Mercurial > repos > imgteam > colorize_labels

annotate colorize_labels.xml @ 4:5907be5a8d7c draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
author imgteam
date Tue, 24 Sep 2024 17:30:20 +0000
parents 2d1de6e7b113
children
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
imgteam
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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
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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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
imgteam
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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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5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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7 <token name="@VERSION_SUFFIX@">3</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>
2
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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9 <creator>
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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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>
0
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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3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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16 <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
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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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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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29
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
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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33
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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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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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>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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42 <outputs>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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43 <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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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>
4
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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46 <!-- int64 -->
0
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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47 <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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48 <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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49 <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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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="#5a5a5a" />
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52 <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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53 <has_image_channels channels="3"/>
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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54 </expand>
1
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>
4
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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56 <!-- uint8 -->
1
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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57 <test>
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="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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59 <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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60 <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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61 <param name="bg_color" value="#ffffff" />
2
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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62 <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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63 <has_image_channels channels="3"/>
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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64 </expand>
0
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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65 </test>
4
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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66 <!-- uint16 -->
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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67 <test>
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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68 <param name="input" value="input3.tif" />
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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69 <param name="radius" value="100" />
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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70 <param name="bg_label" value="0" />
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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71 <param name="bg_color" value="#ffffff" />
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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72 <expand macro="tests/intensity_image_diff" name="output" value="output3.png" ftype="png">
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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73 <has_image_channels channels="3"/>
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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74 </expand>
5907be5a8d7c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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75 </test>
0
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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76 </tests>
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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77 <help>
2
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78
3aa2d054848a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f
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79 **Colorizes a 2-D label map for visualization using greedy coloring.**
0
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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80
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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81 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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82 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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83 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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84 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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85 To facilitate the visual inspection of label maps, this tools converts
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86 label maps to color images, by assigning each label a unique color.
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87
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88 </help>
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89 <citations>
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90 <citation type="bibtex">
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91 @inproceedings{networkx,
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92 author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},
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93 title = {Exploring network structure, dynamics, and function using {NetworkX}},
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94 booktitle = {Proc. of the 7th Python in Science Conference (SciPy 2008)},
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95 pages = {11--15},
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96 year = {2008},
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97 }
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98 </citation>
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99 </citations>
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100 </tool>