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Backport new WDL test cases from GATK. (#171)
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3 files changed

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-273
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3 files changed

+773
-273
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‎src/test/java/org/broadinstitute/barclay/help/wdltestinputs/TestWDLTool.java

Lines changed: 183 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -37,72 +37,206 @@ public class TestWDLTool {
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public static final String GROUP_NAME = "WDL feature group name";
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@PositionalArguments(doc = "Positional args doc")
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@WorkflowInput(requiredCompanions ={"posDictionary", "posIndex"}, localizationOptional = true)
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@WorkflowInput(requiredCompanions={"posDictionary", "posIndex"}, localizationOptional = true)
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public List<File> positionalListFileInput;
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// required Files
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@Argument(fullName = "requiredScalarFileInput",
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shortName = "requiredScalarFileInput",
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doc = "requiredScalarFileInput doc",
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// required input Files
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@Argument(fullName = "requiredScalarFileInputNoCompanions",
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shortName = "requiredScalarFileInputNoCompanions",
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doc = "requiredScalarFileInputNoCompanions doc",
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optional = false)
48-
@WorkflowInput(requiredCompanions = {"requiredScalarFileInputDictionary", "requiredScalarFileInputIndex"},
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optionalCompanions = {"requiredScalarFileInputOptionalCompanion"},
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localizationOptional = true)
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public File requiredScalarFileInput;
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@Argument(fullName = "requiredListFileInput",
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shortName = "requiredListFileInput",
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doc = "requiredListFileInput doc",
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@WorkflowInput
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public File requiredScalarFileInputNoCompanions;
51+
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@Argument(fullName = "requiredScalarFileInputRequiredCompanions",
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shortName = "requiredScalarFileInputRequiredCompanions",
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doc = "requiredScalarFileInputRequiredCompanions doc",
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optional = false)
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@WorkflowInput(requiredCompanions ={"requiredListFileInputDictionary", "requiredListFileInputIndex"})
58-
public List<File> requiredListFileInput;
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@WorkflowInput(requiredCompanions={"requiredScalarFileInputRequiredCompanionsDictionary", "requiredScalarFileInputRequiredCompanionsIndex"}, localizationOptional = true)
57+
public File requiredScalarFileInputRequiredCompanions;
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// outputs
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@Argument(fullName = "requiredScalarFileOutput",
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shortName = "requiredScalarFileOutput",
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doc = "requiredScalarFileOutput doc",
59+
@Argument(fullName = "requiredScalarFileInputOptionalCompanions",
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shortName = "requiredScalarFileInputOptionalCompanions",
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doc = "requiredScalarFileInputOptionalCompanions doc",
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optional = false)
65-
@WorkflowOutput(
66-
requiredCompanions = {"requiredScalarFileOutputDictionary", "requiredScalarFileOutputIndex"},
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optionalCompanions = {"requiredScalarFileOutputOptionalCompanion"})
68-
public File requiredScalarFileOutput;
63+
@WorkflowInput(optionalCompanions={"requiredScalarFileInputOptionalCompanionsDictionary", "requiredScalarFileInputOptionalCompanionsIndex"}, localizationOptional = true)
64+
public File requiredScalarFileInputOptionalCompanions;
65+
66+
@Argument(fullName = "requiredListFileInputNoCompanions",
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shortName = "requiredListFileInputNoCompanions",
68+
doc = "requiredListFileInputNoCompanions doc",
69+
optional = false)
70+
@WorkflowInput
71+
public List<File> requiredListFileInputNoCompanions;
72+
73+
@Argument(fullName = "requiredListFileInputRequiredCompanions",
74+
shortName = "requiredListFileInputRequiredCompanions",
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doc = "requiredListFileInputRequiredCompanions doc",
76+
optional = false)
77+
@WorkflowInput(requiredCompanions={"requiredListFileInputRequiredCompanionsDictionary", "requiredListFileInputRequiredCompanionsIndex"}, localizationOptional = true)
78+
public List<File> requiredListFileInputRequiredCompanions;
79+
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@Argument(fullName = "requiredListFileInputOptionalCompanions",
81+
shortName = "requiredListFileInputOptionalCompanions",
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doc = "requiredListFileInputOptionalCompanions doc",
83+
optional = false)
84+
@WorkflowInput(optionalCompanions={"requiredListFileInputOptionalCompanionsDictionary", "requiredListFileInputOptionalCompanionsIndex"}, localizationOptional = true)
85+
public List<File> requiredListFileInputOptionalCompanions;
86+
87+
@Argument(fullName = "requiredListFileInputMixedCompanions",
88+
shortName = "requiredListFileInputMixedCompanions",
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doc = "requiredListFileInputMixedCompanions doc",
90+
optional = false)
91+
@WorkflowInput(
92+
requiredCompanions = {"requiredListFileInputMixedCompanionsRequired"},
93+
optionalCompanions = {"requiredListFileInputMixedCompanionsOptional"})
94+
public List<File> requiredListFileInputMixedCompanions;
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70-
@Argument(fullName = "requiredListFileOutput",
71-
shortName = "requiredListFileOutput",
72-
doc = "requiredListFileOutput doc",
96+
// required output Files
97+
98+
@Argument(fullName = "requiredScalarFileOutputNoCompanions",
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shortName = "requiredScalarFileOutputNoCompanions",
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doc = "requiredScalarFileOutputNoCompanions doc",
101+
optional = false)
102+
@WorkflowOutput
103+
public File requiredScalarFileOutputNoCompanions;
104+
105+
@Argument(fullName = "requiredScalarFileOutputRequiredCompanions",
106+
shortName = "requiredScalarFileOutputRequiredCompanions",
107+
doc = "requiredScalarFileOutputRequiredCompanions doc",
73108
optional = false)
74-
@WorkflowOutput(requiredCompanions ={"requiredListFileOutputDictionary", "requiredListFileOutputIndex"})
75-
public List<File> requiredListFileOutput;
109+
@WorkflowOutput(requiredCompanions={"requiredScalarFileOutputRequiredCompanionsDictionary", "requiredScalarFileOutputRequiredCompanionsIndex"})
110+
public File requiredScalarFileOutputRequiredCompanions;
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112+
@Argument(fullName = "requiredScalarFileOutputOptionalCompanions",
113+
shortName = "requiredScalarFileOutputOptionalCompanions",
114+
doc = "requiredScalarFileOutputOptionalCompanions doc",
115+
optional = false)
116+
@WorkflowOutput(optionalCompanions={"requiredScalarFileOutputOptionalCompanionsDictionary", "requiredScalarFileOutputOptionalCompanionsIndex"})
117+
public File requiredScalarFileOutputOptionalCompanions;
118+
119+
@Argument(fullName = "requiredListFileOutputNoCompanions",
120+
shortName = "requiredListFileOutputNoCompanions",
121+
doc = "requiredListFileOutputNoCompanions doc",
122+
optional = false)
123+
@WorkflowOutput
124+
public List<File> requiredListFileOutputNoCompanions;
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78-
// optional Files
79-
@Argument(fullName = "optionalScalarFileInput",
80-
shortName = "optionalScalarFileInput",
81-
doc = "optionalScalarFileInput doc",
126+
@Argument(fullName = "requiredListFileOutputRequiredCompanions",
127+
shortName = "requiredListFileOutputRequiredCompanions",
128+
doc = "requiredListFileOutputRequiredCompanions doc",
129+
optional = false)
130+
@WorkflowOutput(requiredCompanions={"requiredListFileOutputRequiredCompanionsDictionary", "requiredListFileOutputRequiredCompanionsIndex"})
131+
public List<File> requiredListFileOutputRequiredCompanions;
132+
133+
@Argument(fullName = "requiredListFileOutputOptionalCompanions",
134+
shortName = "requiredListFileOutputOptionalCompanions",
135+
doc = "requiredListFileOutputOptionalCompanions doc",
136+
optional = false)
137+
@WorkflowOutput(optionalCompanions={"requiredListFileOutputOptionalCompanionsDictionary", "requiredListFileOutputOptionalCompanionsIndex"})
138+
public List<File> requiredListFileOutputOptionalCompanions;
139+
140+
@Argument(fullName = "requiredListFileOutputMixedCompanions",
141+
shortName = "requiredListFileOutputMixedCompanions",
142+
doc = "requiredListFileOutputMixedCompanions doc",
143+
optional = false)
144+
@WorkflowOutput(
145+
requiredCompanions = {"requiredListFileOutputMixedCompanionsRequired"},
146+
optionalCompanions = {"requiredListFileOutputMixedCompanionsOptional"})
147+
public List<File> requiredListFileOutputMixedCompanions;
148+
149+
// optional input Files
150+
151+
@Argument(fullName = "optionalScalarFileInputNoCompanions",
152+
shortName = "optionalScalarFileInputNoCompanions",
153+
doc = "optionalScalarFileInputNoCompanions doc",
82154
optional = true)
83-
@WorkflowInput(requiredCompanions ={"optionalScalarFileInputDictionary", "optionalScalarFileInputIndex"})
84-
public File optionalScalarFileInput;
155+
@WorkflowInput
156+
public File optionalScalarFileInputNoCompanions;
85157

86-
@Argument(fullName = "optionalListFileInput",
87-
shortName = "optionalListFileInput",
88-
doc = "optionalListFileInput doc",
158+
@Argument(fullName = "optionalScalarFileInputOptionalCompanions",
159+
shortName = "optionalScalarFileInputOptionalCompanions",
160+
doc = "optionalScalarFileInputOptionalCompanions doc",
89161
optional = true)
90-
@WorkflowInput(requiredCompanions ={"optionalListFileInputDictionary", "optionalListFileInputIndex"})
91-
public List<File> optionalListFileInput;
162+
@WorkflowInput(optionalCompanions={"optionalScalarFileInputOptionalCompanionsDictionary", "optionalScalarFileInputOptionalCompanionsIndex"})
163+
public File optionalScalarFileInputOptionalCompanions;
92164

93-
@Argument(fullName = "optionaldScalarFileOutput",
94-
shortName = "optionalScalarFileOutput",
95-
doc = "optionalScalarFileOutput doc",
165+
@Argument(fullName = "optionalScalarFileInputRequiredCompanions",
166+
shortName = "optionalScalarFileInputRequiredCompanions",
167+
doc = "optionalScalarFileInputRequiredCompanions doc",
96168
optional = true)
97-
@WorkflowOutput(requiredCompanions ={"optionalScalarFileOutputDictionary", "optionalScalarFileOutputIndex"})
98-
public File optionalScalarFileOutput;
169+
@WorkflowInput(requiredCompanions={"optionalScalarFileInputRequiredCompanionsDictionary", "optionalScalarFileInputRequiredCompanionsIndex"})
170+
public File optionalScalarFileInputRequiredCompanions;
99171

100-
@Argument(fullName = "optionaldListFileOutput",
101-
shortName = "optionalListFileOutput",
102-
doc = "optionalListFileOutput doc",
172+
@Argument(fullName = "optionalListFileInputNoCompanions",
173+
shortName = "optionalListFileInputNoCompanions",
174+
doc = "optionalListFileInputNoCompanions doc",
103175
optional = true)
104-
@WorkflowOutput(requiredCompanions ={"optionalListFileOutputDictionary", "optionalListFileOutputIndex"})
105-
public List<File> optionalListFileOutput;
176+
@WorkflowInput
177+
public List<File> optionalListFileInputNoCompanions;
178+
179+
@Argument(fullName = "optionalListFileInputRequiredCompanions",
180+
shortName = "optionalListFileInputRequiredCompanions",
181+
doc = "optionalListFileInputRequiredCompanions doc",
182+
optional = true)
183+
@WorkflowInput(requiredCompanions={"optionalListFileInputRequiredCompanionsDictionary", "optionalListFileInputRequiredCompanionsIndex"})
184+
public List<File> optionalListFileInputRequiredCompanions;
185+
186+
@Argument(fullName = "optionalListFileInputOptionalCompanions",
187+
shortName = "optionalListFileInputOptionalCompanions",
188+
doc = "optionalListFileInputOptionalCompanions doc",
189+
optional = true)
190+
@WorkflowInput(optionalCompanions={"optionalListFileInputOptionalCompanionsDictionary", "optionalListFileInputOptionalCompanionsIndex"})
191+
public List<File> optionalListFileInputOptionalCompanions;
192+
193+
@Argument(fullName = "optionalListFileInputMixedCompanions",
194+
shortName = "optionalListFileInputMixedCompanions",
195+
doc = "optionalListFileInputMixedCompanions doc",
196+
optional = true)
197+
@WorkflowInput(
198+
requiredCompanions = {"optionalListFileInputMixedCompanionsRequired"},
199+
optionalCompanions = {"optionalListFileInputMixedCompanionsOptional"})
200+
public List<File> optionalListFileInputMixedCompanions;
201+
202+
// optional output Files
203+
204+
@Argument(fullName = "optionalScalarFileOutputNoCompanions",
205+
shortName = "optionalScalarFileOutputNoCompanions",
206+
doc = "optionalScalarFileOutputNoCompanions doc",
207+
optional = true)
208+
@WorkflowOutput
209+
public File optionalScalarFileOutputNoCompanions;
210+
211+
@Argument(fullName = "optionalScalarFileOutputRequiredCompanions",
212+
shortName = "optionalScalarFileOutputRequiredCompanions",
213+
doc = "optionalScalarFileOutputRequiredCompanions doc",
214+
optional = true)
215+
@WorkflowOutput(requiredCompanions={"optionalScalarFileOutputRequiredCompanionsDictionary", "optionalScalarFileOutputRequiredCompanionsIndex"})
216+
public File optionalScalarFileOutputRequiredCompanions;
217+
218+
@Argument(fullName = "optionalScalarFileOutputOptionalCompanions",
219+
shortName = "optionalScalarFileOutputOptionalCompanions",
220+
doc = "optionalScalarFileOutputOptionalCompanions doc",
221+
optional = true)
222+
@WorkflowOutput(requiredCompanions={"optionalScalarFileOutputOptionalCompanionsDictionary", "optionalScalarFileOutputOptionalCompanionsIndex"})
223+
public File optionalScalarFileOutputOptionalCompanions;
224+
225+
@Argument(fullName = "optionalListFileOutputRequiredCompanions",
226+
shortName = "optionalListFileOutputRequiredCompanions",
227+
doc = "optionalListFileOutputRequiredCompanions doc",
228+
optional = true)
229+
@WorkflowOutput(requiredCompanions={"optionalListFileOutputRequiredCompanionsDictionary", "optionalListFileOutputRequiredCompanionsIndex"})
230+
public List<File> optionalListFileOutputRequiredCompanions;
231+
232+
@Argument(fullName = "optionalListFileOutputMixedCompanions",
233+
shortName = "optionalListFileOutputMixedCompanions",
234+
doc = "optionalListFileOutputMixedCompanions doc",
235+
optional = true)
236+
@WorkflowOutput(
237+
requiredCompanions = {"optionalListFileOutputMixedCompanionsRequired"},
238+
optionalCompanions = {"optionalListFileOutputMixedCompanionsOptional"})
239+
public List<File> optionalListFileOutputMixedCompanions;
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// non-File types
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