1version 1.0
2
3# Run TestWDLTool (WDL auto generated from GATK Version 1.2.3.4)
4#
5# WDL Test Tool to test WDL Generation
6#
7#  General Workflow (non-tool) Arguments
8#    dockerImage                                        Docker image for this workflow
9#    gatk                                               Location of gatk to run for this workflow
10#    memoryRequirements                                 Runtime memory requirements for this workflow
11#    diskRequirements                                   Runtime disk requirements for this workflow
12#    cpuRequirements                                    Runtime CPU count for this workflow
13#    preemptibleRequirements                            Runtime preemptible count for this workflow
14#    bootdisksizegbRequirements                         Runtime boot disk size for this workflow
15#
16#  Positional Tool Arguments
17#    positionalArgs                                     Positional args doc
18#    posDictionary                                      Companion resource for positionalArgs
19#    posIndex                                           Companion resource for positionalArgs
20#
21#  Required Tool Arguments
22#    requiredListFileInputMixedCompanions               requiredListFileInputMixedCompanions doc
23#    requiredListFileInputMixedCompanionsRequired       Companion resource for requiredListFileInputMixedCompanions
24#    requiredListFileInputMixedCompanionsOptional       Optional Companion resource for requiredListFileInputMixedCompanions
25#    requiredListFileInputNoCompanions                  requiredListFileInputNoCompanions doc
26#    requiredListFileInputOptionalCompanions            requiredListFileInputOptionalCompanions doc
27#    requiredListFileInputOptionalCompanionsDictionary  Optional Companion resource for requiredListFileInputOptionalCompanions
28#    requiredListFileInputOptionalCompanionsIndex       Optional Companion resource for requiredListFileInputOptionalCompanions
29#    requiredListFileInputRequiredCompanions            requiredListFileInputRequiredCompanions doc
30#    requiredListFileInputRequiredCompanionsDictionary  Companion resource for requiredListFileInputRequiredCompanions
31#    requiredListFileInputRequiredCompanionsIndex       Companion resource for requiredListFileInputRequiredCompanions
32#    requiredListFileOutputMixedCompanions              requiredListFileOutputMixedCompanions doc
33#    requiredListFileOutputMixedCompanionsRequired      Companion resource for requiredListFileOutputMixedCompanions
34#    requiredListFileOutputMixedCompanionsOptional      Optional Companion resource for requiredListFileOutputMixedCompanions
35#    requiredListFileOutputNoCompanions                 requiredListFileOutputNoCompanions doc
36#    requiredListFileOutputOptionalCompanions           requiredListFileOutputOptionalCompanions doc
37#    requiredListFileOutputOptionalCompanionsDictionary Optional Companion resource for requiredListFileOutputOptionalCompanions
38#    requiredListFileOutputOptionalCompanionsIndex      Optional Companion resource for requiredListFileOutputOptionalCompanions
39#    requiredListFileOutputRequiredCompanions           requiredListFileOutputRequiredCompanions doc
40#    requiredListFileOutputRequiredCompanionsDictionary Companion resource for requiredListFileOutputRequiredCompanions
41#    requiredListFileOutputRequiredCompanionsIndex      Companion resource for requiredListFileOutputRequiredCompanions
42#    requiredScalarFileInputNoCompanions                requiredScalarFileInputNoCompanions doc
43#    requiredScalarFileInputOptionalCompanions          requiredScalarFileInputOptionalCompanions doc
44#    requiredScalarFileInputOptionalCompanionsDictionary Optional Companion resource for requiredScalarFileInputOptionalCompanions
45#    requiredScalarFileInputOptionalCompanionsIndex     Optional Companion resource for requiredScalarFileInputOptionalCompanions
46#    requiredScalarFileInputRequiredCompanions          requiredScalarFileInputRequiredCompanions doc
47#    requiredScalarFileInputRequiredCompanionsDictionary Companion resource for requiredScalarFileInputRequiredCompanions
48#    requiredScalarFileInputRequiredCompanionsIndex     Companion resource for requiredScalarFileInputRequiredCompanions
49#    requiredScalarFileOutputNoCompanions               requiredScalarFileOutputNoCompanions doc
50#    requiredScalarFileOutputOptionalCompanions         requiredScalarFileOutputOptionalCompanions doc
51#    requiredScalarFileOutputOptionalCompanionsDictionary Optional Companion resource for requiredScalarFileOutputOptionalCompanions
52#    requiredScalarFileOutputOptionalCompanionsIndex    Optional Companion resource for requiredScalarFileOutputOptionalCompanions
53#    requiredScalarFileOutputRequiredCompanions         requiredScalarFileOutputRequiredCompanions doc
54#    requiredScalarFileOutputRequiredCompanionsDictionary Companion resource for requiredScalarFileOutputRequiredCompanions
55#    requiredScalarFileOutputRequiredCompanionsIndex    Companion resource for requiredScalarFileOutputRequiredCompanions
56#
57
58workflow TestWDLTool {
59
60  input {
61    #Docker to use
62    String dockerImage
63    #App location
64    String gatk
65    #Memory to use
66    String memoryRequirements
67    #Disk requirements for this workflow
68    String diskRequirements
69    #CPU requirements for this workflow
70    String cpuRequirements
71    #Preemptible requirements for this workflow
72    String preemptibleRequirements
73    #Boot disk size requirements for this workflow
74    String bootdisksizegbRequirements
75
76    # Positional Arguments
77    Array[File] positionalArgs
78    Array[File] posDictionary
79    Array[File] posIndex
80
81    # Required Arguments
82    Array[File] requiredListFileInputMixedCompanions
83    Array[File] requiredListFileInputMixedCompanionsRequired
84    Array[File]? requiredListFileInputMixedCompanionsOptional
85    Array[File] requiredListFileInputNoCompanions
86    Array[File] requiredListFileInputOptionalCompanions
87    Array[File]? requiredListFileInputOptionalCompanionsDictionary
88    Array[File]? requiredListFileInputOptionalCompanionsIndex
89    Array[File] requiredListFileInputRequiredCompanions
90    Array[File] requiredListFileInputRequiredCompanionsDictionary
91    Array[File] requiredListFileInputRequiredCompanionsIndex
92    Array[String] requiredListFileOutputMixedCompanions
93    Array[String] requiredListFileOutputMixedCompanionsRequired
94    Array[String]? requiredListFileOutputMixedCompanionsOptional
95    Array[String] requiredListFileOutputNoCompanions
96    Array[String] requiredListFileOutputOptionalCompanions
97    Array[String]? requiredListFileOutputOptionalCompanionsDictionary
98    Array[String]? requiredListFileOutputOptionalCompanionsIndex
99    Array[String] requiredListFileOutputRequiredCompanions
100    Array[String] requiredListFileOutputRequiredCompanionsDictionary
101    Array[String] requiredListFileOutputRequiredCompanionsIndex
102    File requiredScalarFileInputNoCompanions
103    File requiredScalarFileInputOptionalCompanions
104    File? requiredScalarFileInputOptionalCompanionsDictionary
105    File? requiredScalarFileInputOptionalCompanionsIndex
106    File requiredScalarFileInputRequiredCompanions
107    File requiredScalarFileInputRequiredCompanionsDictionary
108    File requiredScalarFileInputRequiredCompanionsIndex
109    String requiredScalarFileOutputNoCompanions
110    String requiredScalarFileOutputOptionalCompanions
111    String? requiredScalarFileOutputOptionalCompanionsDictionary
112    String? requiredScalarFileOutputOptionalCompanionsIndex
113    String requiredScalarFileOutputRequiredCompanions
114    String requiredScalarFileOutputRequiredCompanionsDictionary
115    String requiredScalarFileOutputRequiredCompanionsIndex
116
117  }
118
119  call TestWDLTool {
120
121    input:
122
123        #Docker
124        dockerImage                                        = dockerImage,
125        #App location
126        gatk                                               = gatk,
127        #Memory to use
128        memoryRequirements                                 = memoryRequirements,
129        #Disk requirements for this workflow
130        diskRequirements                                   = diskRequirements,
131        #CPU requirements for this workflow
132        cpuRequirements                                    = cpuRequirements,
133        #Preemptible requirements for this workflow
134        preemptibleRequirements                            = preemptibleRequirements,
135        #Boot disk size requirements for this workflow
136        bootdisksizegbRequirements                         = bootdisksizegbRequirements,
137
138
139        # Positional Arguments
140        positionalArgs                                     = positionalArgs,
141        posDictionary                                      = posDictionary,
142        posIndex                                           = posIndex,
143
144        # Required Arguments
145        requiredListFileInputMixedCompanions               = requiredListFileInputMixedCompanions,
146        requiredListFileInputMixedCompanionsRequired       = requiredListFileInputMixedCompanionsRequired,
147        requiredListFileInputMixedCompanionsOptional       = requiredListFileInputMixedCompanionsOptional,
148        requiredListFileInputNoCompanions                  = requiredListFileInputNoCompanions,
149        requiredListFileInputOptionalCompanions            = requiredListFileInputOptionalCompanions,
150        requiredListFileInputOptionalCompanionsDictionary  = requiredListFileInputOptionalCompanionsDictionary,
151        requiredListFileInputOptionalCompanionsIndex       = requiredListFileInputOptionalCompanionsIndex,
152        requiredListFileInputRequiredCompanions            = requiredListFileInputRequiredCompanions,
153        requiredListFileInputRequiredCompanionsDictionary  = requiredListFileInputRequiredCompanionsDictionary,
154        requiredListFileInputRequiredCompanionsIndex       = requiredListFileInputRequiredCompanionsIndex,
155        requiredListFileOutputMixedCompanions              = requiredListFileOutputMixedCompanions,
156        requiredListFileOutputMixedCompanionsRequired      = requiredListFileOutputMixedCompanionsRequired,
157        requiredListFileOutputMixedCompanionsOptional      = requiredListFileOutputMixedCompanionsOptional,
158        requiredListFileOutputNoCompanions                 = requiredListFileOutputNoCompanions,
159        requiredListFileOutputOptionalCompanions           = requiredListFileOutputOptionalCompanions,
160        requiredListFileOutputOptionalCompanionsDictionary = requiredListFileOutputOptionalCompanionsDictionary,
161        requiredListFileOutputOptionalCompanionsIndex      = requiredListFileOutputOptionalCompanionsIndex,
162        requiredListFileOutputRequiredCompanions           = requiredListFileOutputRequiredCompanions,
163        requiredListFileOutputRequiredCompanionsDictionary = requiredListFileOutputRequiredCompanionsDictionary,
164        requiredListFileOutputRequiredCompanionsIndex      = requiredListFileOutputRequiredCompanionsIndex,
165        requiredScalarFileInputNoCompanions                = requiredScalarFileInputNoCompanions,
166        requiredScalarFileInputOptionalCompanions          = requiredScalarFileInputOptionalCompanions,
167        requiredScalarFileInputOptionalCompanionsDictionary = requiredScalarFileInputOptionalCompanionsDictionary,
168        requiredScalarFileInputOptionalCompanionsIndex     = requiredScalarFileInputOptionalCompanionsIndex,
169        requiredScalarFileInputRequiredCompanions          = requiredScalarFileInputRequiredCompanions,
170        requiredScalarFileInputRequiredCompanionsDictionary = requiredScalarFileInputRequiredCompanionsDictionary,
171        requiredScalarFileInputRequiredCompanionsIndex     = requiredScalarFileInputRequiredCompanionsIndex,
172        requiredScalarFileOutputNoCompanions               = requiredScalarFileOutputNoCompanions,
173        requiredScalarFileOutputOptionalCompanions         = requiredScalarFileOutputOptionalCompanions,
174        requiredScalarFileOutputOptionalCompanionsDictionary = requiredScalarFileOutputOptionalCompanionsDictionary,
175        requiredScalarFileOutputOptionalCompanionsIndex    = requiredScalarFileOutputOptionalCompanionsIndex,
176        requiredScalarFileOutputRequiredCompanions         = requiredScalarFileOutputRequiredCompanions,
177        requiredScalarFileOutputRequiredCompanionsDictionary = requiredScalarFileOutputRequiredCompanionsDictionary,
178        requiredScalarFileOutputRequiredCompanionsIndex    = requiredScalarFileOutputRequiredCompanionsIndex,
179
180  }
181
182  output {
183    # Workflow Outputs
184    File TestWDLToolrequiredScalarFileOutputNoCompanions = TestWDLTool.TestWDLTool_requiredScalarFileOutputNoCompanions
185    File TestWDLToolrequiredScalarFileOutputRequiredCompanions = TestWDLTool.TestWDLTool_requiredScalarFileOutputRequiredCompanions
186    File TestWDLToolrequiredScalarFileOutputRequiredCompanionsDictionary = TestWDLTool.TestWDLTool_requiredScalarFileOutputRequiredCompanionsDictionary
187    File TestWDLToolrequiredScalarFileOutputRequiredCompanionsIndex = TestWDLTool.TestWDLTool_requiredScalarFileOutputRequiredCompanionsIndex
188    File TestWDLToolrequiredScalarFileOutputRequiredCompanionsDictionary = TestWDLTool.TestWDLTool_requiredScalarFileOutputRequiredCompanionsDictionary
189    File TestWDLToolrequiredScalarFileOutputRequiredCompanionsIndex = TestWDLTool.TestWDLTool_requiredScalarFileOutputRequiredCompanionsIndex
190    File TestWDLToolrequiredScalarFileOutputOptionalCompanions = TestWDLTool.TestWDLTool_requiredScalarFileOutputOptionalCompanions
191    File? TestWDLToolrequiredScalarFileOutputOptionalCompanionsDictionary = TestWDLTool.TestWDLTool_requiredScalarFileOutputOptionalCompanionsDictionary
192    File? TestWDLToolrequiredScalarFileOutputOptionalCompanionsIndex = TestWDLTool.TestWDLTool_requiredScalarFileOutputOptionalCompanionsIndex
193    Array[File] TestWDLToolrequiredListFileOutputNoCompanions = TestWDLTool.TestWDLTool_requiredListFileOutputNoCompanions
194    Array[File] TestWDLToolrequiredListFileOutputRequiredCompanions = TestWDLTool.TestWDLTool_requiredListFileOutputRequiredCompanions
195    Array[File] TestWDLToolrequiredListFileOutputRequiredCompanionsDictionary = TestWDLTool.TestWDLTool_requiredListFileOutputRequiredCompanionsDictionary
196    Array[File] TestWDLToolrequiredListFileOutputRequiredCompanionsIndex = TestWDLTool.TestWDLTool_requiredListFileOutputRequiredCompanionsIndex
197    Array[File] TestWDLToolrequiredListFileOutputRequiredCompanionsDictionary = TestWDLTool.TestWDLTool_requiredListFileOutputRequiredCompanionsDictionary
198    Array[File] TestWDLToolrequiredListFileOutputRequiredCompanionsIndex = TestWDLTool.TestWDLTool_requiredListFileOutputRequiredCompanionsIndex
199    Array[File] TestWDLToolrequiredListFileOutputOptionalCompanions = TestWDLTool.TestWDLTool_requiredListFileOutputOptionalCompanions
200    Array[File]? TestWDLToolrequiredListFileOutputOptionalCompanionsDictionary = TestWDLTool.TestWDLTool_requiredListFileOutputOptionalCompanionsDictionary
201    Array[File]? TestWDLToolrequiredListFileOutputOptionalCompanionsIndex = TestWDLTool.TestWDLTool_requiredListFileOutputOptionalCompanionsIndex
202    Array[File] TestWDLToolrequiredListFileOutputMixedCompanions = TestWDLTool.TestWDLTool_requiredListFileOutputMixedCompanions
203    Array[File] TestWDLToolrequiredListFileOutputMixedCompanionsRequired = TestWDLTool.TestWDLTool_requiredListFileOutputMixedCompanionsRequired
204    Array[File]? TestWDLToolrequiredListFileOutputMixedCompanionsOptional = TestWDLTool.TestWDLTool_requiredListFileOutputMixedCompanionsOptional
205    Array[File] TestWDLToolrequiredListFileOutputMixedCompanionsRequired = TestWDLTool.TestWDLTool_requiredListFileOutputMixedCompanionsRequired
206  }
207
208  parameter_meta {
209    dockerImage: { description: "Docker image for this task" }
210    gatk: { description: "Location of gatk to run for this task" }
211    memoryRequirements: { description: "Runtime memory requirements for this task" }
212    diskRequirements: { description: "Runtime disk requirements for this task" }
213    cpuRequirements: { description: "Runtime CPU count for this task" }
214    preemptibleRequirements: { description: "Runtime preemptible count for this task" }
215    bootdisksizegbRequirements: { description: "Runtime boot disk size for this task" }
216
217    # Positional Arguments
218    positionalArgs: { description: "Positional args doc" }
219    posDictionary: { description: "Companion resource for positionalArgs" }
220    posIndex: { description: "Companion resource for positionalArgs" }
221
222    # Required Arguments
223    requiredListFileInputMixedCompanions: { description: "requiredListFileInputMixedCompanions doc" }
224    requiredListFileInputMixedCompanionsRequired: { description: "Companion resource for requiredListFileInputMixedCompanions" }
225    requiredListFileInputMixedCompanionsOptional: { description: "Companion resource for requiredListFileInputMixedCompanions" }
226    requiredListFileInputNoCompanions: { description: "requiredListFileInputNoCompanions doc" }
227    requiredListFileInputOptionalCompanions: {
228        description: "requiredListFileInputOptionalCompanions doc",
229        localization_optional : true
230    }
231    requiredListFileInputOptionalCompanionsDictionary: {
232      description: "Companion resource for requiredListFileInputOptionalCompanions",
233      localization_optional : true
234    }
235    requiredListFileInputOptionalCompanionsIndex: {
236      description: "Companion resource for requiredListFileInputOptionalCompanions",
237      localization_optional : true
238    }
239    requiredListFileInputRequiredCompanions: {
240        description: "requiredListFileInputRequiredCompanions doc",
241        localization_optional : true
242    }
243    requiredListFileInputRequiredCompanionsDictionary: {
244      description: "Companion resource for requiredListFileInputRequiredCompanions",
245      localization_optional : true
246    }
247    requiredListFileInputRequiredCompanionsIndex: {
248      description: "Companion resource for requiredListFileInputRequiredCompanions",
249      localization_optional : true
250    }
251    requiredListFileOutputMixedCompanions: { description: "requiredListFileOutputMixedCompanions doc" }
252    requiredListFileOutputMixedCompanionsRequired: { description: "Companion resource for requiredListFileOutputMixedCompanions" }
253    requiredListFileOutputMixedCompanionsOptional: { description: "Companion resource for requiredListFileOutputMixedCompanions" }
254    requiredListFileOutputNoCompanions: { description: "requiredListFileOutputNoCompanions doc" }
255    requiredListFileOutputOptionalCompanions: { description: "requiredListFileOutputOptionalCompanions doc" }
256    requiredListFileOutputOptionalCompanionsDictionary: { description: "Companion resource for requiredListFileOutputOptionalCompanions" }
257    requiredListFileOutputOptionalCompanionsIndex: { description: "Companion resource for requiredListFileOutputOptionalCompanions" }
258    requiredListFileOutputRequiredCompanions: { description: "requiredListFileOutputRequiredCompanions doc" }
259    requiredListFileOutputRequiredCompanionsDictionary: { description: "Companion resource for requiredListFileOutputRequiredCompanions" }
260    requiredListFileOutputRequiredCompanionsIndex: { description: "Companion resource for requiredListFileOutputRequiredCompanions" }
261    requiredScalarFileInputNoCompanions: { description: "requiredScalarFileInputNoCompanions doc" }
262    requiredScalarFileInputOptionalCompanions: {
263        description: "requiredScalarFileInputOptionalCompanions doc",
264        localization_optional : true
265    }
266    requiredScalarFileInputOptionalCompanionsDictionary: {
267      description: "Companion resource for requiredScalarFileInputOptionalCompanions",
268      localization_optional : true
269    }
270    requiredScalarFileInputOptionalCompanionsIndex: {
271      description: "Companion resource for requiredScalarFileInputOptionalCompanions",
272      localization_optional : true
273    }
274    requiredScalarFileInputRequiredCompanions: {
275        description: "requiredScalarFileInputRequiredCompanions doc",
276        localization_optional : true
277    }
278    requiredScalarFileInputRequiredCompanionsDictionary: {
279      description: "Companion resource for requiredScalarFileInputRequiredCompanions",
280      localization_optional : true
281    }
282    requiredScalarFileInputRequiredCompanionsIndex: {
283      description: "Companion resource for requiredScalarFileInputRequiredCompanions",
284      localization_optional : true
285    }
286    requiredScalarFileOutputNoCompanions: { description: "requiredScalarFileOutputNoCompanions doc" }
287    requiredScalarFileOutputOptionalCompanions: { description: "requiredScalarFileOutputOptionalCompanions doc" }
288    requiredScalarFileOutputOptionalCompanionsDictionary: { description: "Companion resource for requiredScalarFileOutputOptionalCompanions" }
289    requiredScalarFileOutputOptionalCompanionsIndex: { description: "Companion resource for requiredScalarFileOutputOptionalCompanions" }
290    requiredScalarFileOutputRequiredCompanions: { description: "requiredScalarFileOutputRequiredCompanions doc" }
291    requiredScalarFileOutputRequiredCompanionsDictionary: { description: "Companion resource for requiredScalarFileOutputRequiredCompanions" }
292    requiredScalarFileOutputRequiredCompanionsIndex: { description: "Companion resource for requiredScalarFileOutputRequiredCompanions" }
293  }
294}
295
296task TestWDLTool {
297
298  input {
299    String dockerImage
300    String gatk
301    String memoryRequirements
302    String diskRequirements
303    String cpuRequirements
304    String preemptibleRequirements
305    String bootdisksizegbRequirements
306    Array[File] positionalArgs
307    Array[File] requiredListFileInputMixedCompanions
308    Array[File] requiredListFileInputMixedCompanionsRequired
309    Array[File]? requiredListFileInputMixedCompanionsOptional
310    Array[File] requiredListFileInputNoCompanions
311    Array[File] requiredListFileInputOptionalCompanions
312    Array[File]? requiredListFileInputOptionalCompanionsDictionary
313    Array[File]? requiredListFileInputOptionalCompanionsIndex
314    Array[File] requiredListFileInputRequiredCompanions
315    Array[File] requiredListFileInputRequiredCompanionsDictionary
316    Array[File] requiredListFileInputRequiredCompanionsIndex
317    Array[String] requiredListFileOutputMixedCompanions
318    Array[String] requiredListFileOutputMixedCompanionsRequired
319    Array[String]? requiredListFileOutputMixedCompanionsOptional
320    Array[String] requiredListFileOutputNoCompanions
321    Array[String] requiredListFileOutputOptionalCompanions
322    Array[String]? requiredListFileOutputOptionalCompanionsDictionary
323    Array[String]? requiredListFileOutputOptionalCompanionsIndex
324    Array[String] requiredListFileOutputRequiredCompanions
325    Array[String] requiredListFileOutputRequiredCompanionsDictionary
326    Array[String] requiredListFileOutputRequiredCompanionsIndex
327    File requiredScalarFileInputNoCompanions
328    File requiredScalarFileInputOptionalCompanions
329    File? requiredScalarFileInputOptionalCompanionsDictionary
330    File? requiredScalarFileInputOptionalCompanionsIndex
331    File requiredScalarFileInputRequiredCompanions
332    File requiredScalarFileInputRequiredCompanionsDictionary
333    File requiredScalarFileInputRequiredCompanionsIndex
334    String requiredScalarFileOutputNoCompanions
335    String requiredScalarFileOutputOptionalCompanions
336    String? requiredScalarFileOutputOptionalCompanionsDictionary
337    String? requiredScalarFileOutputOptionalCompanionsIndex
338    String requiredScalarFileOutputRequiredCompanions
339    String requiredScalarFileOutputRequiredCompanionsDictionary
340    String requiredScalarFileOutputRequiredCompanionsIndex
341
342  }
343
344  command <<<
345    ~{gatk} TestWDLTool \
346    ~{sep=' ' positionalArgs} \
347    --requiredListFileInputMixedCompanions ~{sep=' --requiredListFileInputMixedCompanions ' requiredListFileInputMixedCompanions} \
348    --requiredListFileInputNoCompanions ~{sep=' --requiredListFileInputNoCompanions ' requiredListFileInputNoCompanions} \
349    --requiredListFileInputOptionalCompanions ~{sep=' --requiredListFileInputOptionalCompanions ' requiredListFileInputOptionalCompanions} \
350    --requiredListFileInputRequiredCompanions ~{sep=' --requiredListFileInputRequiredCompanions ' requiredListFileInputRequiredCompanions} \
351    --requiredListFileOutputMixedCompanions ~{sep=' --requiredListFileOutputMixedCompanions ' requiredListFileOutputMixedCompanions} \
352    --requiredListFileOutputNoCompanions ~{sep=' --requiredListFileOutputNoCompanions ' requiredListFileOutputNoCompanions} \
353    --requiredListFileOutputOptionalCompanions ~{sep=' --requiredListFileOutputOptionalCompanions ' requiredListFileOutputOptionalCompanions} \
354    --requiredListFileOutputRequiredCompanions ~{sep=' --requiredListFileOutputRequiredCompanions ' requiredListFileOutputRequiredCompanions} \
355    --requiredScalarFileInputNoCompanions ~{sep=' --requiredScalarFileInputNoCompanions ' requiredScalarFileInputNoCompanions} \
356    --requiredScalarFileInputOptionalCompanions ~{sep=' --requiredScalarFileInputOptionalCompanions ' requiredScalarFileInputOptionalCompanions} \
357    --requiredScalarFileInputRequiredCompanions ~{sep=' --requiredScalarFileInputRequiredCompanions ' requiredScalarFileInputRequiredCompanions} \
358    --requiredScalarFileOutputNoCompanions ~{sep=' --requiredScalarFileOutputNoCompanions ' requiredScalarFileOutputNoCompanions} \
359    --requiredScalarFileOutputOptionalCompanions ~{sep=' --requiredScalarFileOutputOptionalCompanions ' requiredScalarFileOutputOptionalCompanions} \
360    --requiredScalarFileOutputRequiredCompanions ~{sep=' --requiredScalarFileOutputRequiredCompanions ' requiredScalarFileOutputRequiredCompanions} \
361
362  >>>
363
364  runtime {
365      docker: dockerImage
366      memory: memoryRequirements
367      disks: diskRequirements
368      cpu: cpuRequirements
369      preemptible: preemptibleRequirements
370      bootDiskSizeGb: bootdisksizegbRequirements
371  }
372
373  output {
374    # Task Outputs
375    File TestWDLTool_requiredScalarFileOutputNoCompanions = requiredScalarFileOutputNoCompanions
376    File TestWDLTool_requiredScalarFileOutputRequiredCompanions = requiredScalarFileOutputRequiredCompanions
377    File TestWDLTool_requiredScalarFileOutputRequiredCompanionsDictionary = requiredScalarFileOutputRequiredCompanionsDictionary
378    File TestWDLTool_requiredScalarFileOutputRequiredCompanionsIndex = requiredScalarFileOutputRequiredCompanionsIndex
379    File TestWDLTool_requiredScalarFileOutputRequiredCompanionsDictionary = requiredScalarFileOutputRequiredCompanionsDictionary
380    File TestWDLTool_requiredScalarFileOutputRequiredCompanionsIndex = requiredScalarFileOutputRequiredCompanionsIndex
381    File TestWDLTool_requiredScalarFileOutputOptionalCompanions = requiredScalarFileOutputOptionalCompanions
382    File? TestWDLTool_requiredScalarFileOutputOptionalCompanionsDictionary = requiredScalarFileOutputOptionalCompanionsDictionary
383    File? TestWDLTool_requiredScalarFileOutputOptionalCompanionsIndex = requiredScalarFileOutputOptionalCompanionsIndex
384    Array[File] TestWDLTool_requiredListFileOutputNoCompanions = requiredListFileOutputNoCompanions
385    Array[File] TestWDLTool_requiredListFileOutputRequiredCompanions = requiredListFileOutputRequiredCompanions
386    Array[File] TestWDLTool_requiredListFileOutputRequiredCompanionsDictionary = requiredListFileOutputRequiredCompanionsDictionary
387    Array[File] TestWDLTool_requiredListFileOutputRequiredCompanionsIndex = requiredListFileOutputRequiredCompanionsIndex
388    Array[File] TestWDLTool_requiredListFileOutputRequiredCompanionsDictionary = requiredListFileOutputRequiredCompanionsDictionary
389    Array[File] TestWDLTool_requiredListFileOutputRequiredCompanionsIndex = requiredListFileOutputRequiredCompanionsIndex
390    Array[File] TestWDLTool_requiredListFileOutputOptionalCompanions = requiredListFileOutputOptionalCompanions
391    Array[File]? TestWDLTool_requiredListFileOutputOptionalCompanionsDictionary = requiredListFileOutputOptionalCompanionsDictionary
392    Array[File]? TestWDLTool_requiredListFileOutputOptionalCompanionsIndex = requiredListFileOutputOptionalCompanionsIndex
393    Array[File] TestWDLTool_requiredListFileOutputMixedCompanions = requiredListFileOutputMixedCompanions
394    Array[File] TestWDLTool_requiredListFileOutputMixedCompanionsRequired = requiredListFileOutputMixedCompanionsRequired
395    Array[File]? TestWDLTool_requiredListFileOutputMixedCompanionsOptional = requiredListFileOutputMixedCompanionsOptional
396    Array[File] TestWDLTool_requiredListFileOutputMixedCompanionsRequired = requiredListFileOutputMixedCompanionsRequired
397  }
398
399  parameter_meta {
400    dockerImage: { description: "Docker image for this task" }
401    gatk: { description: "Location of gatk to run for this task" }
402    memoryRequirements: { description: "Runtime memory requirements for this task" }
403    diskRequirements: { description: "Runtime disk requirements for this task" }
404    cpuRequirements: { description: "Runtime CPU count for this task" }
405    preemptibleRequirements: { description: "Runtime preemptible count for this task" }
406    bootdisksizegbRequirements: { description: "Runtime boot disk size for this task" }
407
408    # Positional Arguments
409    positionalArgs: { description: "Positional args doc" }
410    posDictionary: { description: "Companion resource for positionalArgs" }
411    posIndex: { description: "Companion resource for positionalArgs" }
412
413    # Required Arguments
414    requiredListFileInputMixedCompanions: { description: "requiredListFileInputMixedCompanions doc" }
415    requiredListFileInputMixedCompanionsRequired: { description: "Companion resource for requiredListFileInputMixedCompanions" }
416    requiredListFileInputMixedCompanionsOptional: { description: "Companion resource for requiredListFileInputMixedCompanions" }
417    requiredListFileInputNoCompanions: { description: "requiredListFileInputNoCompanions doc" }
418    requiredListFileInputOptionalCompanions: {
419        description: "requiredListFileInputOptionalCompanions doc",
420        localization_optional : true
421    }
422    requiredListFileInputOptionalCompanionsDictionary: {
423      description: "Companion resource for requiredListFileInputOptionalCompanions",
424      localization_optional : true
425    }
426    requiredListFileInputOptionalCompanionsIndex: {
427      description: "Companion resource for requiredListFileInputOptionalCompanions",
428      localization_optional : true
429    }
430    requiredListFileInputRequiredCompanions: {
431        description: "requiredListFileInputRequiredCompanions doc",
432        localization_optional : true
433    }
434    requiredListFileInputRequiredCompanionsDictionary: {
435      description: "Companion resource for requiredListFileInputRequiredCompanions",
436      localization_optional : true
437    }
438    requiredListFileInputRequiredCompanionsIndex: {
439      description: "Companion resource for requiredListFileInputRequiredCompanions",
440      localization_optional : true
441    }
442    requiredListFileOutputMixedCompanions: { description: "requiredListFileOutputMixedCompanions doc" }
443    requiredListFileOutputMixedCompanionsRequired: { description: "Companion resource for requiredListFileOutputMixedCompanions" }
444    requiredListFileOutputMixedCompanionsOptional: { description: "Companion resource for requiredListFileOutputMixedCompanions" }
445    requiredListFileOutputNoCompanions: { description: "requiredListFileOutputNoCompanions doc" }
446    requiredListFileOutputOptionalCompanions: { description: "requiredListFileOutputOptionalCompanions doc" }
447    requiredListFileOutputOptionalCompanionsDictionary: { description: "Companion resource for requiredListFileOutputOptionalCompanions" }
448    requiredListFileOutputOptionalCompanionsIndex: { description: "Companion resource for requiredListFileOutputOptionalCompanions" }
449    requiredListFileOutputRequiredCompanions: { description: "requiredListFileOutputRequiredCompanions doc" }
450    requiredListFileOutputRequiredCompanionsDictionary: { description: "Companion resource for requiredListFileOutputRequiredCompanions" }
451    requiredListFileOutputRequiredCompanionsIndex: { description: "Companion resource for requiredListFileOutputRequiredCompanions" }
452    requiredScalarFileInputNoCompanions: { description: "requiredScalarFileInputNoCompanions doc" }
453    requiredScalarFileInputOptionalCompanions: {
454        description: "requiredScalarFileInputOptionalCompanions doc",
455        localization_optional : true
456    }
457    requiredScalarFileInputOptionalCompanionsDictionary: {
458      description: "Companion resource for requiredScalarFileInputOptionalCompanions",
459      localization_optional : true
460    }
461    requiredScalarFileInputOptionalCompanionsIndex: {
462      description: "Companion resource for requiredScalarFileInputOptionalCompanions",
463      localization_optional : true
464    }
465    requiredScalarFileInputRequiredCompanions: {
466        description: "requiredScalarFileInputRequiredCompanions doc",
467        localization_optional : true
468    }
469    requiredScalarFileInputRequiredCompanionsDictionary: {
470      description: "Companion resource for requiredScalarFileInputRequiredCompanions",
471      localization_optional : true
472    }
473    requiredScalarFileInputRequiredCompanionsIndex: {
474      description: "Companion resource for requiredScalarFileInputRequiredCompanions",
475      localization_optional : true
476    }
477    requiredScalarFileOutputNoCompanions: { description: "requiredScalarFileOutputNoCompanions doc" }
478    requiredScalarFileOutputOptionalCompanions: { description: "requiredScalarFileOutputOptionalCompanions doc" }
479    requiredScalarFileOutputOptionalCompanionsDictionary: { description: "Companion resource for requiredScalarFileOutputOptionalCompanions" }
480    requiredScalarFileOutputOptionalCompanionsIndex: { description: "Companion resource for requiredScalarFileOutputOptionalCompanions" }
481    requiredScalarFileOutputRequiredCompanions: { description: "requiredScalarFileOutputRequiredCompanions doc" }
482    requiredScalarFileOutputRequiredCompanionsDictionary: { description: "Companion resource for requiredScalarFileOutputRequiredCompanions" }
483    requiredScalarFileOutputRequiredCompanionsIndex: { description: "Companion resource for requiredScalarFileOutputRequiredCompanions" }
484  }
485}
486
487