Workflow: sorter.cwl
Fetched 2024-11-25 04:56:31 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| codebook | https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/sorter.cwl#codebook/csv (Optional) | ||
| dir_size | Long (Optional) |
Size of input_dir, in MiB. If provided, will be used to calculate ResourceRequirement. |
|
| cycle_yml | File |
PyYML-formatted dictionary outlining how the truerounds in imaging relate to the pseudorounds in the decoding codebook. The keys are truerounds and the values are the corresponding pseudorounds. |
|
| file_vars | String[] (Optional) |
Variables to get substituted into the file_format string. |
|
| fov_count | Integer (Optional) |
The number of FOVs that are included in this experiment |
|
| input_dir | Directory |
The root directory containing all images. |
|
| fov_offset | Integer (Optional) |
The index of the first FOV (for file names). |
|
| channel_yml | File |
PyYML-formatted list containing a dictionary outlining how the truechannels in imaging relate to the pseudochannels in the decoding codebook. The index of each dict within the list is the trueround % (count of pseudorounds). The keys of the dict are the channels within the image and the values are the pseudochannels in the converted notebook. |
|
| file_format | String (Optional) |
String with layout for .tiff files. Will be formatted via str.format(). |
|
| aux_tilesets | https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/sorter.cwl#aux_tilesets/aux_tilesets (Optional) | ||
| codebook_csv | File (Optional) |
Flattened csv input, refer to record entry. |
|
| round_offset | Integer (Optional) |
The index of the first round (for file names). |
|
| channel_slope | Float (Optional) | ||
| codebook_json | File (Optional) |
Flattened json input, refer to record entry. |
|
| channel_offset | Integer (Optional) |
The index of the first channel (for file names). |
|
| parameter_json | File (Optional) |
json file containing parameters for conversion |
|
| cache_read_order | String[] (Optional) |
Order of x,y,z,ch dimensions within each image. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tmpname |
tmpdir.cwl
(ExpressionTool)
|
||
| stage_sort |
inputParser.cwl
(ExpressionTool)
|
||
| read_schema |
870188c7dfbf91f8b45c8093489a5b02
(CommandLineTool)
|
||
| execute_sort |
c8773d6922fc17a28fa5d8c3ed65c9ee
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| pseudosorted_dir | Directory |
https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/sorter.cwl
