def outputs(self):
return [
ToolOutput(
"summaryMetrics",
File(),
glob=WildcardSelector(
"*.genotype_concordance_summary_metrics", select_first=True
),
),
ToolOutput(
"detailMetrics",
File(),
glob=WildcardSelector(
"*.genotype_concordance_detail_metrics", select_first=True
),
),
ToolOutput(
"contingencyMetrics",
File(),
glob=WildcardSelector(
"*.genotype_concordance_contingency_metrics", select_first=True
),
),
# ToolOutput("vcf", VcfIdx(optional=True), glob=WildcardSelector("*.vcf"))
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput(
"out",
ZipFile(),
glob=WildcardSelector(wildcard="*.zip", select_first=True),
),
ToolOutput(
"out_datafile",
File,
glob=WildcardSelector(wildcard="*/fastqc_data.txt",
select_first=True),
),
ToolOutput(
"out_html",
HtmlFile,
glob=WildcardSelector(wildcard="*.html", select_first=True),
),
ToolOutput(
"out_directory",
Directory,
selector=InputSelector("read", remove_file_extension=True) +
"_fastqc",
),
]
def outputs(self):
return [
ToolOutput(
"out_predictions",
Csv,
selector=WildcardSelector("predictions.csv",
select_first=True),
),
ToolOutput(
"out_probabilities",
Csv,
selector=WildcardSelector("probabilities.csv",
select_first=True),
),
ToolOutput(
"out_distributions",
File,
selector=WildcardSelector("distributions.png",
select_first=True),
),
ToolOutput(
"out_waterfalls",
File,
selector=WildcardSelector("waterfalls.png", select_first=True),
),
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput("pairedOut",
FastqGzPair,
glob=WildcardSelector("*trimmed.fastq.gz")),
ToolOutput("unpairedOut",
FastqGzPair,
glob=WildcardSelector("*unpaired.fastq.gz")),
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput(
"out", Array(ZipFile()), glob=WildcardSelector(wildcard="*.zip")
),
ToolOutput(
"datafile",
Array(File),
glob=WildcardSelector(wildcard="*/fastqc_data.txt"),
),
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput("vcf", Vcf(), glob=WildcardSelector("*.vcf")),
ToolOutput(
"used_options",
File(optional=True),
glob=WildcardSelector("PiscesLogs/*.json"),
),
ToolOutput(
"strandmetrics",
File(optional=True),
glob=WildcardSelector("*ReadStrandBias.txt"),
),
]
def outputs(self):
return [
ToolOutput(
"unalignedReads",
output_type=Array(FastqGz()),
glob=WildcardSelector("*/*.fastq.gz"),
),
ToolOutput("stats",
output_type=Array(File()),
glob=WildcardSelector("Stats/*")),
ToolOutput("interop",
output_type=Array(File()),
glob=WildcardSelector("InterOp/*")),
]
def test_input_value_wildcard(self):
self.assertRaises(
Exception,
wdl.get_input_value_from_potential_selector_or_generator,
value=WildcardSelector("*"),
tool_id=None,
)
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(Bam())),
ToolOutput(
"metrics",
File(),
glob=WildcardSelector("metrics.txt", select_first=True),
),
]
def outputs(self):
return [
ToolOutput(
"out",
Array(Vcf),
glob=WildcardSelector("*.refiltered.vcf"),
doc="To determine type",
)
]
def outputs(self):
return [
ToolOutput(
"meg",
TextFile(),
glob=WildcardSelector("*_CloneFinder.meg"),
doc="To determine type",
),
ToolOutput(
"clonalFractions",
TextFile(),
glob=WildcardSelector("*_CloneFinder.txt"),
doc="To determine type",
),
ToolOutput(
"summary",
TextFile(),
glob=WildcardSelector("*_summary.txt"),
doc="To determine type",
),
]
def outputs(self):
return [
ToolOutput("out", Bam(), glob=InputSelector("outputFilename")),
ToolOutput(
"temporaryOutputs",
Array(Bam(), optional=True),
glob=WildcardSelector("*.tmp.*.bam"),
doc=
"By default, any temporary files are written alongside the output file, "
"as out.bam.tmp.nnnn.bam, or if output is to standard output, "
"in the current directory as samtools.mmm.mmm.tmp.nnnn.bam.",
),
]
def outputs(self):
return [ToolOutput("out", String(), glob=WildcardSelector("*"))]
def outputs(self):
return [
ToolOutput("out", Array(File), glob=WildcardSelector("*.java"))
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput("out", FastqGzPair, glob=WildcardSelector("*.fastq.gz"))
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput(
"out", Directory, selector=WildcardSelector(".", select_first=True)
)
]
def outputs(self):
return [ToolOutput("outs", Array(File()), glob=WildcardSelector("*"))]
def outputs(self):
return [
ToolOutput("out",
File(),
glob=WildcardSelector("*.class", select_first=True))
]
from janis_core import (
CommandToolBuilder,
ToolInput,
ToolOutput,
File,
WildcardSelector,
String,
ToolArgument,
)
ToolWithOptionalWildcardOutput = CommandToolBuilder(
tool="optional_wildcard_output_tool",
version="v0.1.0",
container="ubuntu:latest",
base_command=[],
arguments=[ToolArgument("echo 1 > ", shell_quote=False)],
inputs=[
ToolInput(
"outputFilename", String(optional=True), default="out.csv", position=1
)
],
outputs=[
ToolOutput("out", File(optional=True), selector=WildcardSelector("*.txt"))
],
)