Beispiel #1
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 def outputs(self):
     return [
         ToolOutput(
             "out", Stdout(Bam(),
                           stdoutname=InputSelector("outputFilename"))),
         ToolOutput("metrics", File(),
                    glob=WildcardSelector("metrics.txt")),
     ]
Beispiel #2
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 def outputs(self):
     return [
         ToolOutput(
             "out",
             Stdout(Vcf),
             doc=
             "VCF with length of the variant record added to each record",
         )
     ]
Beispiel #3
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 def outputs(self):
     return [
         ToolOutput("out", Stdout(Bam())),
         ToolOutput(
             "metrics",
             File(),
             glob=WildcardSelector("metrics.txt", select_first=True),
         ),
     ]
Beispiel #4
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 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"),
         ),
     ]
Beispiel #5
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 def outputs(self):
     return [ToolOutput("out", Stdout(Vcf), doc="VCF output")]
Beispiel #6
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 def outputs(self):
     return [ToolOutput(
         "out",
         Stdout(Vcf),
         doc="Filtered VCF",
     )]
 def outputs(self) -> List[ToolOutput]:
     return [ToolOutput("std", Stdout())]
Beispiel #8
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 def outputs(self) -> List[ToolOutput]:
     return [ToolOutput("out", Stdout(CompressedVcf()))]
Beispiel #9
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 def outputs(self):
     return [ToolOutput("out", Stdout(TextFile))]
Beispiel #10
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 def outputs(self):
     return [
         ToolOutput(
             "out",
             Stdout(Cram(), stdoutname=InputSelector("outputFilename")))
     ]
Beispiel #11
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 def outputs(self):
     return [ToolOutput("out", Stdout())]
Beispiel #12
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 def test_stdout_normal(self):
     s1 = Stdout()
     self.assertTrue(True)
Beispiel #13
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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")
Beispiel #14
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 def test_recievefromstdout_subtype(self):
     s1 = Stdout(FileSubclass())
     s2 = File()
     self.assertTrue(s2.can_receive_from(s1))
Beispiel #15
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 def test_recievefromstdout_optional(self):
     s1 = Stdout()
     s2 = File(optional=True)
     self.assertTrue(s2.can_receive_from(s1))
Beispiel #16
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 def test_receivefromstdout_file(self):
     s1 = Stdout()
     s2 = File()
     self.assertTrue(s2.can_receive_from(s1))
Beispiel #17
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 def test_receive_from_nonfile_stdout(self):
     s1 = FileSubclass()
     s2 = Stdout(FileSubclass())
     self.assertTrue(s2.can_receive_from(s1))
Beispiel #18
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 def test_receivefromstdout_reverse(self):
     s1 = File()
     s2 = Stdout(FileSubclass())
     self.assertFalse(s2.can_receive_from(s1))