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annotate spyboat.xml @ 4:8815bc7e9cef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 9b86d7ef6ea6b25984c276df2ea3ff960aa76460
author iuc
date Mon, 10 Oct 2022 17:02:00 +0000
parents 9c53c7da9cbe
children 07a85bc414ba
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4
8815bc7e9cef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 9b86d7ef6ea6b25984c276df2ea3ff960aa76460
iuc
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1 <tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
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2 <description>wavelet analyzes image stacks</description>
0
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3 <macros>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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4 <token name="@TOOL_VERSION@">0.1.1</token>
3
9c53c7da9cbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 169dbae234162ed1e7167e62a3e54de8f89b0268
iuc
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5 <token name="@VERSION_SUFFIX@">1</token>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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6 </macros>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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7 <requirements>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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8 <requirement type="package" version="@TOOL_VERSION@">spyboat</requirement>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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9 </requirements>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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10 <version_command>python '$__tool_directory__/spyboat_cli.py' --version</version_command>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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11 <command detect_errors="exit_code"><![CDATA[
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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12 ## needed for pulsar combat
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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13 cat '$__tool_directory__/output_report.py' > /dev/null &&
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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14 ## run tool
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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15 python '$__tool_directory__/spyboat_cli.py'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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16 --input_path '$movie'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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17 #if str($PreProc.gauss_sigma):
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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18 --gauss_sigma $PreProc.gauss_sigma
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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19 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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20 #if str($PreProc.rescale_factor):
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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21 --rescale $PreProc.rescale_factor
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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22 #end if
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23
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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24 #if $masking.selection_mode == "create_static_mask":
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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25 --masking static
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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26 --mask_frame $masking.mask_frame
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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27 --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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28 #else if $masking.selection_mode == "create_dynamic_mask":
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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29 --masking dynamic
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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30 --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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31 #end if
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32
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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33 --dt $wavana.dt
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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34 --Tmin $wavana.tmin
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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35 --Tmax $wavana.tmax
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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36 --nT $wavana.nt
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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37 #if str($wavana.tcutoff)
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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38 --Tcutoff $wavana.tcutoff
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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39 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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40 #if str($wavana.win_size):
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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41 --win_size $wavana.win_size
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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42 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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43
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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44 #if 'save_phase' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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45 --phase_out '$phase_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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46 #end if
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47
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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48 #if 'save_period' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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49 --period_out '$period_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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50 #end if
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51
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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52 #if 'save_power' in $outputs:
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53 --power_out '$power_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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54 #end if
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55
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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56 #if 'save_amplitude' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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57 --amplitude_out '$amplitude_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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58 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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59
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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60 #if 'save_preprocessed' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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61 --preprocessed_out '$preprocessed_out'
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62 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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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 --html_fname '$html_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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65 --report_img_path '$html_out.extra_files_path'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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66
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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67 --ncpu "\${GALAXY_SLOTS:-8}"
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68
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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69
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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70 ]]></command>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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71 <inputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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72 <param name="movie" type="data" format="tiff" label="Movie to analyze" help="Select a movie to wavelet analyze"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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73
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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74 <!--
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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75 The following Wavelet parameters must have the same numerical type as defined in the
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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76 argparse parser in spyboat_cli.py
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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77 -->
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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78 <section name="PreProc" title="Preprocessing" expanded="true">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
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79 <param argument="gauss_sigma" type="float" min="0" max="100" optional="true" label="Sigma"
0
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80 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" />
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81 <param argument="rescale_factor" type="integer" value="" min="0" max="99" optional="true" label="Rescale factor"
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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82 help="Downsamples the input movie by this factor given in %, leave blank to disable downsampling" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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83 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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84 <section name="wavana" title="Wavelet Analysis" expanded="true">
1
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85 <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"
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86 <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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87 <param name="tmax" type="float" value="30" min="0" max="10000" label="Largest period"
0
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88 help="Largest period for the wavelet transform" />
1
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iuc
parents: 0
diff changeset
89 <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
parents:
diff changeset
90 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
91 <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:
diff changeset
92 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
93 <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"
iuc
parents:
diff changeset
94 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
95 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
96 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
97 <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
parents:
diff changeset
98 <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
99 <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
100 <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
101 </param>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
102 <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
103 <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
104 <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"
iuc
parents:
diff changeset
105 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
106 <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
parents:
diff changeset
107 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
108 </when>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
109 <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
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
parents:
diff changeset
111 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
112 </when>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
113 </conditional>
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="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
parents:
diff changeset
115 <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
116 <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
117 <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
parents:
diff changeset
118 <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
119 <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
parents:
diff changeset
120 </param>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
121 </inputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
122
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
123 <outputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
124 <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
125 <filter>outputs and 'save_phase' in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
126 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
127 <data name="period_out" format="tiff" label="${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
128 <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
129 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
130 <data name="power_out" format="tiff" label="${movie.name[:-4]}_power">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
131 <filter>outputs and "save_power" in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
132 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
133 <data name="amplitude_out" format="tiff" label="${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
134 <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
135 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
136 <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
137 <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
parents:
diff changeset
138 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
139 <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"
iuc
parents:
diff changeset
140 </outputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
141
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
142 <tests>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
143 <test expect_num_outputs="2">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
144 <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
parents:
diff changeset
145 <param name="outputs" value="save_phase"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
146 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
147 <param name="selection_mode" value="no_masking" />
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
148 </conditional>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
149 <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
150 <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
151 <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
parents:
diff changeset
152 </assert_contents>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
153 </output>
3
9c53c7da9cbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 169dbae234162ed1e7167e62a3e54de8f89b0268
iuc
parents: 2
diff changeset
154 <!--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
155 <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"
iuc
parents:
diff changeset
156 </test>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
157 <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
158 <section name="wavana">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
159 <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
160 <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
161 <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
162 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
163 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
164 <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
165 </conditional>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
166 <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
parents:
diff changeset
167 <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
168 <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
169 <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
170 <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
parents:
diff changeset
171 </assert_contents>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
172 </output>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
173 </test>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
174 <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
175 <section name="wavana">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
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176 <param name="tmin" value="20"/>
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177 <param name="nt" value="150"/>
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178 <param name="tcutoff" value="40"/>
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179 </section>
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180 <conditional name="masking">
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181 <param name="selection_mode" value="create_dynamic_mask" />
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182 </conditional>
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183 <param name="movie" value="test-movie.tif" ftype="tiff"/>
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184 <param name="outputs" value="save_phase,save_preprocessed,save_power"/>
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185 <output name="phase_out" ftype="tiff">
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186 <assert_contents>
2
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187 <has_size value="1764430" delta="10000" />
0
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188 </assert_contents>
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189 </output>
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190 </test>
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191 </tests>
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192 <help><![CDATA[
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193 .. class:: infomark
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194
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195 **What it does**
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196
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197 -------------------
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198
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199 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.
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200 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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201
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202 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable.
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203
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204 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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205 Trimming away parts of the movie with no relevant data (e.g. outer dark edges) also speeds up the processing.
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206
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207 If multiple channels are present in your data, extract the channel of interest beforehand (e.g. with Fiji).
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208
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209 **Author**: Gregor Mönke (gregor.moenke@embl.de).
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210
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211 **Wrapper by**: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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212
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213 **Know what you are doing**
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214
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215 .. class:: warningmark
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216
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217 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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218
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219 -------------------
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220
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221 **Parameter List**
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222
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223 - Sigma:
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224 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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225
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226 - Rescale factor:
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227 Given in %, downsamples the spatial resolution of the input movie. This speeds up the whole analysis by a lot.
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228
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229 - Masking:
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230 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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231
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232 - Sampling interval:
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233 Time passed between consecutive measurements, e.g 'an image every 10 minutes'.
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234
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235 - Smallest Period:
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236 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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237
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238 - Largest period:
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239 The maximal period to scan for, this is the lower (in frequency) end of the spectrum. The inbuild Sinc filter will remove any periods larger than this form the data. Due to the 'roll off' of the filter, this value should be chosen generously. A warning will be given during processing if the chosen value exceeds the length of the time series.
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240
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241 - Number of periods to scan for:
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242 This is the the number of convolutions computed per pixel.
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243
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244 Spectral resolution = ( biggest period - smallest period ) / number of periods
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245
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246 - Tcutoff:
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247 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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248 be removed from the signal before the transform. If no value is given,
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249 no detrending is performed. At least a gracious cut-off of around ~3 times
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250 the largest period to be expected is recommended.
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251
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252 - Sliding window size
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253 Length (in time units, e.g. hours) of the sliding window to estimate
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254 an amplitude envelope. The signal then gets normalized by this envelope,
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255 meaning that all amplitudes will be around ~1 after the transform. The
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256 advantage is that signal with strong amplitude trends will have more
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257 meaningful Wavelet powers after normalization.
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258
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259
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260 ]]></help>
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261 <citations>
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262 <citation type="doi">10.1101/2020.04.29.067744</citation>
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263 </citations>
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264 </tool>