Workflow: processing.cwl
Fetched 2025-04-30 20:18:09 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| rescale | Boolean (Optional) |
Whether to iteratively rescale images before running the decoder. If true, will skip clip and scale at the end of this step. |
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| clip_max | Float (Optional) |
Pixels above this percentile are set to 1. |
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| clip_min | Float (Optional) |
Pixels below this percentile are set to 0. |
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| dir_size | Long (Optional) |
The size of input_dir in MiB. If provided, will be used to specify storage space requests. |
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| fov_count | Integer (Optional) |
The number of FOVs that are included in this experiment |
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| input_dir | Directory |
Root directory containing space_tx formatted experiment |
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| is_volume | Boolean (Optional) |
Whether to treat the zplanes as a 3D image. |
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| low_sigma | Integer (Optional) |
Sigma value for low pass gaussian filter. Will not be run if not provided. |
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| high_sigma | Integer (Optional) |
Sigma value for high pass gaussian filter. Will not be run if not provided. |
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| anchor_view | String (Optional) |
The name of the auxillary view to be processed in parallel with primary view, such as for anchor round in ISS processing. Will not be included if not provided. |
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| n_processes | Integer (Optional) |
If provided, the number of processes that will be spawned for processing. Otherwise, the maximum number of available CPUs will be used. |
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| level_method | String (Optional) |
Levelling method for clip and scale application. Defaults to SCALE_BY_CHUNK. If rescaling is configured in parameter_json, will be set to SCALE_BY_CHUNK if true, SCALE_BY_IMAGE if false. |
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| selected_fovs | Integer[] (Optional) |
If provided, processing will only be run on FOVs with these indices. |
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| tophat_radius | Integer (Optional) |
Radius for white top hat filter. Should be slightly larger than the expected spot radius. Will not be run if not provided. |
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| parameter_json | File (Optional) |
json containing step parameters. |
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| rolling_radius | Integer (Optional) |
Radius for rolling ball background subtraction. Larger values lead to increased intensity evening effect. The value of 3 will work for most datasets. Will not be run if not provided. |
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| background_view | String (Optional) |
The name of the auxillary view to be used for background subtraction. Background will be estimated if not provided. |
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| deconvolve_iter | Integer (Optional) |
Number of iterations to perform for deconvolution. High values remove more noise while lower values remove less. The value 15 will work for most datasets unless image is very noisy. Will not be run if not provided. |
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| match_histogram | Boolean (Optional) |
If true, histograms will be equalized. |
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| channels_per_reg | Integer (Optional) |
The number of images associated with each channel in the registration image. Will be calculated from aux view if provided through parameter_json, otherwise defaults to one. |
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| deconvolve_sigma | Integer (Optional) |
Sigma value for deconvolution. Should be approximately the expected spot size. |
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| register_aux_view | String (Optional) |
The name of the auxillary view to be used for image registration. |
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| register_background | Boolean (Optional) |
If true, the `background_view` will be aligned to the `aux_view`. |
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| register_to_primary | Boolean (Optional) |
If true, registration will be performed between the first round of register_aux_view and the primary images. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tmpname |
tmpdir.cwl
(ExpressionTool)
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| read_schema |
26e478a0af2d41067f47a672d0b2d3d3
(CommandLineTool)
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| stage_processing |
inputParser.cwl
(ExpressionTool)
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| execute_processing |
6db6aed18bfa0b9451d75abade99bf14
(CommandLineTool)
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Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| processed_exp | Directory |
https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/processing.cwl
