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Backport new WDL test cases from GATK. (#171)
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cmnbroad authored Sep 23, 2020
1 parent d150508 commit 2a4e57c
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Original file line number Diff line number Diff line change
Expand Up @@ -37,72 +37,206 @@ public class TestWDLTool {
public static final String GROUP_NAME = "WDL feature group name";

@PositionalArguments(doc = "Positional args doc")
@WorkflowInput(requiredCompanions ={"posDictionary", "posIndex"}, localizationOptional = true)
@WorkflowInput(requiredCompanions={"posDictionary", "posIndex"}, localizationOptional = true)
public List<File> positionalListFileInput;

// required Files
@Argument(fullName = "requiredScalarFileInput",
shortName = "requiredScalarFileInput",
doc = "requiredScalarFileInput doc",
// required input Files

@Argument(fullName = "requiredScalarFileInputNoCompanions",
shortName = "requiredScalarFileInputNoCompanions",
doc = "requiredScalarFileInputNoCompanions doc",
optional = false)
@WorkflowInput(requiredCompanions = {"requiredScalarFileInputDictionary", "requiredScalarFileInputIndex"},
optionalCompanions = {"requiredScalarFileInputOptionalCompanion"},
localizationOptional = true)
public File requiredScalarFileInput;

@Argument(fullName = "requiredListFileInput",
shortName = "requiredListFileInput",
doc = "requiredListFileInput doc",
@WorkflowInput
public File requiredScalarFileInputNoCompanions;

@Argument(fullName = "requiredScalarFileInputRequiredCompanions",
shortName = "requiredScalarFileInputRequiredCompanions",
doc = "requiredScalarFileInputRequiredCompanions doc",
optional = false)
@WorkflowInput(requiredCompanions ={"requiredListFileInputDictionary", "requiredListFileInputIndex"})
public List<File> requiredListFileInput;
@WorkflowInput(requiredCompanions={"requiredScalarFileInputRequiredCompanionsDictionary", "requiredScalarFileInputRequiredCompanionsIndex"}, localizationOptional = true)
public File requiredScalarFileInputRequiredCompanions;

// outputs
@Argument(fullName = "requiredScalarFileOutput",
shortName = "requiredScalarFileOutput",
doc = "requiredScalarFileOutput doc",
@Argument(fullName = "requiredScalarFileInputOptionalCompanions",
shortName = "requiredScalarFileInputOptionalCompanions",
doc = "requiredScalarFileInputOptionalCompanions doc",
optional = false)
@WorkflowOutput(
requiredCompanions = {"requiredScalarFileOutputDictionary", "requiredScalarFileOutputIndex"},
optionalCompanions = {"requiredScalarFileOutputOptionalCompanion"})
public File requiredScalarFileOutput;
@WorkflowInput(optionalCompanions={"requiredScalarFileInputOptionalCompanionsDictionary", "requiredScalarFileInputOptionalCompanionsIndex"}, localizationOptional = true)
public File requiredScalarFileInputOptionalCompanions;

@Argument(fullName = "requiredListFileInputNoCompanions",
shortName = "requiredListFileInputNoCompanions",
doc = "requiredListFileInputNoCompanions doc",
optional = false)
@WorkflowInput
public List<File> requiredListFileInputNoCompanions;

@Argument(fullName = "requiredListFileInputRequiredCompanions",
shortName = "requiredListFileInputRequiredCompanions",
doc = "requiredListFileInputRequiredCompanions doc",
optional = false)
@WorkflowInput(requiredCompanions={"requiredListFileInputRequiredCompanionsDictionary", "requiredListFileInputRequiredCompanionsIndex"}, localizationOptional = true)
public List<File> requiredListFileInputRequiredCompanions;

@Argument(fullName = "requiredListFileInputOptionalCompanions",
shortName = "requiredListFileInputOptionalCompanions",
doc = "requiredListFileInputOptionalCompanions doc",
optional = false)
@WorkflowInput(optionalCompanions={"requiredListFileInputOptionalCompanionsDictionary", "requiredListFileInputOptionalCompanionsIndex"}, localizationOptional = true)
public List<File> requiredListFileInputOptionalCompanions;

@Argument(fullName = "requiredListFileInputMixedCompanions",
shortName = "requiredListFileInputMixedCompanions",
doc = "requiredListFileInputMixedCompanions doc",
optional = false)
@WorkflowInput(
requiredCompanions = {"requiredListFileInputMixedCompanionsRequired"},
optionalCompanions = {"requiredListFileInputMixedCompanionsOptional"})
public List<File> requiredListFileInputMixedCompanions;

@Argument(fullName = "requiredListFileOutput",
shortName = "requiredListFileOutput",
doc = "requiredListFileOutput doc",
// required output Files

@Argument(fullName = "requiredScalarFileOutputNoCompanions",
shortName = "requiredScalarFileOutputNoCompanions",
doc = "requiredScalarFileOutputNoCompanions doc",
optional = false)
@WorkflowOutput
public File requiredScalarFileOutputNoCompanions;

@Argument(fullName = "requiredScalarFileOutputRequiredCompanions",
shortName = "requiredScalarFileOutputRequiredCompanions",
doc = "requiredScalarFileOutputRequiredCompanions doc",
optional = false)
@WorkflowOutput(requiredCompanions ={"requiredListFileOutputDictionary", "requiredListFileOutputIndex"})
public List<File> requiredListFileOutput;
@WorkflowOutput(requiredCompanions={"requiredScalarFileOutputRequiredCompanionsDictionary", "requiredScalarFileOutputRequiredCompanionsIndex"})
public File requiredScalarFileOutputRequiredCompanions;

@Argument(fullName = "requiredScalarFileOutputOptionalCompanions",
shortName = "requiredScalarFileOutputOptionalCompanions",
doc = "requiredScalarFileOutputOptionalCompanions doc",
optional = false)
@WorkflowOutput(optionalCompanions={"requiredScalarFileOutputOptionalCompanionsDictionary", "requiredScalarFileOutputOptionalCompanionsIndex"})
public File requiredScalarFileOutputOptionalCompanions;

@Argument(fullName = "requiredListFileOutputNoCompanions",
shortName = "requiredListFileOutputNoCompanions",
doc = "requiredListFileOutputNoCompanions doc",
optional = false)
@WorkflowOutput
public List<File> requiredListFileOutputNoCompanions;

// optional Files
@Argument(fullName = "optionalScalarFileInput",
shortName = "optionalScalarFileInput",
doc = "optionalScalarFileInput doc",
@Argument(fullName = "requiredListFileOutputRequiredCompanions",
shortName = "requiredListFileOutputRequiredCompanions",
doc = "requiredListFileOutputRequiredCompanions doc",
optional = false)
@WorkflowOutput(requiredCompanions={"requiredListFileOutputRequiredCompanionsDictionary", "requiredListFileOutputRequiredCompanionsIndex"})
public List<File> requiredListFileOutputRequiredCompanions;

@Argument(fullName = "requiredListFileOutputOptionalCompanions",
shortName = "requiredListFileOutputOptionalCompanions",
doc = "requiredListFileOutputOptionalCompanions doc",
optional = false)
@WorkflowOutput(optionalCompanions={"requiredListFileOutputOptionalCompanionsDictionary", "requiredListFileOutputOptionalCompanionsIndex"})
public List<File> requiredListFileOutputOptionalCompanions;

@Argument(fullName = "requiredListFileOutputMixedCompanions",
shortName = "requiredListFileOutputMixedCompanions",
doc = "requiredListFileOutputMixedCompanions doc",
optional = false)
@WorkflowOutput(
requiredCompanions = {"requiredListFileOutputMixedCompanionsRequired"},
optionalCompanions = {"requiredListFileOutputMixedCompanionsOptional"})
public List<File> requiredListFileOutputMixedCompanions;

// optional input Files

@Argument(fullName = "optionalScalarFileInputNoCompanions",
shortName = "optionalScalarFileInputNoCompanions",
doc = "optionalScalarFileInputNoCompanions doc",
optional = true)
@WorkflowInput(requiredCompanions ={"optionalScalarFileInputDictionary", "optionalScalarFileInputIndex"})
public File optionalScalarFileInput;
@WorkflowInput
public File optionalScalarFileInputNoCompanions;

@Argument(fullName = "optionalListFileInput",
shortName = "optionalListFileInput",
doc = "optionalListFileInput doc",
@Argument(fullName = "optionalScalarFileInputOptionalCompanions",
shortName = "optionalScalarFileInputOptionalCompanions",
doc = "optionalScalarFileInputOptionalCompanions doc",
optional = true)
@WorkflowInput(requiredCompanions ={"optionalListFileInputDictionary", "optionalListFileInputIndex"})
public List<File> optionalListFileInput;
@WorkflowInput(optionalCompanions={"optionalScalarFileInputOptionalCompanionsDictionary", "optionalScalarFileInputOptionalCompanionsIndex"})
public File optionalScalarFileInputOptionalCompanions;

@Argument(fullName = "optionaldScalarFileOutput",
shortName = "optionalScalarFileOutput",
doc = "optionalScalarFileOutput doc",
@Argument(fullName = "optionalScalarFileInputRequiredCompanions",
shortName = "optionalScalarFileInputRequiredCompanions",
doc = "optionalScalarFileInputRequiredCompanions doc",
optional = true)
@WorkflowOutput(requiredCompanions ={"optionalScalarFileOutputDictionary", "optionalScalarFileOutputIndex"})
public File optionalScalarFileOutput;
@WorkflowInput(requiredCompanions={"optionalScalarFileInputRequiredCompanionsDictionary", "optionalScalarFileInputRequiredCompanionsIndex"})
public File optionalScalarFileInputRequiredCompanions;

@Argument(fullName = "optionaldListFileOutput",
shortName = "optionalListFileOutput",
doc = "optionalListFileOutput doc",
@Argument(fullName = "optionalListFileInputNoCompanions",
shortName = "optionalListFileInputNoCompanions",
doc = "optionalListFileInputNoCompanions doc",
optional = true)
@WorkflowOutput(requiredCompanions ={"optionalListFileOutputDictionary", "optionalListFileOutputIndex"})
public List<File> optionalListFileOutput;
@WorkflowInput
public List<File> optionalListFileInputNoCompanions;

@Argument(fullName = "optionalListFileInputRequiredCompanions",
shortName = "optionalListFileInputRequiredCompanions",
doc = "optionalListFileInputRequiredCompanions doc",
optional = true)
@WorkflowInput(requiredCompanions={"optionalListFileInputRequiredCompanionsDictionary", "optionalListFileInputRequiredCompanionsIndex"})
public List<File> optionalListFileInputRequiredCompanions;

@Argument(fullName = "optionalListFileInputOptionalCompanions",
shortName = "optionalListFileInputOptionalCompanions",
doc = "optionalListFileInputOptionalCompanions doc",
optional = true)
@WorkflowInput(optionalCompanions={"optionalListFileInputOptionalCompanionsDictionary", "optionalListFileInputOptionalCompanionsIndex"})
public List<File> optionalListFileInputOptionalCompanions;

@Argument(fullName = "optionalListFileInputMixedCompanions",
shortName = "optionalListFileInputMixedCompanions",
doc = "optionalListFileInputMixedCompanions doc",
optional = true)
@WorkflowInput(
requiredCompanions = {"optionalListFileInputMixedCompanionsRequired"},
optionalCompanions = {"optionalListFileInputMixedCompanionsOptional"})
public List<File> optionalListFileInputMixedCompanions;

// optional output Files

@Argument(fullName = "optionalScalarFileOutputNoCompanions",
shortName = "optionalScalarFileOutputNoCompanions",
doc = "optionalScalarFileOutputNoCompanions doc",
optional = true)
@WorkflowOutput
public File optionalScalarFileOutputNoCompanions;

@Argument(fullName = "optionalScalarFileOutputRequiredCompanions",
shortName = "optionalScalarFileOutputRequiredCompanions",
doc = "optionalScalarFileOutputRequiredCompanions doc",
optional = true)
@WorkflowOutput(requiredCompanions={"optionalScalarFileOutputRequiredCompanionsDictionary", "optionalScalarFileOutputRequiredCompanionsIndex"})
public File optionalScalarFileOutputRequiredCompanions;

@Argument(fullName = "optionalScalarFileOutputOptionalCompanions",
shortName = "optionalScalarFileOutputOptionalCompanions",
doc = "optionalScalarFileOutputOptionalCompanions doc",
optional = true)
@WorkflowOutput(requiredCompanions={"optionalScalarFileOutputOptionalCompanionsDictionary", "optionalScalarFileOutputOptionalCompanionsIndex"})
public File optionalScalarFileOutputOptionalCompanions;

@Argument(fullName = "optionalListFileOutputRequiredCompanions",
shortName = "optionalListFileOutputRequiredCompanions",
doc = "optionalListFileOutputRequiredCompanions doc",
optional = true)
@WorkflowOutput(requiredCompanions={"optionalListFileOutputRequiredCompanionsDictionary", "optionalListFileOutputRequiredCompanionsIndex"})
public List<File> optionalListFileOutputRequiredCompanions;

@Argument(fullName = "optionalListFileOutputMixedCompanions",
shortName = "optionalListFileOutputMixedCompanions",
doc = "optionalListFileOutputMixedCompanions doc",
optional = true)
@WorkflowOutput(
requiredCompanions = {"optionalListFileOutputMixedCompanionsRequired"},
optionalCompanions = {"optionalListFileOutputMixedCompanionsOptional"})
public List<File> optionalListFileOutputMixedCompanions;

// non-File types

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