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comparison SpyBOAT.xml @ 3:4d7f30a7e2f6 draft

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"planemo upload commit d070f1ba04a5141a65487f45b29c22767639e44b"
author gregor.m
date Tue, 24 Nov 2020 13:06:26 +0000
parents c59d1373230e
children a4c6fcf2c456
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2:c59d1373230e 3:4d7f30a7e2f6
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: