lib/cheripic/cmd.rb in cheripic-1.2.5 vs lib/cheripic/cmd.rb in cheripic-1.2.6

@@ -43,28 +43,30 @@
         version Cheripic::VERSION
         banner cmds.help_message
         opt :assembly, 'Assembly file in FASTA format',
             :short => '-f',
             :type => String
-        opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam',
+        opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam or vcf',
             :short => '-F',
             :type => String,
             :default => 'pileup'
         opt :mut_bulk, 'Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1',
             :short => '-a',
             :type => String
         opt :mut_bulk_vcf, 'vcf file for variants from mutant/trait of interest bulk 1',
-            :type => String
+            :type => String,
+            :default => ''
         opt :bg_bulk, 'Pileup or sorted BAM file alignments from background/wildtype bulk 2',
             :short => '-b',
             :type => String
         opt :bg_bulk_vcf, 'vcf file for variants from background/wildtype bulk 2',
-            :type => String
+            :type => String,
+            :default => ''
         opt :output, 'custom name tag to include in the output file name',
             :default => 'cheripic_results'
         opt :loglevel, 'Choose any one of "info / warn / debug" level for logs generated',
-            :default => 'debug'
+            :default => 'info'
         opt :hmes_adjust, 'factor added to snp count of each contig to adjust for hme score calculations',
             :type => Float,
             :default => 0.5
         opt :htlow, 'lower level for categorizing heterozygosity',
             :type => Float,
@@ -77,23 +79,23 @@
             :default => 6
         opt :max_d_multiple, "multiplication factor for average coverage to calculate maximum read coverage
 if set zero no calculation will be made from bam file.\nsetting this value will override user set max depth",
             :type => Integer,
             :default => 5
-        opt :maxdepth, "maximum read depth at a position to consider for variant calls
-if set to zero no user max depth will be used",
+        opt :maxdepth, 'maximum read depth at a position to consider for variant calls
+if set to zero no user max depth will be used',
             :type => Integer,
             :default => 0
         opt :min_non_ref_count, 'minimum read depth supporting non reference base at each position',
             :type => Integer,
             :default => 3
         opt :min_indel_count_support, 'minimum read depth supporting an indel at each position',
             :type => Integer,
             :default => 3
         opt :ambiguous_ref_bases, 'including variant at completely ambiguous bases in the reference',
-            :type => FalseClass,
-            :default => false
+            :type => String,
+            :default => 'false'
         opt :mapping_quality, 'minimum mapping quality of read covering the position',
             :short => '-q',
             :type => Integer,
             :default => 20
         opt :base_quality, 'minimum base quality of bases covering the position',
@@ -105,19 +107,19 @@
             :default => 0.1
         opt :cross_type, 'type of cross used to generated mapping population - back or out',
             :type => String,
             :default => 'back'
         opt :use_all_contigs, 'option to select all contigs or only contigs containing variants for analysis',
-            :type => FalseClass,
-            :default => false
+            :type => String,
+            :default => 'false'
         opt :include_low_hmes, 'option to include or discard variants from contigs with
 low hme-score or bfr score to list in the final output',
-            :type => FalseClass,
-            :default => false
+            :type => String,
+            :default => 'false'
         opt :polyploidy, 'Set if the data input is from polyploids',
-            :type => FalseClass,
-            :default => false
+            :type => String,
+            :default => 'false'
         opt :mut_parent, 'Pileup or sorted BAM file alignments from mutant/trait of interest parent',
             :short => '-p',
             :type => String,
             :default => ''
         opt :bg_parent, 'Pileup or sorted BAM file alignments from background/wildtype parent',
@@ -185,12 +187,36 @@
       exit(0)
     end
 
     # calls other methods to check if command line inputs are valid
     def check_arguments
+      convert_boolean_strings
       check_output
       check_log_level
+      check_input_entry
       check_input_types
+    end
+
+    # convert true or false options to boolean
+    def convert_boolean_strings
+      %i{ambiguous_ref_bases use_all_contigs include_low_hmes polyploidy}.each do | symbol |
+        if @options.key?(symbol)
+          @options[symbol] = @options[symbol] == 'false' ? false : true
+        end
+      end
+    end
+
+    # set file given option to false if input is nil or None or ''
+    def check_input_entry
+      %i{assembly mut_bulk bg_bulk mut_bulk_vcf bg_bulk_vcf mut_parent bg_parent repeats_file}.each do | symbol |
+        if @options.key?(symbol)
+          if @options[symbol] == 'None'
+            param = (symbol.to_s + '_given').to_sym
+            @options[symbol] = ''
+            @options.delete(param)
+          end
+        end
+      end
     end
 
     # checks input files based on bulk file type
     def check_input_types
       inputfiles = {}