Workflow: spaceTxConversion.cwl
Fetched 2024-05-19 00:44:30 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
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- Default Values
- Nested Workflows
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| tiffs | Directory |
The directory containing all .tiff files |
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| codebook | https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/spaceTxConversion.cwl#codebook/csv (Optional) | ||
| dir_size | Long (Optional) |
Size of tiffs, in MiB. If provided, will be used to calculate ResourceRequirement. |
|
| 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 |
|
| locs_json | File (Optional) |
Flattened json input, refer to record entry. |
|
| add_blanks | Boolean (Optional) |
If true, will add blanks with a hamming distance 1 from the existing codes. |
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| fov_offset | Integer (Optional) |
The index of the first FOV (for file names). |
|
| file_format | String (Optional) |
String with layout for .tiff files |
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| round_count | Integer (Optional) |
The number of imaging rounds in the experiment |
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| aux_tilesets | https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/spaceTxConversion.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). |
|
| zplane_count | Integer (Optional) |
The number of z-planes in each image |
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| channel_count | Integer (Optional) |
The number of total channels per imaging round |
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| codebook_json | File (Optional) |
Flattened json input, refer to record entry. |
|
| data_org_file | File (Optional) |
The data org file used to describe .dax formatted images. |
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| zplane_offset | Integer (Optional) |
The index of the first zplane (for file names). |
|
| channel_offset | Integer (Optional) |
The index of the first channel (for file names). |
|
| parameter_json | File (Optional) |
json file with values to be read into other input variables. |
|
| fov_positioning | https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/spaceTxConversion.cwl#fov_positioning/locs (Optional) | ||
| cache_read_order | String[] (Optional) |
Order of non x,y dimensions within each image. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tmpname |
tmpdir.cwl
(ExpressionTool)
|
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| read_schema |
aeba4da96c3befb9ea398cd010830870
(CommandLineTool)
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| stage_conversion |
inputParser.cwl
(ExpressionTool)
|
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| execute_conversion |
de672a2b24d846b21d57fb9ca5c74211
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| spaceTx_converted | Directory |
https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/spaceTxConversion.cwl
