def outputs(self) -> List[j.ToolOutput]:
return [
j.ToolOutput(
"extended",
Csv(),
glob=j.InputSelector("reportPrefix") + ".extended.csv",
),
j.ToolOutput("summary",
Csv(),
glob=j.InputSelector("reportPrefix") +
".summary.csv"),
j.ToolOutput(
"metrics",
j.File(),
glob=j.InputSelector("reportPrefix") + ".metrics.json.gz",
),
j.ToolOutput("vcf",
VcfTabix(),
glob=j.InputSelector("reportPrefix") + ".vcf.gz"),
j.ToolOutput(
"runinfo",
JsonFile(),
glob=j.InputSelector("reportPrefix") + ".runinfo.json",
),
j.ToolOutput(
"rocOut",
j.File(),
glob=j.InputSelector("reportPrefix") + ".roc.all.csv.gz",
),
j.ToolOutput(
"indelLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.INDEL.csv.gz",
),
j.ToolOutput(
"indelPassLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.INDEL.PASS.csv.gz",
),
j.ToolOutput(
"snpLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.SNP.csv.gz",
),
j.ToolOutput(
"snpPassLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.SNP.PASS.csv.gz",
),
]
def test_csv_optional(self):
d = Csv(optional=True)
self.assertEqual("Csv(optional=True)", get_string_repr(d))
def test_csv_nooptional(self):
d = Csv(optional=False)
self.assertEqual("Csv()", get_string_repr(d))