Mercurial > repos > imgteam > imagej2_analyze_skeleton

annotate imagej2_analyze_skeleton.xml @ 1:3272e0439968 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:52:29 +0000
parents bb84f130a4e1
children bdee06a1bcfa
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bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 <tool id="imagej2_analyze_skeleton" name="Analyze skeleton" version="@WRAPPER_VERSION@.0">
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 <description></description>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <macros>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 <import>imagej2_macros.xml</import>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 </macros>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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6 <expand macro="fiji_requirements"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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7 <command detect_errors="exit_code"><![CDATA[
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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8 #import os
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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9 #set error_log = 'output_log.txt'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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10 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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11 #set input_with_ext = '.'.join([input_sans_ext, $input.ext])
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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12 ln -s '$input.file_name' '$input_with_ext' &&
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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13 ImageJ --ij2 --headless --debug
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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14 --jython '$__tool_directory__/imagej2_analyze_skeleton_jython_script.py'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 '$error_log'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 '$input_with_ext'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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17 '$black_background'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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18 '$prune_cycle_method'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 '$prune_ends'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 '$calculate_largest_shortest_path'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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21 'no'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 '$output'
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 &>'$error_log';
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 if [[ $? -ne 0 ]]; then
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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25 cat '$error_log' >&2;
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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26 fi
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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27 ]]></command>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 <inputs>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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29 <expand macro="param_input"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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30 <expand macro="black_background_param"/>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 <param name="prune_cycle_method" type="select" label="Prune cycle method">
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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32 <option value="none" selected="True">None</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 <option value="shortest_branch">Shortest branch</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 <option value="lowest_intensity_voxel">Lowest intensity voxel</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 <option value="lowest_intensity_branch">Lowest intensity branch</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 </param>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 <param name="prune_ends" type="select" label="Prune ends">
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 <option value="no" selected="True">No</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 <option value="yes">Yes</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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40 </param>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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41 <param name="calculate_largest_shortest_path" type="select" label="Calculate largest shortest path">
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 <option value="no" selected="True">No</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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43 <option value="yes">Yes</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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44 </param>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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45 <!-- TODO: Uncomment this option when the tool has been enhanced to use the
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 future "Display labeled skeletons" option. See http://fiji.sc/AnalyzeSkeleton.
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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47 <param name="show_detailed_info" type="select" label="Show detailed info">
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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48 <option value="no" selected="True">No</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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49 <option value="yes">Yes</option>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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50 </param>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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51 -->
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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52 </inputs>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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53 <outputs>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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54 <data name="output" format="tabular"/>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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55 </outputs>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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56 <tests>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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57 <test>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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58 <param name="input" value="skeletonized_blobs.gif"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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59 <output name="output" file="basic.tabular" ftype="tabular"/>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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60 </test>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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61 <test>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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62 <param name="input" value="skeletonized_clown.jpg"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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63 <param name="prune_cycle_method" value="shortest_branch"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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64 <output name="output" file="shortest_branch_basic.tabular" ftype="tabular"/>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 </test>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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66 <test>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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67 <param name="input" value="skeletonized_blobs.gif"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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68 <param name="calculate_largest_shortest_path" value="yes"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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69 <output name="output" file="largest_shortest_path_basic.tabular" ftype="tabular"/>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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70 </test>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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71 <test>
1
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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72 <param name="input" value="skeletonized_clown.jpg"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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73 <param name="prune_cycle_method" value="shortest_branch"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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74 <param name="calculate_largest_shortest_path" value="yes"/>
3272e0439968 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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75 <output name="output" file="shortest_branch_all_yes.tabular" ftype="tabular"/>
0
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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76 </test>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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77 </tests>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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78 <help>
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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79
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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80 .. class:: warningmark
bb84f130a4e1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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81
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82 The underlying AnalyzeSkeleton Fiji plugin works on binary images, so other image types will
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83 automatically be converted to binary before they are analyzed. This step is performed using the
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84 ImageJ2 **Make Binary** command with the following settings: **Iterations:** 1, **Count:** 1,
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85 **Black background:** No, **Pad edges when eroding:** No. If these settings are not appropriate,
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86 first manually convert the image to binary using the **Convert to binary (black and white) with
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87 ImageJ2** tool, which allows you to change them.
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88
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89 .. class:: warningmark
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90
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91 The **Skeletonize images** tool produces skeleton images that can be used as input to this tool.
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92 Images that have not been skeletonized will not result in errors, but the results may or may not
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93 be useful.
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94
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95 **What it does**
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96
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97 <![CDATA[
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98 Tags all pixel/voxels in a skeleton image and then counts all its junctions, triple and quadruple
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99 points and branches, and measures their average and maximum length. The voxels are classified into
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100 three different categories depending on their 26 neighbors:
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101
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102 - **End-point** voxels: if they have less than 2 neighbors.
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103 - **Junction** voxels: if they have more than 2 neighbors.
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104 - **Slab** voxels: if they have exactly 2 neighbors.
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105
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106 -----
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107
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108 **Options**
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109
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110 - **Prune cycle method**: prune the possible loops in the skeleton.
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111 - **Prune ends**: prunes any branch that ends in an end-point.
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112 - **Calculate largest shortest path**: calculate the largest shortest path of each skeleton using the APSP (all pairs shortest path).
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113 ]]>
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114 </help>
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115 <citations>
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116 <citation type="doi">10.1002/jemt.20829</citation>
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117 <citation type="doi">10.1038/nmeth.2102</citation>
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118 </citations>
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119 </tool>