Mercurial > repos > gregor.m > spyboat
comparison SpyBOAT.xml @ 3:4d7f30a7e2f6 draft
"planemo upload commit d070f1ba04a5141a65487f45b29c22767639e44b"
author | gregor.m |
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date | Tue, 24 Nov 2020 13:06:26 +0000 |
parents | c59d1373230e |
children | a4c6fcf2c456 |
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2:c59d1373230e | 3:4d7f30a7e2f6 |
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1 <tool id="SpyBOAT" name="SpyBOAT" version="0.0.2"> | 1 <tool id="SpyBOAT" name="SpyBOAT" version="0.1.0"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="0.0.4">spyboat</requirement> | 3 <requirement type="package" version="0.1.0">spyboat</requirement> |
4 </requirements> | 4 </requirements> |
5 <version_command>python $__tool_directory__/cl_wrapper.py --version</version_command> | 5 <version_command>python $__tool_directory__/spyboat_cli.py --version</version_command> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 python $__tool_directory__/cl_wrapper.py | 7 python $__tool_directory__/spyboat_cli.py |
8 --input_path '$movie' | 8 --input_path '$movie' |
9 #if $gauss_sigma: | 9 #if $gauss_sigma: |
10 --gauss_sigma $gauss_sigma | 10 --gauss_sigma $gauss_sigma |
11 #end if | 11 #end if |
12 #if $rescale_factor: | 12 #if $rescale_factor: |
13 --rescale $rescale_factor | 13 --rescale $rescale_factor |
14 #end if | 14 #end if |
15 | 15 |
16 #if $masking.selection_mode == "create_fixed_mask": | 16 #if $masking.selection_mode == "create_static_mask": |
17 --masking fixed | 17 --masking static |
18 --mask_frame $masking.mask_frame | 18 --mask_frame $masking.mask_frame |
19 --mask_thresh $masking.mask_thresh | 19 --mask_thresh $masking.mask_thresh |
20 #else if $masking.selection_mode == "create_dynamic_mask": | 20 #else if $masking.selection_mode == "create_dynamic_mask": |
21 --masking dynamic | 21 --masking dynamic |
22 --mask_thresh $masking.mask_thresh | 22 --mask_thresh $masking.mask_thresh |
52 <param name="movie" type="data" format="tiff" label="Movie to process" | 52 <param name="movie" type="data" format="tiff" label="Movie to process" |
53 help="Select a movie to Wavelet process"/> | 53 help="Select a movie to Wavelet process"/> |
54 | 54 |
55 <!-- | 55 <!-- |
56 The following Wavelet parameters must have the same numerical type as defined in the | 56 The following Wavelet parameters must have the same numerical type as defined in the |
57 argparse parser in cl_wrapper.py | 57 argparse parser in spyboat_cli.py |
58 --> | 58 --> |
59 | 59 |
60 <param name="gauss_sigma" type="float" label="Sigma" | 60 <param name="gauss_sigma" type="float" label="Sigma" |
61 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired." optional="true"> | 61 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired." optional="true"> |
62 <validator type="in_range" min="0" max="9999999"/> | 62 <validator type="in_range" min="0" max="9999999"/> |
69 </param> | 69 </param> |
70 | 70 |
71 <conditional name="masking"> | 71 <conditional name="masking"> |
72 <param label="Masking the output" name="selection_mode" type="select" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output"> | 72 <param label="Masking the output" name="selection_mode" type="select" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output"> |
73 <option selected="true" value="no_masking">No masking</option> | 73 <option selected="true" value="no_masking">No masking</option> |
74 <option value="create_fixed_mask">Create a fixed mask</option> | 74 <option value="create_static_mask">Create a static mask</option> |
75 <option value="create_dynamic_mask">Create a dynamic mask</option> | 75 <option value="create_dynamic_mask">Create a dynamic mask</option> |
76 </param> | 76 </param> |
77 <when value="create_fixed_mask"> | 77 <when value="create_static_mask"> |
78 <param name="mask_frame" type="integer" value="1" label="Create mask from frame" | 78 <param name="mask_frame" type="integer" value="1" label="Create mask from frame" |
79 help="Creates a fixed mask from the chosen frame of the input movie."> | 79 help="Creates a static mask from the chosen frame of the input movie."> |
80 <validator type="in_range" min="1" max="99999"/> | 80 <validator type="in_range" min="1" max="99999"/> |
81 </param> | 81 </param> |
82 <param name="mask_thresh" type="float" value="0" label="Threshold" | 82 <param name="mask_thresh" type="float" value="0" label="Threshold" |
83 help="All pixels below this threshold will be masked in the output."> | 83 help="All pixels below this threshold will be masked in the output."> |
84 <validator type="in_range" min="0" max="999999"/> | 84 <validator type="in_range" min="0" max="999999"/> |
152 </test> | 152 </test> |
153 </tests> | 153 </tests> |
154 <help><![CDATA[ | 154 <help><![CDATA[ |
155 **What it does** | 155 **What it does** |
156 | 156 |
157 Wavelet transforms a 3d-image stack (time,Y,X) pixel by pixel and extracts/evaluates the wavelet ridge. Removal of low-frequency trends is provided via sinc filtering. | 157 Wavelet transforms a 3d-image stack (time,Y,X) pixel by pixel along the time axis and extracts/evaluates the wavelet ridge. Removal of low-frequency trends is provided via sinc filtering. |
158 There are four output movies generated (phase, period, amplitude and power). They have exactly the same dimensions (time,Y,X) as the (rescaled) input. | 158 There are four output movies generated (phase, period, amplitude and power). They have exactly the same dimensions (time,Y,X) as the (rescaled) input. |
159 | 159 |
160 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable. | 160 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable. |
161 | 161 |
162 To limit the number of Wavelet transformations (computing time), downscaling of the input movie resolution is recommended. | 162 To limit the number of Wavelet transformations (computing time), downscaling of the input movie resolution is recommended. |
183 - Rescale factor: | 183 - Rescale factor: |
184 | 184 |
185 Given in %, downsamples the spatial resolution of the input movie. This speeds | 185 Given in %, downsamples the spatial resolution of the input movie. This speeds |
186 up the whole analysis by a lot. | 186 up the whole analysis by a lot. |
187 | 187 |
188 - Masking: | |
189 SpyBOAT offers 'static' and 'dynamic' masking. 'static' means that a single mask is created by thresholding from a user selected frame. 'dynamic' creates a mask for each frame by thresholding, works better for moving/expanding/shrinking oscillatory fields. | |
188 - Sampling interval: | 190 - Sampling interval: |
189 | 191 |
190 Time passed between consecutive measurements, e.g 'an image every 10 minutes'. | 192 Time passed between consecutive measurements, e.g 'an image every 10 minutes'. |
191 | 193 |
192 - Smallest Period: | 194 - Smallest Period: |