Modifier and Type | Interface and Description |
---|---|
static class |
JstacsTool.ResultEntry
Representation of default results.
|
Modifier and Type | Method and Description |
---|---|
JstacsTool.ResultEntry[] |
getDefaultResultInfos()
Returns
JstacsTool.ResultEntry s for the default results of this JstacsTool . |
String |
getDescription()
Returns a short description (half a sentence) on what this tool does.
|
String |
getHelpText()
Returns a detailed help text for this tool, describing the purpose of the tool, all parameters and results.
|
String |
getShortName()
Returns a name (preferably short and without spaces) for referring to this tool on the command line.
|
String |
getToolName()
Returns a descriptive, human readable name for this tool.
|
ParameterSet |
getToolParameters()
Returns the input parameters of this tool.
|
String |
getToolVersion()
Returns a descriptive, human readable version for this tool.
|
ToolResult |
run(ParameterSet parameters,
Protocol protocol,
ProgressUpdater progress,
int threads)
Runs the tool using the provided (now filled) parameters, which are in structure identical to those returned by
getToolParameters() . |
ParameterSet getToolParameters()
ToolResult run(ParameterSet parameters, Protocol protocol, ProgressUpdater progress, int threads) throws Exception
getToolParameters()
. These parameters should only be used for this run and should not affect subsequent runs of the same tool.
Protocol
and ProgressUpdater
may be used for indicating the tool's progress. Depending on the implementation and interface variant, these may be rendered differently (or not at all). This method returns all results of this tool encapsulated in a ToolResult
.parameters
- the input parametersprotocol
- the protocolprogress
- the progress updaterthreads
- the maximum number of threads that may be used for this run of the toolException
- if the tool can not be run properlyString getToolName()
String getToolVersion()
String getShortName()
String getDescription()
String getHelpText()
JstacsTool.ResultEntry[] getDefaultResultInfos()
JstacsTool.ResultEntry
s for the default results of this JstacsTool
. These results must be a subset of
all results that are returned by successful runs of this tool regardless of the input parameters.
If no results should be defined as defaults, this method may return null
.
Currently, this information is only used in the Galaxy
environment, but may be used
in the JavaFX GUI in the future for building workflows as well.
For each entry either the format or the result class should be supplied. If a format is specified this overrides the default formats
for this Result
type. Default formats for a given Result
class may be obtained from
GalaxyAdaptor.getDefaultExtension(Class)
. If this method returns null
, the output format
may be guessed by the environment (e.g., Galaxy).
Results are matched to default results by their name (AnnotatedEntity.getName()
) and result class, so the name supplied to JstacsTool.ResultEntry.JstacsTool.ResultEntry(Class, String, String)
must be identical to that of the final Result
and should be unique (otherwise only one appearance of this name will be considered a default result) within a result class.
The set of default results must always be returned in the same order.null
for no default results).