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annotate spyboat.xml @ 2:4626a83601d4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit b5cdb8bbc5334d5ff05b3e2fcc13c574832d2dd9"
author iuc
date Sat, 06 Feb 2021 12:00:33 +0000
parents 639d2031d998
children 9c53c7da9cbe
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639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
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1 <tool id="spyboat" name="SpyBOAT" version="@TOOL_VERSION@" profile="20.01" license="GPL-3.0-or-later">
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
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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>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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5 </macros>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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6 <requirements>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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7 <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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8 </requirements>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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9 <version_command>python '$__tool_directory__/spyboat_cli.py' --version</version_command>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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10 <command detect_errors="exit_code"><![CDATA[
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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11 ## needed for pulsar combat
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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12 cat '$__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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13 ## run tool
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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14 python '$__tool_directory__/spyboat_cli.py'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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15 --input_path '$movie'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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16 #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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17 --gauss_sigma $PreProc.gauss_sigma
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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18 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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19 #if str($PreProc.rescale_factor):
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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20 --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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21 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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22
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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23 #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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24 --masking static
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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25 --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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26 --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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27 #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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28 --masking dynamic
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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29 --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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30 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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31
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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32 --dt $wavana.dt
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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33 --Tmin $wavana.tmin
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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34 --Tmax $wavana.tmax
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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35 --nT $wavana.nt
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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36 #if str($wavana.tcutoff)
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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37 --Tcutoff $wavana.tcutoff
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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38 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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39 #if str($wavana.win_size):
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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40 --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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41 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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42
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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43 #if 'save_phase' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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44 --phase_out '$phase_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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45 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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46
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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47 #if 'save_period' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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48 --period_out '$period_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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49 #end if
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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50
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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51 #if 'save_power' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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52 --power_out '$power_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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53 #end if
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54
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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55 #if 'save_amplitude' in $outputs:
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56 --amplitude_out '$amplitude_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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57 #end if
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58
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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59 #if 'save_preprocessed' in $outputs:
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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60 --preprocessed_out '$preprocessed_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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61 #end if
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62
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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63 --html_fname '$html_out'
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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64 --report_img_path '$html_out.extra_files_path'
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65
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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66 --ncpu "\${GALAXY_SLOTS:-8}"
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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67
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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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 ]]></command>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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70 <inputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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71 <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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72
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 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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75 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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76 -->
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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77 <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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78 <param argument="gauss_sigma" type="float" min="0" max="100" optional="true" label="Sigma"
0
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79 help="Width of the Gaussian smoothing kernel, leave blank if no pre-smoothing desired" />
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80 <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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81 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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82 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
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83 <section name="wavana" title="Wavelet Analysis" expanded="true">
1
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84 <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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85 <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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86 <param name="tmax" type="float" value="30" min="0" max="10000" label="Largest period"
0
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87 help="Largest period for the wavelet transform" />
1
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88 <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
89 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
90 <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
91 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
92 <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
93 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
94 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
95 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
96 <param name="selection_mode" type="select" label="Masking the output" help="Create a mask from the (blurred/rescaled) input to mask out regions without oscillations/signal in the output">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
97 <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
98 <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
99 <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
100 </param>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
101 <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
102 <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
103 <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
104 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
105 <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
106 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
107 </when>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
108 <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
109 <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
110 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
111 </when>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
112 </conditional>
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 </param>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
120 </inputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
121
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
122 <outputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
123 <data name="phase_out" format="tiff" label="${movie.name[:-4]}_phase">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
124 <filter>outputs and 'save_phase' in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
125 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
126 <data name="period_out" format="tiff" label="${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
127 <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
128 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
129 <data name="power_out" format="tiff" label="${movie.name[:-4]}_power">
1
639d2031d998 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 88e9d9a220d160f55e0472719bb463143a4eefa5"
iuc
parents: 0
diff changeset
130 <filter>outputs and "save_power" in outputs</filter>
0
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
131 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
132 <data name="amplitude_out" format="tiff" label="${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
133 <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
134 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
135 <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
136 <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
137 </data>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
138 <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
139 </outputs>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
140
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
141 <tests>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
142 <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
143 <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
144 <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
145 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
146 <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
147 </conditional>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
148 <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
149 <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
150 <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
151 </assert_contents>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
152 </output>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
153 <output name="html_out" file="output1.html" ftype="html"/>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
154 </test>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
155 <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
156 <section name="wavana">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
157 <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
158 <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
159 <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
160 </section>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
161 <conditional name="masking">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
162 <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
163 </conditional>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
164 <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
165 <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
166 <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
167 <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
168 <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
169 </assert_contents>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
170 </output>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
171 </test>
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
172 <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
173 <section name="wavana">
76733d05d8ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"
iuc
parents:
diff changeset
174 <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
175 <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
176 <param name="tcutoff" value="40"/>
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177 </section>
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178 <conditional name="masking">
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179 <param name="selection_mode" value="create_dynamic_mask" />
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180 </conditional>
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181 <param name="movie" value="test-movie.tif" ftype="tiff"/>
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182 <param name="outputs" value="save_phase,save_preprocessed,save_power"/>
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183 <output name="phase_out" ftype="tiff">
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184 <assert_contents>
2
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185 <has_size value="1764430" delta="10000" />
0
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186 </assert_contents>
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187 </output>
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188 </test>
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189 </tests>
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190 <help><![CDATA[
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191 .. class:: infomark
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192
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193 **What it does**
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194
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195 -------------------
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196
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197 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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198 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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199
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200 Pre-smoothing of the data with Gaussian kernels is supported and often recommendable.
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201
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202 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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203 Trimming away parts of the movie with no relevant data (e.g. outer dark edges) also speeds up the processing.
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204
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205 If multiple channels are present in your data, extract the channel of interest beforehand (e.g. with Fiji).
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206
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207 **Author**: Gregor Mönke (gregor.moenke@embl.de).
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208
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209 **Wrapper by**: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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210
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211 **Know what you are doing**
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212
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213 .. class:: warningmark
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214
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215 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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216
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217 -------------------
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218
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219 **Parameter List**
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220
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221 - Sigma:
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222 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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223
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224 - Rescale factor:
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225 Given in %, downsamples the spatial resolution of the input movie. This speeds up the whole analysis by a lot.
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226
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227 - Masking:
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228 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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229
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230 - Sampling interval:
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231 Time passed between consecutive measurements, e.g 'an image every 10 minutes'.
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232
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233 - Smallest Period:
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234 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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235
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236 - Largest period:
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237 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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238
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239 - Number of periods to scan for:
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240 This is the the number of convolutions computed per pixel.
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241
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242 Spectral resolution = ( biggest period - smallest period ) / number of periods
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243
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244 - Tcutoff:
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245 The cut-off period for the sinc filter, periods larger than this one will
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246 be removed from the signal before the transform. If no value is given,
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247 no detrending is performed. At least a gracious cut-off of around ~3 times
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248 the largest period to be expected is recommended.
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249
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250 - Sliding window size
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251 Length (in time units, e.g. hours) of the sliding window to estimate
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252 an amplitude envelope. The signal then gets normalized by this envelope,
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253 meaning that all amplitudes will be around ~1 after the transform. The
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254 advantage is that signal with strong amplitude trends will have more
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255 meaningful Wavelet powers after normalization.
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256
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257
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258 ]]></help>
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259 <citations>
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260 <citation type="doi">10.1101/2020.04.29.067744</citation>
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261 </citations>
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262 </tool>