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comparison spyboat.xml @ 1:639d2031d998 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
author iuc
date Mon, 30 Nov 2020 21:11:23 +0000
parents 76733d05d8ef
children 4626a83601d4
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0:76733d05d8ef 1:639d2031d998
1 <tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@" profile="20.01" license="GPL-3.0-or-later"> 1 <tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@" profile="20.01" license="GPL-3.0-or-later">
2 <description>wavelet transforms image stacks</description> 2 <description>wavelet analyzes image stacks</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.1.1</token> 4 <token name="@TOOL_VERSION@">0.1.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">spyboat</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">spyboat</requirement>
73 <!-- 73 <!--
74 The following Wavelet parameters must have the same numerical type as defined in the 74 The following Wavelet parameters must have the same numerical type as defined in the
75 argparse parser in spyboat_cli.py 75 argparse parser in spyboat_cli.py
76 --> 76 -->
77 <section name="PreProc" title="Preprocessing" expanded="true"> 77 <section name="PreProc" title="Preprocessing" expanded="true">
78 <param argument="gauss_sigma" type="float" min="0" max="9999999" optional="true" label="Sigma" 78 <param argument="gauss_sigma" type="float" min="0" max="100" optional="true" label="Sigma"
79 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" /> 79 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" />
80 <param argument="rescale_factor" type="integer" value="" min="0" max="99" optional="true" label="Rescale factor" 80 <param argument="rescale_factor" type="integer" value="" min="0" max="99" optional="true" label="Rescale factor"
81 help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling" /> 81 help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling" />
82 </section> 82 </section>
83 <section name="wavana" title="Wavelet Analysis" expanded="true"> 83 <section name="wavana" title="Wavelet Analysis" expanded="true">
84 <param name="dt" type="float" value="1" min="0" max="9999999" label="Sampling interval" help="Time span between two frames" /> 84 <param name="dt" type="float" value="1" min="0" max="1000" label="Sampling interval" help="Time span between two frames" />
85 <param name="tmin" type="float" value="20" min="0" max="9999999" label="Smallest period" help="Lowest period for the wavelet transform" /> 85 <param name="tmin" type="float" value="20" min="0" max="2000" label="Smallest period" help="Lowest period for the wavelet transform" />
86 <param name="tmax" type="float" value="30" min="0" max="9999999" label="Largest period" 86 <param name="tmax" type="float" value="30" min="0" max="10000" label="Largest period"
87 help="Largest period for the wavelet transform" /> 87 help="Largest period for the wavelet transform" />
88 <param name="nt" type="integer" value="150" min="0" max="9999999" label="Number of periods to scan for" 88 <param name="nt" type="integer" value="150" min="0" max="1000" label="Number of periods to scan for"
89 help="Determines period resolution of the Wavelet power spectra" /> 89 help="Determines period resolution of the Wavelet power spectra" />
90 <param name="tcutoff" type="float" value="40" min="0" max="9999999" label="T cutoff" 90 <param name="tcutoff" type="float" value="40" min="0" max="10000" label="T cutoff"
91 help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true" /> 91 help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true" />
92 <param name="win_size" type="float" value="" min="0" max="9999999" optional="true" label="Sliding window size" 92 <param name="win_size" type="float" value="" min="0" max="10000" optional="true" label="Sliding window size"
93 help="Window size for amplitude envelope estimation, leave blank to disable normalization" /> 93 help="Window size for amplitude envelope estimation, leave blank to disable normalization" />
94 </section> 94 </section>
95 <conditional name="masking"> 95 <conditional name="masking">
96 <param name="selection_mode" type="select" label="Masking the output" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output"> 96 <param name="selection_mode" type="select" label="Masking the output" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output">
97 <option selected="true" value="no_masking">No masking</option> 97 <option selected="true" value="no_masking">No masking</option>
98 <option value="create_static_mask">Create a static mask</option> 98 <option value="create_static_mask">Create a static mask</option>
99 <option value="create_dynamic_mask">Create a dynamic mask</option> 99 <option value="create_dynamic_mask">Create a dynamic mask</option>
100 </param> 100 </param>
101 <when value="no_masking" /> 101 <when value="no_masking" />
102 <when value="create_static_mask"> 102 <when value="create_static_mask">
103 <param name="mask_frame" type="integer" value="1" min="1" max="99999" label="Create mask from frame" 103 <param name="mask_frame" type="integer" value="1" min="1" max="5000" label="Create mask from frame"
104 help="Creates a static mask from the chosen frame of the input movie." /> 104 help="Creates a static mask from the chosen frame of the input movie." />
105 <param name="mask_thresh" type="float" value="0" min="0" max="999999" label="Threshold" 105 <param name="mask_thresh" type="float" value="0" min="0" max="65000" label="Threshold"
106 help="All pixels below this threshold will be masked in the output." /> 106 help="All pixels below this threshold will be masked in the output." />
107 </when> 107 </when>
108 <when value="create_dynamic_mask"> 108 <when value="create_dynamic_mask">
109 <param name="mask_thresh" type="float" value="0" min="0" max="999999" label="Threshold" 109 <param name="mask_thresh" type="float" value="0" min="0" max="65000" label="Threshold"
110 help="For each frame of the input, all pixels below this threshold will be masked in the output." /> 110 help="For each frame of the input, all pixels below this threshold will be masked in the output." />
111 </when> 111 </when>
112 </conditional> 112 </conditional>
113 <param name="outputs" type="select" optional="true" multiple="true" label="Select optional outputs" help=""> 113 <param name="outputs" type="select" optional="true" multiple="true" label="Select optional outputs" help="" display="checkboxes">
114 <option value="save_phase">Phase Movie</option> 114 <option value="save_phase">Phase Movie</option>
115 <option value="save_period">Period Movie</option> 115 <option value="save_period">Period Movie</option>
116 <option value="save_amplitude">Amplitude Movie</option> 116 <option value="save_amplitude">Amplitude Movie</option>
117 <option value="save_power">Power Movie</option> 117 <option value="save_power">Power Movie</option>
118 <option value="save_preprocessed">Preprocessed Movie</option> 118 <option value="save_preprocessed">Preprocessed Movie</option>
119 </param> 119 </param>
120 </inputs> 120 </inputs>
121 121
122 <outputs> 122 <outputs>
123 <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase"> 123 <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase">
124 <filter>'save_phase' in ouputs</filter> 124 <filter>outputs and 'save_phase' in outputs</filter>
125 </data> 125 </data>
126 <data name="period_out" format="tiff" label="${movie.name[:-4]}_period"> 126 <data name="period_out" format="tiff" label="${movie.name[:-4]}_period">
127 <filter>'save_period' in outputs</filter> 127 <filter>outputs and 'save_period' in outputs</filter>
128 </data> 128 </data>
129 <data name="power_out" format="tiff" label="${movie.name[:-4]}_power"> 129 <data name="power_out" format="tiff" label="${movie.name[:-4]}_power">
130 <filter>'save_power' in outputs</filter> 130 <filter>outputs and "save_power" in outputs</filter>
131 </data> 131 </data>
132 <data name="amplitude_out" format="tiff" label="${movie.name[:-4]}_amplitude"> 132 <data name="amplitude_out" format="tiff" label="${movie.name[:-4]}_amplitude">
133 <filter>'save_amplitude' in outputs</filter> 133 <filter>outputs and 'save_amplitude' in outputs</filter>
134 </data> 134 </data>
135 <data name="preprocessed_out" format="tiff" label="${movie.name[:-4]}_preproc"> 135 <data name="preprocessed_out" format="tiff" label="${movie.name[:-4]}_preproc">
136 <filter>'save_preprocessed' in outputs</filter> 136 <filter>outputs and 'save_preprocessed' in outputs</filter>
137 </data> 137 </data>
138 <data name="html_out" format="html" label="Report ${movie.name[:-4]}" /> 138 <data name="html_out" format="html" label="Report ${movie.name[:-4]}" />
139 </outputs> 139 </outputs>
140 140
141 <tests> 141 <tests>
166 <output name="phase_out" ftype="tiff"> 166 <output name="phase_out" ftype="tiff">
167 <assert_contents> 167 <assert_contents>
168 <has_size value="1764430" delta="100" /> 168 <has_size value="1764430" delta="100" />
169 </assert_contents> 169 </assert_contents>
170 </output> 170 </output>
171 <output name="html_out" file="output1.html" ftype="html"/>
172 </test> 171 </test>
173 <test expect_num_outputs="4"> 172 <test expect_num_outputs="4">
174 <section name="wavana"> 173 <section name="wavana">
175 <param name="tmin" value="20"/> 174 <param name="tmin" value="20"/>
176 <param name="nt" value="150"/> 175 <param name="nt" value="150"/>
184 <output name="phase_out" ftype="tiff"> 183 <output name="phase_out" ftype="tiff">
185 <assert_contents> 184 <assert_contents>
186 <has_size value="1764430" delta="100" /> 185 <has_size value="1764430" delta="100" />
187 </assert_contents> 186 </assert_contents>
188 </output> 187 </output>
189 <output name="html_out" file="output1.html" ftype="html"/>
190 </test> 188 </test>
191 </tests> 189 </tests>
192 <help><![CDATA[ 190 <help><![CDATA[
193 .. class:: infomark 191 .. class:: infomark
194 192