GalaxyClasses: Galaxy Parameter Classes

In dtenenba/RGalaxy_refactor: Make an R function available in the Galaxy web platform

Description

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

Usage

  GalaxyIntegerParam(...)

  GalaxyNumericParam(...)

  GalaxyCharacterParam(...)

  GalaxyLogicalParam(...)

Arguments

...

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

	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 15, 2019, 4:55 p.m.