def test_commandtool_string(self):
t = CommandToolBuilder(
tool="id",
base_command=None,
inputs=[ToolInput("inp", Optional[str])],
outputs=[
ToolOutput("out", str, glob=InputSelector("inp").assert_not_null())
],
version=None,
container=None,
)
cwltool = t.translate("cwl", allow_empty_container=True, to_console=False)
print(cwltool)
def from_container(
container: str,
basecommand: List[str],
helpcommand="-h",
containersoftware="docker",
optionsmarker: Optional[str] = None,
name: Optional[str] = None,
version: Optional[str] = None,
type: ToolTemplateType = ToolTemplateType.base,
):
helpstr = get_help_from_container(
container=container,
basecommand=basecommand,
help_param=helpcommand,
containersoftware=containersoftware,
)
tooldoc, args = parse_str(helpstr, option_marker=optionsmarker)
if not version:
comps = container.split(":")
version = comps[-1] if len(comps) > 1 else "Latest"
if not version:
version = get_version_from_container(
container,
basecommand,
versionparam="-v",
containersoftware=containersoftware,
)
tool_id = name or basecommand
if isinstance(tool_id, list):
tool_id = "".join(s.title() for s in tool_id)
else:
tool_id = tool_id[0].upper() + tool_id[1:]
t = CommandToolBuilder(
tool=tool_id,
base_command=basecommand,
inputs=args,
outputs=[],
metadata=ToolMetadata(documentation=tooldoc) if tooldoc else None,
version=version,
container=container,
)
return t.translate("janis", to_console=False), helpstr