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import pprint
from pbcommand.models.common import (
FileTypes, ResourceTypes, SymbolTypes, TaskTypes)
from pbcommand.models.parser import get_pbparser
from pbcommand.models.tool_contract import ToolDriver
def _example_options(p):
p.add_input_file_type(
FileTypes.BAM,
"ubam",
"Unaligned BAM",
"A General description of BAM")
p.add_input_file_type(
FileTypes.DS_REF,
"ref",
"Reference",
"Reference Dataset XML")
p.add_int("mytool.task_options.myoption", "myopt", 7,
"My Option", "My Option which does this and that")
p.add_str(
"mytool.task_options.myopt2",
"mylabel",
"Stuff",
"My Option name",
"My Option2 description")
p.add_output_file_type(
FileTypes.REPORT,
"rpt",
"Json Report",
"Mapping Stats Report Task",
"mapping-stats.report.json")
return p
def example_01():
driver = ToolDriver("my-exe --config")
resource_types = (ResourceTypes.TMP_DIR, ResourceTypes.LOG_FILE)
p = get_pbparser(
"pbcommand.tools.example",
"0.1.2",
"My Description",
driver,
TaskTypes.DISTRIBUTED,
SymbolTypes.MAX_NPROC,
resource_types)
return _example_options(p)
def example_02():
p = example_01()
print("Generated Manifest")
pprint.pprint(p.parsers[1].to_tool_contract())
# ipython will dump out here. with non-zero exitcode. blah...
print("Running Argparse --help")
p.parsers[0].parser.parse_args(["--help"])
return p
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