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annotate colorize_labels.xml @ 3:2d1de6e7b113 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:12:15 +0000
parents 3aa2d054848a
children 5907be5a8d7c
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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1 <tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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2 <description>with NetworkX</description>
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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3 <macros>
2
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4 <import>creators.xml</import>
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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5 <import>tests.xml</import>
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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6 <token name="@TOOL_VERSION@">3.2.1</token>
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2d1de6e7b113 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c86a1b93cb7732f7331a981d13465653cc1a2790
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7 <token name="@VERSION_SUFFIX@">2</token>
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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8 </macros>
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9 <creator>
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10 <expand macro="creators/bmcv" />
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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11 </creator>
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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12 <edam_operations>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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13 <edam_operation>operation_3443</edam_operation>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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14 </edam_operations>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
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17 <requirement type="package" version="1.22">numpy</requirement>
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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18 <requirement type="package" version="0.18.1">scikit-image</requirement>
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2d1de6e7b113 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c86a1b93cb7732f7331a981d13465653cc1a2790
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19 <requirement type="package" version="0.1">giatools</requirement>
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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20 </requirements>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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21 <command><![CDATA[
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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23 ## Inputs
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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25 python '$__tool_directory__/colorize_labels.py' '$input'
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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26 --radius $radius
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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27 --bg_label $bg_label
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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28 --bg_color '$bg_color'
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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30 ## Outputs
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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31
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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32 --output output.png
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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34 ]]>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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35 </command>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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36 <inputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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37 <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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38 <param argument="--radius" type="integer" min="1" value="10" label="Radius of the neighborhood" help="Defines the neighborhood (in pixels) where labels are considered to be adjacent." />
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39 <param argument="--bg_label" type="integer" value="0" label="Background label" />
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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40 <param argument="--bg_color" type="color" value="#000000" label="Background color"/>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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41 </inputs>
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42 <outputs>
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43 <data format="png" name="output" from_work_dir="output.png" />
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44 </outputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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45 <tests>
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46 <test>
1
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47 <param name="input" value="input1.tif" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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48 <param name="radius" value="1" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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49 <param name="bg_label" value="0" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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50 <param name="bg_color" value="#5a5a5a" />
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51 <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
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52 <has_image_channels channels="3"/>
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53 </expand>
1
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54 </test>
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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55 <test>
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56 <param name="input" value="input2.tif" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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57 <param name="radius" value="10" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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58 <param name="bg_label" value="0" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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59 <param name="bg_color" value="#ffffff" />
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60 <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
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61 <has_image_channels channels="3"/>
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62 </expand>
0
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63 </test>
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64 </tests>
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65 <help>
2
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66
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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67 **Colorizes a 2-D label map for visualization using greedy coloring.**
0
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68
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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69 Label maps are produced by segmentation and other image analysis steps.
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70 Direct inspection of label maps can be difficult,
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71 because labels usually correspond to gray values which are difficult to
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72 distinguish visually from each other and from the image background.
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73 To facilitate the visual inspection of label maps, this tools converts
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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74 label maps to color images, by assigning each label a unique color.
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75
0
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76 </help>
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77 <citations>
1
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78 <citation type="bibtex">
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79 @inproceedings{networkx,
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80 author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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81 title = {Exploring network structure, dynamics, and function using {NetworkX}},
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82 booktitle = {Proc. of the 7th Python in Science Conference (SciPy 2008)},
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83 pages = {11--15},
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84 year = {2008},
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85 }
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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86 </citation>
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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87 </citations>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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88 </tool>