Workflow: spaceTxConversion.cwl
Fetched 2023-03-24 21:36:25 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| tiffs | Directory |
The directory containing all .tiff files |
|
| codebook | https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/spaceTxConversion.cwl#codebook/csv (Optional) | ||
| 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 |
|
| add_blanks | Boolean (Optional) |
If true, will add blanks with a hamming distance 1 from the existing codes. |
|
| fov_offset | Integer (Optional) |
The index of the first FOV (for file names). |
|
| file_format | String (Optional) |
String with layout for .tiff files |
|
| round_count | Integer (Optional) |
The number of imaging rounds in the experiment |
|
| aux_tilesets | https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/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 |
|
| channel_count | Integer (Optional) |
The number of total channels per imaging round |
|
| codebook_json | File (Optional) |
Flattened json input, refer to record entry. |
|
| 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/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/spaceTxConversion.cwl#fov_positioning/dummy (Optional) | ||
| cache_read_order | String[] (Optional) |
Order of non x,y dimensions within each image. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| read_schema |
56f0a87fbdee55c41bce5c199b347e25
(CommandLineTool)
|
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| stage_conversion |
inputParser.cwl
(ExpressionTool)
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| execute_conversion |
2eabb320fbaf3ae27ecb7ed0f2b0d22c
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| spaceTx_converted | Directory |
https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/spaceTxConversion.cwl
