GalaxyClasses: Galaxy Parameter Classes

Description Usage Arguments Details Examples

Description

Galaxy Parameter Classes These classes encapsulate parameters to be passed to functions exposed in Galaxy.

Usage

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Arguments

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Arguments can be a single unnamed argument, corresponding to the name of the class, e.g., integer, numeric, character, or logical.

The first argument can be missing, can be of length 1 or can be a vector of a greater length, in which case it is rendered as a dropdown (select) list.

testValues:

(optional) Either an integer(1), numeric(1), character(1), or logical(1), depending on the class used. A value to be used in functional testing (running your function with a fixed set of inputs and checking that the outputs match what is expected).

Additional parameters are as follows:

label:

A character(1). The friendly name for this parameter. By default, RGalaxy will use the parameter's name ("fooBar" is changed to "Foo Bar") if this is not supplied.

min:

(optional) An integer(1). If the parameter is integer or numeric, this specifies a minimum value for the parameter. Galaxy will not allow lower values.

max:

(optional) An integer(1). If the parameter is integer or numeric, this specifies a maximum value for the parameter. Galaxy will not allow higher values.

force_select:

(default: FALSE) A logical(1). If this parameter is a dropdown list (i.e., the first argument is a vector of length > 1), a TRUE value forces the user to select an item.

display:

(optional) A character(1). If parameter is a dropdown list, this can be set to "checkboxes" or "radio" which renders the list as a set of check boxes or radio buttons. Defaults to a drop-down menu select list.

checked:

(default: FALSE) A logical(1). Whether the rendered checkbox should be checked. Only applicable if the parameter is a logical of length < 2.

size:

(default: 60L) An integer(1) The width of the field, in characters. For character parameters only.

required:

(default: FALSE) A logical(1). Whether Galaxy will require this field be filled in.

requiredMsg:

(default: "This field is required.") A character(1) If required is TRUE, the message to display to the user when the leave the field empty.

Details

The arguments to these classes are based on http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set

Examples

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	GalaxyIntegerParam()
	GalaxyIntegerParam(1L)
	GalaxyIntegerParam(c(a=1L, b=2L)) # a select list

	GalaxyNumericParam(2.0, required=TRUE)

	GalaxyCharacterParam(c("First Choice"="one",
		"Second Choice"="two")) # a select list
	GalaxyLogicalParam(checked=TRUE)

dtenenba/RGalaxy_refactor documentation built on May 13, 2017, 8:41 a.m.