.rb

@@ -19,9 +19,13 @@ class MiGA::Cli < MiGA::MiGA
   attr_accessor :task
 
   ##
-  # The CLI parameters (except the task), and Array of String
+  # The unparsed CLI parameters (except the task), an Array of String
   attr_accessor :argv
 
+  ##
+  # The original ARGV passed to the CLI, an Array of String
+  attr_accessor :original_argv
+
   ##
   # Action to launch, an object inheriting from MiGA::Cli::Action
   attr_accessor :action
@@ -62,6 +66,7 @@ def initialize(argv)
     @data = {}
     @defaults = { verbose: false, tabular: false }
     @opt_common = true
+    @original_argv = argv.dup
     @objects = {}
     if argv[0].nil? or argv[0].to_s[0] == '-'
       @task = :generic

lib/miga/cli/action/get.rb

@@ -77,6 +77,9 @@ def parse_cli
         'Path to an NCBI Taxonomy dump directory to query instead of API calls',
         'If the path is not passed, the dump is automatically downloaded'
       ) { |v| cli[:ncbi_taxonomy_dump] = v || true }
+      opt.on(
+        '--ignore-file', '::HIDE::' # Only for internal use
+      ) { |v| cli[:ignore_file] = v }
     end
   end
 
@@ -100,17 +103,18 @@ def perform
   private
 
   def get_sub_cli
-    return [cli] if cli[:file].nil?
+    return [cli] if cli[:file].nil? || cli[:ignore_file]
 
     glob = []
+    cli_default = cli.original_argv + ['--ignore-file']
     File.open(cli[:file], 'r') do |fh|
       h = nil
       fh.each do |ln|
         r = ln.chomp.split(/\t/)
         if h.nil?
           h = r
         else
-          argv_i = [self.name]
+          argv_i = cli_default.dup
           h.each_with_index do |field, k|
             case field.downcase
             when *%w[query ignore-dup get-metadata only-metadata]

lib/miga/version.rb

@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 13, 3].freeze
+  VERSION = [1.3, 13, 4].freeze
 
   ##
   # Nickname for the current major.minor version.
   VERSION_NAME = 'mezzotint'
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 3, 18)
+  VERSION_DATE = Date.new(2024, 3, 20)
 
   ##
   # References of MiGA