def test_commandtool_string(self):
t = CommandToolBuilder(
tool="id",
base_command=None,
inputs=[ToolInput("inp", Optional[str])],
outputs=[
ToolOutput("out", str, glob=InputSelector("inp").assert_not_null())
],
version=None,
container=None,
)
cwltool = t.translate("cwl", allow_empty_container=True, to_console=False)
print(cwltool)
def from_container(
container: str,
basecommand: List[str],
helpcommand="-h",
containersoftware="docker",
optionsmarker: Optional[str] = None,
name: Optional[str] = None,
version: Optional[str] = None,
type: ToolTemplateType = ToolTemplateType.base,
):
helpstr = get_help_from_container(
container=container,
basecommand=basecommand,
help_param=helpcommand,
containersoftware=containersoftware,
)
tooldoc, args = parse_str(helpstr, option_marker=optionsmarker)
if not version:
comps = container.split(":")
version = comps[-1] if len(comps) > 1 else "Latest"
if not version:
version = get_version_from_container(
container,
basecommand,
versionparam="-v",
containersoftware=containersoftware,
)
tool_id = name or basecommand
if isinstance(tool_id, list):
tool_id = "".join(s.title() for s in tool_id)
else:
tool_id = tool_id[0].upper() + tool_id[1:]
t = CommandToolBuilder(
tool=tool_id,
base_command=basecommand,
inputs=args,
outputs=[],
metadata=ToolMetadata(documentation=tooldoc) if tooldoc else None,
version=version,
container=container,
)
return t.translate("janis", to_console=False), helpstr
def test_create_single_file_from_operator(self):
command = CommandToolBuilder(
**self.initial_params,
files_to_create=[("my-path.txt", InputSelector("inp").contents())],
)
req = CwlTranslator.build_initial_workdir_from_tool(command).listing
self.assertEqual(1, len(req))
self.assertEqual("my-path.txt", req[0].entryname)
self.assertEqual("$(inputs.inp.contents)", req[0].entry)
def test_create_single_directory_from_selector(self):
command = CommandToolBuilder(
**self.initial_params, directories_to_create=InputSelector("name")
)
req = CwlTranslator.build_initial_workdir_from_tool(command).listing
self.assertEqual(1, len(req))
self.assertEqual(
'$({ class: "Directory", basename: inputs.name, listing: [] })', req[0]
)
def test_input_value_removing_extension(self):
clt = CommandToolBuilder(
tool="dev",
base_command="echo",
inputs=[ToolInput("inp", File(extension=".txt"))],
outputs=[ToolOutput("out", str, selector=ReadContents(Stdout()))],
version="v1.0",
container="ubuntu",
)
arg = cwl.translate_tool_argument(
ToolArgument(InputSelector("inp", remove_file_extension=True) + ".bam"),
clt,
inputs_dict={t.id(): t for t in clt.inputs()},
)
self.assertEqual(
'$((inputs.inp.basename.replace(/.txt$/, "") + ".bam"))', arg.valueFrom
)
def test_read_contents_as_int(self):
t = CommandToolBuilder(
tool="test_readcontents",
base_command=["echo", "1"],
inputs=[],
outputs=[ToolOutput("out", Float, glob=ReadContents(Stdout()).as_float())],
container=None,
version="-1",
)
translated = CwlTranslator.translate_tool_internal(
t, allow_empty_container=True
)
self.assertTrue(translated.outputs[0].outputBinding.loadContents)
self.assertEqual("float", translated.outputs[0].type)
def test_create_single_file_path_from_operator(self):
command = CommandToolBuilder(
**self.initial_params,
files_to_create=[
(
StringFormatter("{name}.txt", name=InputSelector("name")),
"this is contents",
)
],
)
req = CwlTranslator.build_initial_workdir_from_tool(command).listing
self.assertEqual(1, len(req))
self.assertIsInstance(req[0], cwlgen.Dirent)
self.assertEqual(
'$("{name}.txt".replace(/\{name\}/g, inputs.name))', req[0].entryname
)
self.assertEqual("this is contents", req[0].entry)
def test_filter_null(self):
T = CommandToolBuilder(
tool="testsingleinput",
base_command="echo",
inputs=[ToolInput("inp", str, position=0)],
outputs=[ToolOutput("out", Stdout)],
version="v1",
container=None,
)
w = WorkflowBuilder("wf")
w.input("inp", Array(Optional[str], optional=True))
w.step("stp", T(inp=FilterNullOperator(w.inp)), scatter="inp")
w.output("out", source=w.stp.out)
w_cwl = cwl.CwlTranslator().translate_workflow(w, with_container=False)[0]
self.assertEqual(2, len(w_cwl.steps))
self.assertEqual(
"_evaluate_prescatter-stp-inp/out", w_cwl.steps[1].in_[0].source
)
from janis_bioinformatics.data_types import Bam, BamBai, FastaWithIndexes, VcfTabix, Vcf
# Add tool definitions here
Gatk4BaseRecalibrator_4_1_4 = CommandToolBuilder(
tool="Gatk4BaseRecalibrator",
container="broadinstitute/gatk:4.1.4.0",
version="v4.1.4.0",
base_command=["gatk", "BaseRecalibrator"],
inputs=[
ToolInput("bam", BamBai, prefix="--input"),
ToolInput("reference", FastaWithIndexes, prefix="--reference"),
ToolInput("outputFilename",
Filename(extension=".table"),
prefix="--output"),
ToolInput("knownSites",
Array(VcfTabix),
prefix="--known-sites",
prefix_applies_to_all_elements=True),
],
outputs=[
ToolOutput("out_recalibration_report",
File,
selector=InputSelector("outputFilename"))
],
)
Gatk4ApplyBQSR_4_1_4 = CommandToolBuilder(
tool="Gatk4ApplyBqsr",
container="broadinstitute/gatk:4.1.4.0",
version="v4.1.4.0",
self.output("output_vcf", source=self.merge.output_vcf)
Gatk4MergeVcfs_4_1_4 = CommandToolBuilder(
tool="Gatk4MergeVcfs",
base_command=["gatk", "MergeVcfs"],
inputs=[
ToolInput(
"vcfs",
Array(VcfTabix),
prefix="--INPUT",
prefix_applies_to_all_elements=True,
),
ToolInput(
"output_filename",
Filename(suffix=".merged", extension=".vcf.gz"),
prefix="--OUTPUT",
),
],
outputs=[
ToolOutput("output_vcf",
VcfTabix,
glob=InputSelector("output_filename"))
],
version="4.1.4.0",
container="broadinstitute/gatk:4.1.4.0",
)
if __name__ == "__main__":
Gatk4GermlineSnpsIndels().translate("wdl")
# Gatk4MergeVcfs_4_1_4().translate("wdl")
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"))
],
)