Argument container class for testing documentation generation.
The purpose of this paragraph is to test embedded html formatting.
See these additional references for more information.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Positional Arguments | |||
| [NA - Positional] | NA | Positional arguments, min = 2, max = 2 | |
| Required Arguments | |||
| --requiredClpEnum | null | Required Clp enum | |
| --requiredFileList -reqFilList | [] | Required file list | |
| --requiredInputFilesFromArgCollection -rRequiredInputFilesFromArgCollection | [] | Required input files from argument collection | |
| --requiredStringInputFromArgCollection | null | Required string input from argument collection | |
| --requiredStringList -reqStrList | [] | A required list of strings | |
| --usesFieldNameForArgName | null | Use field name if no name in annotation. | |
| Optional Tool Arguments | |||
| --fullAnonymousArgName -anonymousClassArg | [] | Test anonymous class arg | |
| --mutexArg | [] | Undocumented option | |
| --mutexTargetField1 | [] | SAM/BAM/CRAM file(s) with alignment data from the first read of a pair. | |
| --mutexTargetField2 | [] | SAM/BAM file(s) with alignment data from the second read of a pair. | |
| --optionalClpEnum | ENUM_VALUE_1 | Optional Clp enum | |
| --optionalDouble -optDouble | 2.15 | Optionals double with initial value 2.15 | |
| --optionalDoubleList -optDoubleList | [100.0, 99.9, 99.0, 90.0] | optionalDoubleList with initial values: 100.0, 99.9, 99.0, 90.0 | |
| --optionalFileList -optFilList | [] | Optional file list | |
| --optionalFlag -optFlag | false | Optional flag, defaults to false. | |
| --optionalInputFilesFromArgCollection | [] | Optional input files from argument collection | |
| --optionalStringInputFromArgCollection | null | Optional string input from argument collection | |
| --optionalStringList -optStrList | [] | An optional list of strings | |
| --testPlugin | [] | Undocumented option | |
| Advanced Arguments | |||
| --advancedOptionalInt -advancedOptInt | 1 | advancedOptionalInt with initial value 1 | |
| Deprecated Arguments | |||
| --deprecatedString -depStr | 0 | deprecated | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
			Positional arguments, min = 2, max = 2
			Positional arguments, min = 2, max = 2
		
R List[File] NA
			advancedOptionalInt with initial value 1
			Advanced, Optional int
		
int 1 [ [ -∞ ∞ ] ]
			deprecated
			Deprecated string
		
int 0 [ [ -∞ ∞ ] ]
			Test anonymous class arg
			
		
List[File] []
			Undocumented option
			Mutually exclusive args
		
Exclusion: This argument cannot be used at the same time as READ1_ALIGNED_BAM, READ2_ALIGNED_BAM.
List[File] []
			SAM/BAM/CRAM file(s) with alignment data from the first read of a pair.
			
		
Exclusion: This argument cannot be used at the same time as mutexSourceField.
List[File] []
			SAM/BAM file(s) with alignment data from the second read of a pair.
			
		
Exclusion: This argument cannot be used at the same time as mutexSourceField.
List[File] []
			Optional Clp enum
			
		
The --optionalClpEnum argument is an enumerated type (TestEnum), which can have one of the following values:
TestEnum ENUM_VALUE_1
			Optionals double with initial value 2.15
			Required double
		
double 2.15 [ [ -∞ ∞ ] ]
			optionalDoubleList with initial values: 100.0, 99.9, 99.0, 90.0
			Optional double list.
		
List[Double] [100.0, 99.9, 99.0, 90.0]
			Optional file list
			Optional file list.
		
List[File] []
			Optional flag, defaults to false.
			Optional flag.
		
boolean false
			Optional input files from argument collection
			
		
List[File] []
			Optional string input from argument collection
			
		
String null
			An optional list of strings
			Optional string list.
		
List[String] []
			Required Clp enum
			
		
The --requiredClpEnum argument is an enumerated type (TestEnum), which can have one of the following values:
R TestEnum null
			Required file list
			Required file list.
		
R List[File] []
			Required input files from argument collection
			
		
R List[File] []
			Required string input from argument collection
			
		
R String null
			A required list of strings
			Required string list.
		
R List[String] []
			Undocumented option
			
		
List[String] []
			Use field name if no name in annotation.
			
		
R String null
Barclay version 11.1 built at 2016/01/01 01:01:01.