size: "integer" ("1"). The number of elements in the array.

minimum: "float" ("-FLT_MIN"). Lower value limit. Defaults to the boundaries as specified by the systems set-up.

maximum: "float" ("+FLT_MAX"). Upper value limit. Defaults to the boundaries as specified by the systems set-up.

trueminimum: "boolean" ("N"). Used for calculated values of minimum: and maximum:. By default the minimum value is used if the minimum and maximum values overlap.

failrange: "boolean" ("Y"). Used for calculated values of minimum: and maximum:. By default the application fails if the calculated ranges overlap.

rangemessage: "string" (""). Used for calculated values of minimum: and maximum:. Failure message to use if calculated ranges overlap.

sum: "float" ("1.0"). Total for all values in the array (tested unless the sumtest: attribute is false).

sumtest: "boolean" ("Y"). If false, turns off testing for the sum: attribute.

tolerance: "float" ("0.01"). Specifies how closely the sum: should match the total. Most floating point fractions cannot be represented accurately in binary form.

warnrange: "boolean" ("Y"). Controls whether a warning is issued if values are given that are out of range.

increment: "integer" ("0"). Defines the steps the array values may take when iterated. The increment: can be any valid float value. Implemented for GUIs to EMBOSS only and is not used by EMBOSS itself (it is disregarded during ACD file processing).

precision: "integer" ("0"). Defines the maximum number of significant decimal places that will be taken into account for this value. Implemented for GUIs to EMBOSS only and is not used by EMBOSS itself (it is disregarded during ACD file processing).

boolean currently has no specific attributes.

minimum: "float" ("-FLT_MIN"). Lower value limit. Defaults to the boundaries as specified by the systems set-up.

maximum: "float" ("+FLT_MAX"). Upper value limit. Defaults to the boundaries as specified by the systems set-up.

trueminimum: "boolean" ("N"). Used for calculated values of minimum: and maximum:. By default the minimum value is used if the minimum and maximum values overlap.

failrange: "boolean" ("Y"). Used for calculated values of minimum: and maximum:. By default the application fails if the calculated ranges overlap.

rangemessage: "string" (""). Used for calculated values of minimum: and maximum:. Failure message to use if calculated ranges overlap.

increment: "float" ("1"). The steps that this parameter is allowed to take, in case there is a need to iterate this parameter. The increment: attribute can be any valid float value.

precision: "integer" ("3"). The maximum number of significant decimal places that will be taken into account for this value.

warnrange: "boolean" ("Y"). Controls whether a warning is issued if values are given that are out of range.

minimum: "integer" ("INT_MIN"). Lower value limit. Defaults to the boundaries as specified by the systems set-up.

maximum: "integer" ("INT_MAX"). Upper value limit. Defaults to the boundaries as specified by the systems set-up.

trueminimum: "boolean" ("N"). Used for calculated values of minimum: and maximum:. By default the minimum value is used if the minimum and maximum values overlap.

failrange: "boolean" ("Y"). Used for calculated values of minimum: and maximum:. By default the application fails if the calculated ranges overlap.

rangemessage: "string" (""). Used for calculated values of minimum: and maximum:. Failure message to use if calculated ranges overlap.

increment: "integer" ("0"). Defines the steps that this parameter is allowed to take, in case there is a need to iterate this parameter.

warnrange: "boolean" ("Y"). Controls whether a warning is issued if values are given that are out of range.

minimum: "integer" ("1"). Lower value limit.

maximum: "integer" ("INT_MAX"). Upper value limit. Defaults to the boundaries as specified by the systems set-up.

trueminimum: "boolean" ("N"). Used for calculated values of minimum: and maximum:. By default the minimum value is used if the minimum and maximum values overlap.

failrange: "boolean" ("Y"). Used for calculated values of minimum: and maximum:. By default the application fails if the calculated ranges overlap.

rangemessage: "string" (""). Used for calculated values of minimum: and maximum:. Failure message to use if calculated ranges overlap.

minsize: "integer" ("0"). Where multiple ranges are defined minsize: defines the minimum number of ranges that must be defined.

size: "integer" ("0"). Exact number of values required.

Only one of size: or minsize: should be defined for any range.

minlength: "integer" ("1"). The minimum length the regular expression string can be.

maxlength: "integer" ("INT_MAX"). The maximum length the regular expression string can be.

upper: "boolean" ("N"). Convert the regular expression to upper case before compiling.

lower: "boolean" ("N"). Convert the regular expression to lower case before compiling.

maxsize: "integer" ("INT_MAX"). The maximum number of patterns.

type: The type of pattern, currently one of string, nucleotide or protein.

minlength: "integer" ("1"). The minimum length the pattern can be.

maxlength: "integer" ("INT_MAX"). The maximum length the pattern can be.

upper: "boolean" ("N"). Convert the pattern to upper case before compiling.

lower: "boolean" ("N"). Convert the pattern to lower case before compiling.

maxsize: "integer" ("INT_MAX"). The maximum number of patterns.

type: The type of pattern, currently one of string, nucleotide or protein.

minlength: "integer" ("0"). Minimum length of the string. The default minimum length is zero.

maxlength: "integer" ("INT_MAX"). Maximum length of the string. There is no default maximum.

pattern: "string" (""). Defines a regular expression used to validate the string value: an invalid string will be reprompted for. EMBOSS uses the Perl-compatible regular expression library (PCRE) so any Perl-compatible regular expression should be usable.

word: "boolean" ("N"). If set requires the result to be a valid word with no whitespace. Note that the default minimum length of zero allows an empty string however this is not accepted as a word.

upper: "boolean" ("N"). Converts the case of the string internally to upper case.

lower: "boolean" ("N"). Converts the case of the string internally to lower case.

Only one of upper: or lower: should be specified.

Although there are (currently) no specific attributes for a toggle ACD type, care should be taken over the definition of the information: and help: attributes. These are used to prompt the user (interactively or via a GUI), and to provide help text. The text provided in each case should reflect the expected default value of the toggle option, which may be the opposite of what the name implies. For example, if set to "Y" by default, then the command line option would typically be -noFlag where Flag is the qualifier. If set to "N" by default, then the default action may be the opposite of what the information or help text implies. If the value is calculated, the user may need some extra guidance.

name: "string" ("Ehum.cut"). Individual codon data definitions can set their own default codon usage tables with the name: attribute. Alternatively, this can be set via the global attribute default:.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a codon usage table, the nullok: attribute must be set to "Y". In such cases the codon usage file might not be specified (in the ACD file or on the command line) for the data definition. This might occur when the codon usage table is only required by the application under certain circumstances.

name: "string" (""). Individual cpdb inputs can set their own default names with the name: attribute which in the current version has the same effect as setting the default: global attribute.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without clean PDB file input, the nullok: attribute must be set to "Y". In such cases a clean coordinate file might not be specified (in the ACD file or on the command line) for the data definition. This might occur when the file is only required by the application under certain circumstances.

name: "string" (""). Base name of the default datafile.

extension: "string" (""). File extension of the default datafile.

directory: "string" (""). The EMBOSS data subdirectory to be searched.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a datafile, the nullok: attribute must be set to "Y". This allows a default value to be omitted, or -noFlag (where Flag is the name of the definition), to be specified on the command line.

extension: "string" (""). The file extension for all files read from the directory. Files with other extensions will not be read

fullpath: "boolean" ("N"). If set to "Y" will interpret the specified directory as a full path rather than a relative path.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a directory the nullok: attribute must be set to "Y". In such cases a default directory might not be set, or -noFlag, where Flag is the name of the data definition flag, might be given on the command line.

nulldefault: "boolean" ("N"). By default, names for files in the directory are constructed from the path and extension as described above. The nulldefault: attribute overrides the default name generation, and uses an empty string (no directory) by default. This is useful for programs which only occasionally require a directory. If an empty string is specified for the directory on the command line, the default name generation will be used. In combination with the nullok:, this allows qualifiers to be null by default, and turned on from the command line.

extension: "string" (""). The extension for all files read from the directories. Files with other extensions will not be read.

fullpath: "boolean" ("N"). If set to "Y" will interpret the given path as a full rather than a relative path specification.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a directory the nullok: attribute must be set to "Y". In such cases a default directory might not be set, or -noFlag, where Flag is the name of the data definition flag, might be given on the command line.

length: "integer" ("0"). The number of state values (the length of the discrete characters string) in each set

size: "integer" ("1"). The number of sets of values (usually 1) but some programs will accept multiple sets.

characters: "string" ("01"). Defines which discrete state characters can be specified. This is defined as a string containing all possible characters.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a discretestates file, the nullok: attribute must be set to "Y". This allows the application to run without a default value or to be run with -noFlag (where Flag is the name of the data definition) on the command line.

size: "integer" ("1"). The number of rows in the distance matrix.

missval: "boolean" ("N"). If set to "Y" means the matrix can have missing values.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a distance matrix file, the nullok: attribute must be set to "Y". This allows the application to run without a default value or to be run with -noFlag (where Flag is the data definition flag) on the command line.

type: "string" (""). Whether the feature input is "protein" or "nucleotide". There is a default based on the type of any input sequence, but a value should always be specified.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without features input, the nullok: attribute must be set to "Y". This allows the application to run without a default value or to be run with -noFlag (where Flag is the data definition flag) on the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a filelist input, the nullok: attribute must be set to "Y". This specifies that a missing input file is acceptable to the application, and that -noFlag (where Flag is the data definition flag) can be used on the command line.

length: "integer" ("0"). Defines the number of loci (or values) in the frequencies file.

size: "integer" ("1"). The number of sets of values, usually 1 but some programs will accept multiple sets.

continuous: "boolean" ("N"). Specifies a frequencies file with continuous character data values.

genedata: "boolean" ("N"). Specifies a frequencies file with genetic locus data values.

within: "boolean" ("N"). Specifies a frequencies file with continuous data for multiple individuals (additional values on each line).

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a frequencies file, the nullok: attribute must be set to "Y". This allows the application to be run without a default value or with -noFlag (where Flag is the of the data definition flag) on the command line.

nullok: "boolean" ("N"). Specifies that a missing input file is acceptable to the application. The application can then run without a default value or with -noFlag (where Flag is the name of the data definition) on the command line.

directory: "@(value:ENVARNAME". Specifies a directory in which to search for the file. The directory is given by the environment variable ENVARNAME, which is resolved first as EMBOSS_ENVARNAME (in emboss.default or set by a setenv) call. It then checks for ENVARNAME (set using setenv). If an explicit path is given in the filename by the user, the directory is ignored.

protein: "boolean" ("Y"). If set to "Y" will specify that the scoring matrix is a protein matrix. If not set the matrix is presumed to be for nucleic acids.

pname: "string" ("EBLOSUM62"). Defines the default protein matrix to use. The system default is EBLOSUM62 for protein matrices.

nname: "string" ("EDNAFULL"). Defines the default nucleotide matrix to use. The system default is EDNAFULL for nucleotide matrices.

protein: "boolean" ("Y"). If set to "Y" will specify that the scoring matrix is a protein matrix. If not set the matrix is presumed to be for nucleic acids.

pname: "string" ("EBLOSUM62"). Defines the default protein matrix to use. The system default is EBLOSUM62 for protein matrices.

nname: "string" ("EDNAFULL"). Defines the default nucleotide matrix to use. The system default is EDNAFULL for nucleotide matrices.

length: "integer" ("0"). The number of values in the properties file.

size: "integer" ("1"). The number of sets of values, usually 1 but some programs will accept multiple sets.

characters: "string" (""). Defines which property characters can be specified. This is defined as a string containing all possible characters.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without a properties file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nullok: "boolean" ("N"). Used to set defaults for individual scop inputs and has the same effect as setting the default: attribute.

type: "string" (""). Forces the sequence to be of the given type. By default any sequence type is accepted. Ideally the type: attribute will always be set so that the accepted input sequence type is clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

features: "boolean" ("N"). If the features: attribute is set, the sequence input will include feature information either in the same file (if the sequence format supports it) or in a separate file, which by default is in GFF format.

entry: "boolean" ("N"). When set, the sequence input will include the full original text of the input sequence or database entry.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without sequence input, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

type: "string" (""). Forces the sequence(s) to be of the given type. By default any sequence type is accepted. The type: attribute is normally set so that the accepted input sequence type is clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

features: "boolean" ("N"). If the features: attribute is set, the sequence input will include feature information either in the same file (if the sequence format supports it) or in a separate file (by default in GFF format).

entry: "boolean" ("N"). If set, the sequence input will include the full original text of the input sequence or database entry.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without sequence input, the nullok: must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

minseqs: "integer" ("1"). Minimum number of sequences to be read. By default, a minimum of one sequence is acceptable.

maxseqs: "integer" ("INT_MAX"). Maximum number of sequences to be read. By default, there is no maximum.

type: "string" (""). Forces the sequence set to be of the given type. By default any sequence type is accepted. Ideally the type: attribute will always be set so that the accepted input sequence type is always clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

aligned: "boolean" ("N"). If set, specifies that all sequences in the input are expected to be aligned. If false then the sequences are assumed to be unaligned, and are simply read into memory together for processing. We recommend always defining the aligned: attribute so that the nature of the sequence set is clearly defined.

features: "boolean" ("N"). If the features: attribute is set, the sequence input will include feature information either in the same file (if the sequence format supports it) or in a separate file (by default in GFF format).

entry: "boolean" ("N"). If set, the sequence input will include the full original text of the input sequence or database entry.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without sequence input, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no sequence input) as the default for programs where sequence input is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

minseqs: "integer" ("1"). Minimum number of sequences to be read. By default, a minimum of one sequence is acceptable.

maxseqs: "integer" ("INT_MAX"). Maximum number of sequences to be read. By default, there is no maximum.

type: "string" (""). Forces the sequence set(s) to be of the given type. By default any sequence type is accepted. Ideally the type: attribute will be set so that the accepted input sequence type is clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

aligned: "boolean" ("N"). If true, it specifies that all sequences in the input are expected to be aligned. If false then the sequences are assumed to be unaligned, and are simply read into memory together for processing. Ideally the aligned: attribute should always be set so that the nature of the sequence set is clearly defined.

features: "boolean" ("N"). If set, will make the sequence input include feature information either in the same file (if the sequence format supports it) or in a separate file (by default in GFF format).

entry: "boolean" ("N"). If set, the sequence input will include the full original text of the input sequence or database entry.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without sequence input, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no sequence input) as the default for programs where sequence input is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

minsets: "integer" ("1"). Minimum number of sequence sets to be read. By default, a minimum of one sequence set is acceptable.

maxsets: "integer" ("INT_MAX"). Maximum number of sequence sets to be read. By default, there is no maximum (other than system-imposed limits on the size of an integer).

minseqs: "integer" ("1"). Minimum number of sequences to be read. By default, a minimum of one sequence is acceptable.

maxseqs: "integer" ("INT_MAX"). Maximum number of sequences to be read. By default, there is no maximum.

size: "integer" ("0"). The number of trees in the input file. Some can only accept a single tree so the value should be set to "1" for these. A value of "0" means that any number of trees is acceptable.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without tree input, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

minseqs: "integer" ("1"). The minimum number of sequences that are expected in the output alignment.

The minseqs: and maxseqs: attributes can be used to validate application output, for example, when selecting formats on the command line with the -aformat qualifier.

maxseqs: "integer" ("INT_MAX"). The maximum number of sequences that are expected in the output alignment.

The minseqs: and maxseqs: attributes can be used to validate application output, for example, when selecting formats on the command line with the -aformat qualifier.

multiple: "boolean" ("N"). Should be set to "Y" if the output can contain more than one alignment from the same input.

type: The sequence type. Although this will default to the type of the first output sequence, it is recommended that a value is always defined to make the output sequence type clear.

taglist: "string" (""). Defines additional tags to be reported from the internal feature table for the aligned sequences. The tag names and types must match the source code of the application. Each tag is in the format type:tagname[=columnname] for example int:length or string:gc=GC%

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating alignment output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no alignment file) as the default for programs where an alignment file is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead.

name: "string" (""). Base name of output file name. Use of -ofname (see below) is preferred.

extension: "string" (""). Extension of output file name. Use of -offormat (see below) is preferred.

type: "string" (""). Defines whether the feature output is "protein" or "nucleotide". There is a default based on the type of any input sequence, but a value should always be specified.

multiple: "boolean" ("N"). Should be set to "Y" if the feature annotation is for multiple sequences.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating feature output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no feature output) as the default for programs where feature output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

name: "string" (""). Base name of output file name.

extension: "string" (""). Extension of output file name.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating codon output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

extension: "string" (""). Extension of output file name. The extension: attribute will default to the output file format.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating coordinate file output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

type: "string" (""). Defines the output data type. It is recommended that a value is always defined to make the output data type clear.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating formatted data output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

fullpath: "boolean" ("N"). If set to "Y" requires the path to be specified in full when passed to the program, although the user may provide a path from the current working directory.

extension: "string" (""). The default extension for all files written to the directory.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without an output directory, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an output file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating a distance matrix file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an output frequencies file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

name: "string" (""). Base name of output file name. By default, any input file or sequence name will be used. If there is no input file processed so far, the default name is "outfile".

extension: "string" (""). Extension of output file name.

append: "boolean" ("N"). If set, specifies that output is appended to the end of an existing output file. By default the output file will be overwritten.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an output file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no output file) as the default for programs where an output file is only occasionally required. Examples include programs where the original output format is available, usually for users that still require it for parsing in automated scripts. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

The knowntype: global attribute (Section A.4, “Global Attributes”) should always be defined. If the output is not of any of the standard EMBOSS known types, ApplicationName output is the recommended value.

name: "string" (""). Base name of output file name. By default, any input file or sequence name will be used. If there is no input file processed so far, the default name is "outfile".

extension: "string" (""). Extension of output file name.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an output file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no output file) as the default for programs where an output file is only occasionally required. Examples include programs where the original output format is available, usually for users that still require it for parsing in automated scripts. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

The knowntype: global attribute (Section A.4, “Global Attributes”) should always be defined. If the output is not of any of the standard EMBOSS known types (Section A.4, “Global Attributes”, "ApplicationName output" is the recommended value.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an matrix file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an matrix file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating a properties file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating an output file, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

name: "string" (""). Base name of output file name.

extension: "string" (""). Extension of output file name.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating a phylogenetic tree, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no data output) as the default for programs where data output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

multiple: "boolean" ("N"). Should be set to "Y" if the output can contain more than one report from the same input.

precision: "integer" ("3"). The floating point precision of any reported score values. For integer score values this can be set to "0".

type: "string" (""). Where the report format is one of the standard feature table formats (see the EMBOSS Users Guide), the type: attribute defines whether the report output is "protein" or "nucleotide". There is a default based on the type of any input sequence, but a value should always be specified.

taglist: "string" (""). Defines the additional tags to be reported from the internal feature table. The tag names and types must match the source code of the application. Each tag is in the format type:tagname[=columnname] for example int:length or string:gc=GC%.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating report output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no report output) as the default for programs where report output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

name: "string" (""). Base name of output file name.

extension: "string" (""). Extension of output file name.

features: "boolean" ("N"). If set, the sequence output will include feature information either in the same file (if the sequence format supports it) or in a separate file (by default in GFF format).

type: "string" (""). The output sequence type. Although this will default to the type of the first output sequence, it is recommended that a value is always defined to make the output sequence type clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating sequence output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no sequence output) as the default for programs where sequence output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

name: "string" (""). Base name of output file name.

extension: "string" (""). Extension of output file name.

features: "boolean" ("N"). If set, the sequence output will include feature information either in the same file (if the sequence format supports it) or in a separate file (by default in GFF format).

type: "string" (""). The output sequence type. Although this will default to the type of the first output sequence, it is recommended that a value is always defined to make the output sequence type clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

minseqs: "integer" ("1"). The minimum number of sequences that are expected in the output file.

maxseqs: "integer" ("INT_MAX"). The maximum number of sequences that are expected in the output file.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating sequence output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no sequence output) as the default for programs where sequence output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

name: "string" (""). Base name of output file name.

extension: "string" (""). Extension of output file name.

features: "boolean" ("N"). If set, the sequence output will include feature information either in the same file (if the sequence format supports it) or in a separate file (by default in GFF format).

type: "string" (""). Output sequence type. Although this will default to the type of the first output sequence, it is recommended that a value is always defined to make the output sequence type clear. The sequence type must be a standard sequence type (Section A.7, “Sequence Types”).

minseqs: "integer" ("1"). The minimum number of sequences that are expected in the output file.

maxseqs: "integer" ("INT_MAX"). The maximum number of sequences that are expected in the output file.

aligned: "boolean" ("N"). If true, specifies that all sequences in the output are expected to be aligned. If false then the sequences are assumed to be unaligned. We recommend always defining the aligned: attribute so that the nature of the sequence set is clearly defined.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating sequence output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no sequence output) as the default for programs where sequence output is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead. In combination with the nullok: and missing: attributes, this allows qualifiers to be null by default, and turned on from the command line.

values: "string" (""). A string containing a list of option labels and descriptions which define the options the user can choose from. The delimiter: and codedelimiter: attributes specify how to parse this string into individual list items.

delimiter: "string" (";"). The character used in the values: string to separate list items. Defaults to a semi-colon (;).

codedelimiter: "string" (":"). The character used in the values: string to separate option labels from their descriptions. Defaults to a colon :).

minimum: "integer" ("1"). The minimum number of selections required. By default 1 selection is required.

maximum: "integer" ("1"). The maximum number of selections allowed. By default exactly 1 selection is required. A higher value allows multiple selections.

trueminimum: "boolean" ("N"). Used for calculated values of minimum: and maximum:. By default the minimum value is used if the minimum and maximum values overlap.

failrange: "boolean" ("Y"). Used for calculated values of minimum: and maximum:. By default the application fails if the calculated ranges overlap.

rangemessage: "string" (""). Used for calculated values of minimum: and maximum:. Failure message to use if calculated ranges overlap.

header: "string" (""). Text that is displayed to the user above the list of options.

button: "boolean" ("N"). Provided for interface developers. It has a boolean value used to suggest whether a list is best represented as checkboxes or radio buttons in an interface (value of "Y") or if a text box should be used to enter a value ("N").

casesensitive: "boolean" ("N"). Defines whether user input must match the exact case of the list item. Regardless of the case used by the user, the value of the parameter will be exactly what the corresponding list value is.

values: "string" (""). A string containing a list of option descriptions which define the options the user can choose from. The delimiter: attribute specifies how to parse this string into individual selection list items.

delimiter: "string" (":"). The character used in the values: string to separate list items. Defaults to a semi-colon (;).

minimum: "integer" ("1"). The minimum number of selections required. By default 1 selection is required.

maximum: "integer" ("1"). The maximum number of selections allowed. By default exactly 1 selection is required. A higher value allows multiple selections.

trueminimum: "boolean" ("N"). Used for calculated values of minimum: and maximum:. By default the minimum value is used if the minimum and maximum values overlap.

failrange: "boolean" ("Y"). Used for calculated values of minimum: and maximum:. By default the application fails if the calculated ranges overlap.

rangemessage: "string" (""). Used for calculated values of minimum: and maximum:. Failure message to use if calculated ranges overlap.

header: "string" (""). Text that is displayed to the user above the list of options.

button: "boolean" ("N"). Provided for interface developers. It has a boolean value used to suggest whether a list is best represented as checkboxes or radio buttons in an interface (value of "Y") or if a text box should be used to enter a value ("N").

casesensitive: "boolean" ("N"). Defines whether the input must match the exact case of the list item. Regardless of the case used by the user, the value of the parameter will be exactly what the corresponding list value is.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating graphical output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). Overrides the default name generation, and uses an empty string (no graph) as the default for programs where a graph is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead.

multiple: "integer" ("1"). The multiple: attribute specifies the number of multiple XY graphs in a single output. The default value is 1, but any integer value may be defined in the ACD file.

nullok: "boolean" ("N"). If the application can accept a null value for this definition and can run without generating graphical output, the nullok: attribute must be set to "Y". This allows a default value to be omitted or the application to be run with -noFlag on the command line (where Flag is the data definition flag).

nulldefault: "boolean" ("N"). The nulldefault: attribute overrides the default name generation, and uses an empty string (no graph) as the default for programs where a graph is only occasionally required. If an empty string is specified on the command line, the standard default value will be generated instead.