Updated the help menu

docs/tools/VcfToTsv.md

@@ -14,26 +14,33 @@ biopet tool VcfToTsv -h
 Usage: VcfToTsv [options]
 
   -l <value> | --log_level <value>
-        Log level
+        Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
   -h | --help
         Print usage
   -v | --version
         Print version
   -I <file> | --inputFile <file>
-        
+        Input vcf file
   -o <file> | --outputFile <file>
         output file, default to stdout
-  -f <value> | --field <value>
-        
-  -i <value> | --info_field <value>
-        
+  -f Genotype field name | --field Genotype field name
+        Genotype field to use
+  -i Info field name | --info_field Info field name
+        Info field to use
   --all_info
-        
+        Use all info fields in the vcf header
   --all_format
-        
+        Use all genotype fields in the vcf header
   -s <value> | --sample_field <value>
-        
+        Genotype fields to use in the tsv file
   -d | --disable_defaults
+        Don't output the default columns from the vcf file
+  --separator <value>
+        Optional separator. Default is tab-delimited
+  --list_separator <value>
+        Optional list separator. By default, lists are separated by a comma
+  --max_decimals <value>
+        Number of decimal places for numbers. Default is 2
 ~~~
 
 To run the tool: