def outputs(self): return [ ToolOutput( "out", Stdout(Bam(), stdoutname=InputSelector("outputFilename"))), ToolOutput("metrics", File(), glob=WildcardSelector("metrics.txt")), ]
def outputs(self): return [ ToolOutput( "out", Stdout(Vcf), doc= "VCF with length of the variant record added to each record", ) ]
def outputs(self): return [ ToolOutput("out", Stdout(Bam())), ToolOutput( "metrics", File(), glob=WildcardSelector("metrics.txt", select_first=True), ), ]
def outputs(self) -> List[ToolOutput]: return [ ToolOutput( "out", VcfTabix(optional=True), selector=InputSelector("outputFilename") ), ToolOutput("out_stdout", Stdout(TextFile)), ToolOutput( "out_stats", File(optional=True, extension=".html"), selector=InputSelector("statsFile"), ), ToolOutput( "out_warnings", File(optional=True, extension=".txt"), selector=InputSelector("warningFile"), ), ]
def outputs(self): return [ToolOutput("out", Stdout(Vcf), doc="VCF output")]
def outputs(self): return [ToolOutput( "out", Stdout(Vcf), doc="Filtered VCF", )]
def outputs(self) -> List[ToolOutput]: return [ToolOutput("std", Stdout())]
def outputs(self) -> List[ToolOutput]: return [ToolOutput("out", Stdout(CompressedVcf()))]
def outputs(self): return [ToolOutput("out", Stdout(TextFile))]
def outputs(self): return [ ToolOutput( "out", Stdout(Cram(), stdoutname=InputSelector("outputFilename"))) ]
def outputs(self): return [ToolOutput("out", Stdout())]
def test_stdout_normal(self): s1 = Stdout() self.assertTrue(True)
import janis_core as j from janis_core import ToolInput, ToolOutput, Int, Stdout, File from janis_unix.tools import Echo AddTwo = j.CommandToolBuilder( tool="expr", base_command=None, arguments=[j.ToolArgument("expr 2 + ", position=0, shell_quote=False)], version="dev", container="ubuntu:latest", inputs=[ ToolInput("inp", Int(), position=1) ], outputs=[ ToolOutput("out", Stdout()), ] ) w = j.WorkflowBuilder("str_to_int") w.input("str_input", str) w.step("echo", Echo(inp=w.str_input)) w.step("exp", AddTwo(inp=w.echo.out.contents().as_int())) w.output("out", source=w.exp.out) if __name__ == "__main__": w.translate("wdl")
def test_recievefromstdout_subtype(self): s1 = Stdout(FileSubclass()) s2 = File() self.assertTrue(s2.can_receive_from(s1))
def test_recievefromstdout_optional(self): s1 = Stdout() s2 = File(optional=True) self.assertTrue(s2.can_receive_from(s1))
def test_receivefromstdout_file(self): s1 = Stdout() s2 = File() self.assertTrue(s2.can_receive_from(s1))
def test_receive_from_nonfile_stdout(self): s1 = FileSubclass() s2 = Stdout(FileSubclass()) self.assertTrue(s2.can_receive_from(s1))
def test_receivefromstdout_reverse(self): s1 = File() s2 = Stdout(FileSubclass()) self.assertFalse(s2.can_receive_from(s1))