Creating Parameters

Parameters are always a list, consisting of zero to three items. Parameters with three items are generally options that will be visible at the command line.

Zero/One Item Lists

Empty lists followed by a list of one item indicates a section break

[],
['Options'],

At the command line it results in a section break like so:

-v, --verbose         Produce more verbose output

Options:
  --mult [MULT]         Testing mult. (Default: [10]) [Required]

Two Item Lists

Two item lists are aliases for flags/boolean options for backwards compatability. Use them identically to three item lists without the third section.

Three Item Lists

Three item lists are generally inclusive of all option types.

['int', 'An integer parameter', {'required': True, 'validate':'Int', 'default': 10}],

• The first parameter is the name, visible at the command line. It can optionally contain a POSIX style short option (one character), separated by a pipe.

# Python
['int|i', 'An integer parameter', {'required': True, 'validate':'Int', 'default': 10}],

# --help
  -i [INT], --int [INT]
                          An integer parameter (Default: 10) [Required]

• The second parameter provides a description of the parameter, as seen above. This is also used in the help text in Galaxy.
• The third parameter provides attributes that configure the parameter. The following options are always available:

Dict Key	Accepted Values	Notes
required	True/False	whether or not this parameter MUST be specified. If there is a default value, this is sufficient to pass the required requirement
validate	String	The parameter type, choose one of: Int, Float, String, Flag, File/Input, Option, GenomicTagOption
default	{any}	The default value for the parameter. Will be used in lieu of a user supplied value
multiple	True/False	Should this parameter be accepted more than one time on the command line. If this is True, and default is specified, it MUST be a list

['int', 'An integer parameter', {'required': True, 'validate':'Int', 'default': 10}],
['float', 'A float', {'required': True, 'validate': 'Float','default': 1e-4}],
['string', 'A string value', {'required': True, 'multiple': True, 'default': ['Hello', 'World'], 'validate': 'String'}],
['option', 'A selection type parameter', {'required': False,'validate':
                                          'Option','options': {'a': 'Alpha', 'b': 'Bravo'} }],
['file', 'An input file', {'required': True, 'validate':'File/Input'}],

Some parameters have additional data that can be passed to them, like numerical values have minimum and maximum values.

Validation Type	Extra Parameter	Description
Int	min	minimum value, must be greater than this value
Int	max	maximum value, must be less than this value
Float	min	minimum value, must be greater than this value
Float	max	maximum value, must be less than this value
File/Input	file_format	a list of formats, e.g. ['fastq', 'fastqsanger']
Option	options	a dict of options to enforce. At the command line these will be accepted as the key (short string), in galaxy they will be presented as the long version. For example {'a': 'Alpha', 'b': 'Bravo'}, a command line user will write --option a while a galaxy user will select Alpha.