CLI Reference
CLI migration since version 0.32.0
Since version 0.32.0, EOAP CWL Wrap is a Transpiler Mate plugin.
Install transpiler-mate-runtime alongside eoap-cwlwrap and invoke
transpiler-mate cwlwrap instead of eoap-cwlwrap. Pass the application
workflow as the positional SOURCE argument instead of --workflow.
The legacy --workflow-id and --stage-out options are no longer supported;
use a #<process-id> fragment and --directory-stage-out, respectively.
The installed plugin builds and writes a packed orchestrator workflow:
transpiler-mate cwlwrap [OPTIONS] SOURCE
SOURCE is the required application CWL file or URL. Append #<process-id> to
select a process from a packed graph.
Plugin Options
| Option | Default | Description |
|---|---|---|
--directory-stage-in |
None | CWL stage-in file or URL for Directory-compatible inputs. |
--file-stage-in |
None | CWL stage-in file or URL for File-compatible inputs. |
--directory-stage-out |
None | CWL stage-out file or URL for Directory-compatible outputs. |
--file-stage-out |
None | CWL stage-out file or URL for File-compatible outputs. |
--output |
wrapped.cwl |
Output path for the packed CWL document. Parent directories are created automatically; an existing file is overwritten. |
--help |
— | Show the command help and exit. |
Staging options are conditionally required: supply the matching stage-in for
each Directory- or File-compatible input and the matching stage-out for each
compatible output. A missing required component causes wrapping to fail. Other
parameter types are forwarded unchanged. Supplied staging processes must satisfy
the component contracts.
Runtime Authentication Options
Transpiler Mate supplies these options for resolving CWL locations:
| Option | Environment variable | Description |
|---|---|---|
--oci-hostname |
OCI_HOSTNAME |
OCI registry hostname. |
--oci-username |
OCI_USERNAME |
OCI registry username. |
--oci-password |
OCI_PASSWORD |
OCI registry password. |
--oauth2-bearer |
OAUTH2_BEARER |
OAuth2 bearer token. |
Location loading and authentication are managed by the host runtime. Available schemes depend on its configured resolver and loaders.
Process Selection
For a single-process document, use its path directly:
transpiler-mate cwlwrap ./workflow.cwl \
--directory-stage-out ./stage-out.cwl \
--output ./wrapped.cwl
Use fragments to select the application process and staging processes from multi-process documents:
transpiler-mate cwlwrap './workflow.cwl#water-bodies-detection' \
--directory-stage-in './components.cwl#directory-stage-in' \
--directory-stage-out './components.cwl#directory-stage-out' \
--output ./wrapped.cwl
Process fragments work for SOURCE and all four staging options. A staging
document containing multiple processes requires an explicit fragment.
Check the options exposed by your installed runtime and plugin with:
transpiler-mate cwlwrap --help