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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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