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Adjust behavior of command_input_file_expression #128

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Merged
merged 4 commits into from
Oct 6, 2021
Merged

Adjust behavior of command_input_file_expression #128

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cad5d46
Adjust behavior of command_input_file_expression
tetron Oct 5, 2021
585babf
Remove InitialWorkDir requirement
tetron Oct 5, 2021
bbd478c
command_input_file_expression uses ShellCommandRequirement
mr-c Oct 6, 2021
309f5bd
Merge branch '1.2.1_proposed' into command_input_file_expression-test…
mr-c Oct 6, 2021
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20 changes: 8 additions & 12 deletions tests/secondaryfiles/rename-inputs.cwl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
#!/usr/bin/env cwl-runner
id: InputSecondaryFileConformanceTest
baseCommand:
- ls
class: CommandLineTool
cwlVersion: v1.2
doc: |
Expand All @@ -24,7 +22,6 @@ inputs:
touch secondary_file_test.txt.accessory
```
secondaryFiles:
- .accessory
- |
${
function resolveSecondary(base, secPattern) {
Expand All @@ -37,19 +34,21 @@ inputs:
}
return [{
"class": "File",
"location": self.secondaryFiles[0].location,
"location": inputs.accessory.location,
"basename": resolveSecondary(self.basename, '^.accessory')
}];
}
- id: accessory
type: File


arguments:
- "ls"
- $(inputs.inputWithSecondary.dirname)
- valueFrom: "|"
shellQuote: false
position: 0
- valueFrom: "grep"
position: 1
- valueFrom: "secondary"
position: 2
- "grep"
- "secondary"

outputs:
- id: output_file
Expand All @@ -58,6 +57,3 @@ stdout: result
requirements:
InlineJavascriptRequirement: {}
ShellCommandRequirement: {}
InitialWorkDirRequirement:
listing:
- $(inputs.inputWithSecondary)
3 changes: 3 additions & 0 deletions tests/secondaryfiles/rename-inputs.yml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
inputWithSecondary:
class: File
location: secondary_file_test.txt
accessory:
class: File
location: secondary_file_test.txt.accessory
2 changes: 1 addition & 1 deletion tests/secondaryfiles/test-index.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
checksum: sha1$901c3d387a263c57eaed6f24a82517c1fb0e198d
size: 54
location: result
tags: [ inline_javascript, secondary_files, command_line_tool ]
tags: [ inline_javascript, secondary_files, command_line_tool, shell_command ]

- tool: rename-outputs.cwl
doc: Confirm CommandOutputParameter expression can receive a File object
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