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annotate colorize_labels.xml @ 1:43c80f3c3b60 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
author imgteam
date Wed, 13 Mar 2024 19:08:34 +0000
parents 0afb17e107ff
children 3aa2d054848a
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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>
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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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4 <token name="@TOOL_VERSION@">3.2.1</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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5 <token name="@VERSION_SUFFIX@">0</token>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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6 </macros>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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7 <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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8 <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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9 </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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10 <requirements>
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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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11 <requirement type="package" version="3.2.1">networkx</requirement>
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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12 <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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13 <requirement type="package" version="0.18.1">scikit-image</requirement>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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14 </requirements>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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15 <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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17 ## 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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19 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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20 --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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21 --bg_label $bg_label
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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22 --bg_color '$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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23
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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24 ## Outputs
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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26 --output output.png
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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27
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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28 ]]>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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29 </command>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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30 <inputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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31 <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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32 <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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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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33 <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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34 <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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35 </inputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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36 <outputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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37 <data format="png" name="output" from_work_dir="output.png" />
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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38 </outputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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39 <tests>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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40 <test>
1
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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41 <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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42 <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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43 <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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44 <param name="bg_color" value="#5a5a5a" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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45 <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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46 </test>
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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47 <test>
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="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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49 <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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50 <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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51 <param name="bg_color" value="#ffffff" />
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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52 <output name="output" value="output2.png" ftype="png" compare="sim_size" delta_frac="0.1" />
0
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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53 </test>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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54 </tests>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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55 <help>
1
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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56 Colorize a 2-D label map for visualization using greedy coloring.
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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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57
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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58 Label maps are produced by segmentation and other image analysis steps.
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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59 Direct inspection of label maps can be difficult,
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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60 because labels usually correspond to gray values which are difficult to
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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61 distinguish visually from each other and from the image background.
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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62 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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63 label maps to color images, by assigning each label a unique color.
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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64 </help>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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65 <citations>
1
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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66 <citation type="bibtex">
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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67 @inproceedings{networkx,
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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68 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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69 title = {Exploring network structure, dynamics, and function using {NetworkX}},
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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70 booktitle = {Proc. of the 7th Python in Science Conference (SciPy 2008)},
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71 pages = {11--15},
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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72 year = {2008},
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73 }
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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74 </citation>
0
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75 </citations>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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76 </tool>