Tool parameter sets
The parameter sets for tools are used to supply a default set of parameters that the tool should generally always use. If a pipeline is constructed using a tool, any of the tool arguments specified in the tool parameter set will be automatically applied. Any pipeline parameter set data or user defined inputs will override any of the data included in the tool parameter set. In general, tool parameter sets should only be defined when adding a tool to gkno and then are generally left alone. Parameter sets for pipelines are generally the mechanism for handling parameter sets.
The format is similar to parameter set definitions in pipeline configuration files, but is essentially similar. The json provides a list of parameter set all defined by an id, although for tools, only a default parameter set should be included (see the example below). Since tool configuration files should only contain a single default parameter set, the description is essentially moot, but is maintained for consistency with general parameter set definitions. The important section is contained in the data list. This is a list of parameters, each of which must have the following attributes:
id
A unique id for each of the defined parameters.
argument
The tool argument that the values are to be applied to. This must be either the long or short form version of an argument that is defined in the arguments section of the tool configuration file.
values
A list of values that are to be applied to the argument. This list can contain multiple values if the argument is defined as accepting multiple values, otherwise only a single value should be supplied. The value must be of the correct type and have the correct extension as defined in the argument definition.
  • "parameter sets" : [
  •   {
  •     "id" : "default",
  •     "description" : "Default parameter set requires the users input for all files.",
  •     "data" : [
  •       {
  •         "id" : "UNIQUE ID",
  •         "argument" : "VALID TOOL ARGUMENT",
  •         "values" : [LIST OF VALID VALUES]
  •       }
  •     ]
  •   }
  • ]