Workflow: segmentation.cwl
Fetched 2026-09-23 08:51:00 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| exp_loc | Directory |
Location of directory containing the 'experiment.json' file |
|
| aux_name | String (Optional) |
The name of the aux view to look at in the experiment file. |
|
| binary_mask | https://w3id.org/cwl/view/git/6ef7a6399b2ab55c1d3edd4e37631a8234889fd9/steps/segmentation.cwl#binary_mask/basic_watershed (Optional) | ||
| decoded_loc | Directory |
Location of the directory that is the output from the starfishRunner step. |
|
| selected_fovs | Integer[] (Optional) |
If provided, segmentation will only be run on FOVs with these indices. |
|
| mask_roi_files | Directory (Optional) |
Flattened directory input, refer to record entry \"binary_mask\" |
|
| parameter_json | File (Optional) |
File containing parameters to run this step. |
|
| mask_roi_formats | String (Optional) |
Flattened record input, refer to record entry \"binary_mask\" |
|
| mask_labeled_files | Directory (Optional) |
Flattened file input, refer to record entry \"binary_mask\" |
|
| mask_labeled_formats | String (Optional) |
Flattened record input, refer to record entry \"binary_mask\" |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tmpname |
tmpdir.cwl
(ExpressionTool)
|
||
| read_schema |
c3f8a2743aa966ea00962a8e7d86d841
(CommandLineTool)
|
||
| stage_segmentation |
inputParser.cwl
(ExpressionTool)
|
||
| execute_segmentation |
d5ff44b4a2e38b55355708d4e2b9adeb
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| segmented | Directory |
Permalink:
https://w3id.org/cwl/view/git/6ef7a6399b2ab55c1d3edd4e37631a8234889fd9/steps/segmentation.cwl
