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annotate orientationpy.xml @ 0:214f548481eb draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
author imgteam
date Tue, 12 Mar 2024 10:54:40 +0000
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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1 <tool id="orientationpy" name="Compute image orientation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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2 <description>with OrientationPy</description>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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3 <macros>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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4 <token name="@TOOL_VERSION@">0.2.0.4</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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6 </macros>
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7 <edam_operations>
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8 <edam_operation>operation_3443</edam_operation>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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9 </edam_operations>
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10 <xrefs>
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11 <xref type="biii">orientationj</xref>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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12 </xrefs>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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13 <requirements>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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14 <requirement type="package" version="0.2.0.4">orientationpy</requirement>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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15 <requirement type="package" version="0.22.0">scikit-image</requirement>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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16 </requirements>
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17 <command><![CDATA[
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18
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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19 ## Inputs
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20
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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21 python '$__tool_directory__/orientationpy-cli.py' '$image'
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22 --mode $mode
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23 --sigma $sigma
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24 --min_energy $min_energy
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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25 --min_coherency $min_coherency
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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26 --max_precision $max_precision
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27
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28 ## Outputs
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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29
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30 --output_angle_tsv '$output_angle_tsv'
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31
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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32 ]]>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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33 </command>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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34 <inputs>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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35 <param name="image" type="data" format="png,tiff" label="Input image" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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36 <param argument="--mode" type="select" label="Gradient computation">
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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37 <option value="finite_difference" selected="True">Finite differences</option>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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38 <option value="gaussian">Gaussian</option>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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39 <option value="splines">Splines</option>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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40 </param>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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41 <param argument="--sigma" type="float" label="Spatial scale (in pixels)" value="2" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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42 <param argument="--min_energy" type="float" label="Minimum energy" value="0.1" min="0" max="1" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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43 <param argument="--min_coherency" type="float" label="Minimum coherency" value="0.2" min="0" max="1" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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44 <param argument="--max_precision" type="integer" label="Maximum possible precision (in decimals)" value="3" min="0" max="8" help="Governs the histogram bin size (increasing maximum possible precision leads to smaller bin sizes). Note that increasing the maximum possible precision too far may actually decrease the actual precision, because the bin size becomes too small." />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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45 </inputs>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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46 <outputs>
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47 <data format="tabular" name="output_angle_tsv" from_work_dir="output_angle.tsv" />
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48 </outputs>
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49 <tests>
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50 <!-- Test negative angle -->
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51 <test>
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52 <param name="image" value="input1.tif" />
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53 <param name="mode" value="finite_difference" />
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54 <param name="sigma" value="2" />
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55 <param name="min_energy" value="0.1" />
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56 <param name="min_coherency" value="0.2" />
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57 <param name="max_precision" value="1" />
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58 <output name="output_angle_tsv">
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59 <assert_contents>
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60 <has_line line="Angle" />
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61 <has_line line="-45.0" />
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62 <has_n_lines n="2" />
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63 <has_n_columns n="1" />
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <!-- Test positive angle -->
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68 <test>
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69 <param name="image" value="input2.tif" />
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70 <param name="mode" value="finite_difference" />
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71 <param name="sigma" value="2" />
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72 <param name="min_energy" value="0.1" />
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73 <param name="min_coherency" value="0.2" />
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74 <param name="max_precision" value="1" />
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75 <output name="output_angle_tsv">
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76 <assert_contents>
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77 <has_line line="Angle" />
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78 <has_line line="45.0" />
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79 <has_n_lines n="2" />
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80 <has_n_columns n="1" />
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81 </assert_contents>
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82 </output>
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83 </test>
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84 </tests>
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85 <help>
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86 Compute the orientation of 2-D images in degrees using OrientationPy.
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87
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88 OrientationPy is the pythonic successor to the well-loved OrientationJ Fiji Plugin.
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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89 It is a library that takes in images and computes the orientation of the greylevels.
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90 A key step is the computation of image gradients, for a number of different techniques is supported.
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91
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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92 For more information on ``--min_energy`` and ``--min_coherency`` see: https://epfl-center-for-imaging.gitlab.io/orientationpy/orientationpy_examples/plot_fibres_2d.html#plot-hsv-composition
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93 </help>
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94 <citations>
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95 <citation type="doi">10.1007/s10237-011-0325-z</citation>
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96 </citations>
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97 </tool>