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annotate spyboat.xml @ 8:10ae027ab022 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 4b95b96461684de086fe7e8086af9385f3ed7930
author iuc
date Wed, 20 Dec 2023 18:03:23 +0000
parents 4c51f0bac726
children
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117a042eb1b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
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1 <tool id="spyboat" name="Perform wavelet transformation on 3D-image stack" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
117a042eb1b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
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2 <description>with SpyBOAT</description>
0
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3 <macros>
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4c51f0bac726 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 3421a08ab29b58cd514011767f429f6769e3e86d
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4 <token name="@TOOL_VERSION@">0.1.2</token>
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10ae027ab022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 4b95b96461684de086fe7e8086af9385f3ed7930
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5 <token name="@VERSION_SUFFIX@">3</token>
0
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6 </macros>
6
117a042eb1b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
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7 <edam_operations>
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8 <edam_operation>operation_3443</edam_operation>
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9 </edam_operations>
0
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10 <requirements>
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10ae027ab022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 4b95b96461684de086fe7e8086af9385f3ed7930
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11 <!-- TODO replace requirement version with TOOL_VERSION: this tool has been accidentally merged with 0.1.2 which did not exist yet-->
10ae027ab022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 4b95b96461684de086fe7e8086af9385f3ed7930
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12 <requirement type="package" version="0.1.1">spyboat</requirement>
0
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13 </requirements>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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14 <version_command>python '$__tool_directory__/spyboat_cli.py' --version</version_command>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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15 <command detect_errors="exit_code"><![CDATA[
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16 ## needed for pulsar combat
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17 cat '$__tool_directory__/output_report.py' > /dev/null &&
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18 ## run tool
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19 python '$__tool_directory__/spyboat_cli.py'
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20 --input_path '$movie'
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21 #if str($PreProc.gauss_sigma):
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22 --gauss_sigma $PreProc.gauss_sigma
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23 #end if
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24 #if str($PreProc.rescale_factor):
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25 --rescale $PreProc.rescale_factor
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26 #end if
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27
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28 #if $masking.selection_mode == "create_static_mask":
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29 --masking static
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30 --mask_frame $masking.mask_frame
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31 --mask_thresh $masking.mask_thresh
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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32 #else if $masking.selection_mode == "create_dynamic_mask":
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33 --masking dynamic
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34 --mask_thresh $masking.mask_thresh
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35 #end if
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36
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37 --dt $wavana.dt
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38 --Tmin $wavana.tmin
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39 --Tmax $wavana.tmax
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40 --nT $wavana.nt
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41 #if str($wavana.tcutoff)
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42 --Tcutoff $wavana.tcutoff
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43 #end if
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44 #if str($wavana.win_size):
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45 --win_size $wavana.win_size
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46 #end if
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47
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48 #if 'save_phase' in $outputs:
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49 --phase_out '$phase_out'
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50 #end if
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51
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52 #if 'save_period' in $outputs:
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53 --period_out '$period_out'
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54 #end if
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55
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56 #if 'save_power' in $outputs:
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57 --power_out '$power_out'
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58 #end if
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59
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60 #if 'save_amplitude' in $outputs:
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61 --amplitude_out '$amplitude_out'
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62 #end if
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63
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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64 #if 'save_preprocessed' in $outputs:
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65 --preprocessed_out '$preprocessed_out'
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66 #end if
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67
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68 --html_fname '$html_out'
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69 --report_img_path '$html_out.extra_files_path'
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70
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71 --ncpu "\${GALAXY_SLOTS:-8}"
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72
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73
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74 ]]></command>
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75 <inputs>
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76 <param name="movie" type="data" format="tiff" label="Movie to analyze" help="Select a movie to wavelet analyze"/>
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77
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78 <!--
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79 The following Wavelet parameters must have the same numerical type as defined in the
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80 argparse parser in spyboat_cli.py
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81 -->
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82 <section name="PreProc" title="Preprocessing" expanded="true">
1
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83 <param argument="gauss_sigma" type="float" min="0" max="100" optional="true" label="Sigma"
0
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84 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" />
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85 <param argument="rescale_factor" type="integer" value="" min="0" max="99" optional="true" label="Rescale factor"
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86 help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling" />
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87 </section>
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88 <section name="wavana" title="Wavelet Analysis" expanded="true">
1
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89 <param name="dt" type="float" value="1" min="0" max="1000" label="Sampling interval" help="Time span between two frames" />
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
90 <param name="tmin" type="float" value="20" min="0" max="2000" label="Smallest period" help="Lowest period for the wavelet transform" />
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
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parents: 0
diff changeset
91 <param name="tmax" type="float" value="30" min="0" max="10000" label="Largest period"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
92 help="Largest period for the wavelet transform" />
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
93 <param name="nt" type="integer" value="150" min="0" max="1000" label="Number of periods to scan for"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
94 help="Determines period resolution of the Wavelet power spectra" />
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
95 <param name="tcutoff" type="float" value="40" min="0" max="10000" label="T cutoff"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
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96 help="Cut-off-period for sinc filter detrending, a blank field disables detrending" optional="true" />
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
97 <param name="win_size" type="float" value="" min="0" max="10000" optional="true" label="Sliding window size"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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98 help="Window size for amplitude envelope estimation, leave blank to disable normalization" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
99 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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100 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
101 <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">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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102 <option selected="true" value="no_masking">No masking</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
103 <option value="create_static_mask">Create a static mask</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
104 <option value="create_dynamic_mask">Create a dynamic mask</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
105 </param>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
106 <when value="no_masking" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
107 <when value="create_static_mask">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
108 <param name="mask_frame" type="integer" value="1" min="1" max="5000" label="Create mask from frame"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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109 help="Creates a static mask from the chosen frame of the input movie." />
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
110 <param name="mask_thresh" type="float" value="0" min="0" max="65000" label="Threshold"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
111 help="All pixels below this threshold will be masked in the output." />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
112 </when>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
113 <when value="create_dynamic_mask">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
114 <param name="mask_thresh" type="float" value="0" min="0" max="65000" label="Threshold"
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
115 help="For each frame of the input, all pixels below this threshold will be masked in the output." />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
116 </when>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
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117 </conditional>
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
118 <param name="outputs" type="select" optional="true" multiple="true" label="Select optional outputs" help="" display="checkboxes">
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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119 <option value="save_phase">Phase Movie</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
120 <option value="save_period">Period Movie</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
121 <option value="save_amplitude">Amplitude Movie</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
122 <option value="save_power">Power Movie</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
123 <option value="save_preprocessed">Preprocessed Movie</option>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
124 </param>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
125 </inputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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126
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
127 <outputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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128 <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
129 <filter>outputs and 'save_phase' in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
130 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
131 <data name="period_out" format="tiff" label="${movie.name[:-4]}_period">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
132 <filter>outputs and 'save_period' in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
133 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
134 <data name="power_out" format="tiff" label="${movie.name[:-4]}_power">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
135 <filter>outputs and "save_power" in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
136 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
137 <data name="amplitude_out" format="tiff" label="${movie.name[:-4]}_amplitude">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
138 <filter>outputs and 'save_amplitude' in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
139 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
140 <data name="preprocessed_out" format="tiff" label="${movie.name[:-4]}_preproc">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
141 <filter>outputs and 'save_preprocessed' in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
142 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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143 <data name="html_out" format="html" label="Report ${movie.name[:-4]}" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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diff changeset
144 </outputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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145
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
146 <tests>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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147 <test expect_num_outputs="2">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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148 <param name="movie" value="test-movie.tif" ftype="tiff"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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149 <param name="outputs" value="save_phase"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
150 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
151 <param name="selection_mode" value="no_masking" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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152 </conditional>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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153 <output name="phase_out" ftype="tiff">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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154 <assert_contents>
2
4626a83601d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit b5cdb8bbc5334d5ff05b3e2fcc13c574832d2dd9"
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parents: 1
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155 <has_size value="1764430" delta="10000" />
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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156 </assert_contents>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
157 </output>
3
9c53c7da9cbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 169dbae234162ed1e7167e62a3e54de8f89b0268
iuc
parents: 2
diff changeset
158 <!--allow for 1 differing line due to number of CPUs which might change-->
9c53c7da9cbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 169dbae234162ed1e7167e62a3e54de8f89b0268
iuc
parents: 2
diff changeset
159 <output name="html_out" file="output1.html" ftype="html" lines_diff="2"/>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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diff changeset
160 </test>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
161 <test expect_num_outputs="4">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
162 <section name="wavana">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
163 <param name="tmin" value="20"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
164 <param name="nt" value="150"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
165 <param name="tcutoff" value="40"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
166 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
167 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
168 <param name="selection_mode" value="create_static_mask" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
169 </conditional>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
170 <param name="movie" value="test-movie.tif" ftype="tiff"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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diff changeset
171 <param name="outputs" value="save_phase,save_preprocessed,save_power"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
172 <output name="phase_out" ftype="tiff">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
173 <assert_contents>
2
4626a83601d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit b5cdb8bbc5334d5ff05b3e2fcc13c574832d2dd9"
iuc
parents: 1
diff changeset
174 <has_size value="1764430" delta="10000" />
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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175 </assert_contents>
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176 </output>
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177 </test>
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178 <test expect_num_outputs="4">
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179 <section name="wavana">
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180 <param name="tmin" value="20"/>
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181 <param name="nt" value="150"/>
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182 <param name="tcutoff" value="40"/>
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183 </section>
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184 <conditional name="masking">
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185 <param name="selection_mode" value="create_dynamic_mask" />
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186 </conditional>
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187 <param name="movie" value="test-movie.tif" ftype="tiff"/>
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188 <param name="outputs" value="save_phase,save_preprocessed,save_power"/>
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189 <output name="phase_out" ftype="tiff">
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190 <assert_contents>
2
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191 <has_size value="1764430" delta="10000" />
0
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192 </assert_contents>
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193 </output>
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194 </test>
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195 </tests>
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196 <help><![CDATA[
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197 .. class:: infomark
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198
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199 **What it does**
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200
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201 -------------------
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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202
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203 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.
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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204 There are four output movies generated (phase, period, amplitude and power). They have exactly the same dimensions (time,Y,X) as the (rescaled) input.
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205
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206 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable.
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207
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208 To limit the number of Wavelet transformations (computing time), downscaling of the input movie resolution is recommended.
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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209 Trimming away parts of the movie with no relevant data (e.g. outer dark edges) also speeds up the processing.
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210
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211 If multiple channels are present in your data, extract the channel of interest beforehand (e.g. with Fiji).
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212
5
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213 **Author**: Gregor Mönke (github.com/tensionhead).
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214
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215 **SpyBOAT repository**: https://github.com/tensionhead/SpyBOAT
0
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216
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217 **Wrapper by**: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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218
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219 **Know what you are doing**
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220
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221 .. class:: warningmark
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222
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223 You need to have a basic understanding of time-frequency analysis with Wavelets, find more information about the analysis strategy employed at https://github.com/tensionhead/pyBOAT or the publication cited below.
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224
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225 -------------------
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226
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227 **Parameter List**
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228
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229 - Sigma:
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230 The Kernel bandwidth (in pixels) for the Gaussian kernels to use for pre-smoothing the input data. The default value of zero means that no pre-smoothing is done. Set this number to a desired kernel width to turn on pre-smoothing.
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231
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232 - Rescale factor:
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233 Given in %, downsamples the spatial resolution of the input movie. This speeds up the whole analysis by a lot.
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234
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235 - Masking:
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236 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.
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237
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238 - Sampling interval:
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239 Time passed between consecutive measurements, e.g 'an image every 10 minutes'.
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240
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241 - Smallest Period:
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242 The minimal period to scan for, this is the higher (in frequency) end of the spectrum. A warning will be given during processing if the chosen value deceeds the Nyquist limit (2 times the sampling interval).
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243
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244 - Largest period:
5
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245 The maximal period to scan for, this is the lower (in frequency) end of the spectrum. A warning will be given during processing if the chosen value exceeds the length of the time series.
0
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246
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247 - Number of periods to scan for:
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248 This is the the number of convolutions computed per pixel.
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249
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250 Spectral resolution = ( biggest period - smallest period ) / number of periods
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251
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252 - Tcutoff:
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253 The cut-off period for the sinc filter, periods larger than this one will
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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254 be removed from the signal before the transform. If no value is given,
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255 no detrending is performed. At least a gracious cut-off of around ~3 times
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256 the largest period to be expected is recommended.
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257
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258 - Sliding window size
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259 Length (in time units, e.g. hours) of the sliding window to estimate
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260 an amplitude envelope. The signal then gets normalized by this envelope,
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261 meaning that all amplitudes will be around ~1 after the transform. The
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262 advantage is that signal with strong amplitude trends will have more
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263 meaningful Wavelet powers after normalization.
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264
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265
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266 ]]></help>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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267 <citations>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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268 <citation type="doi">10.1101/2020.04.29.067744</citation>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
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269 </citations>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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270 </tool>