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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
author imgteam
date Tue, 14 Nov 2023 08:27:27 +0000
parents 9bb446db4a1e
children
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
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1 <tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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3 <macros>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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4 <token name="@TOOL_VERSION@">0.5</token>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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5 <token name="@VERSION_SUFFIX@">0</token>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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6 </macros>
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7 <edam_operations>
9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 <edam_operation>operation_3443</edam_operation>
9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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9 </edam_operations>
9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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10 <xrefs>
9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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11 <xref type="bio.tools">galaxy_image_analysis</xref>
9bb446db4a1e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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12 </xrefs>
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 <requirements>
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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14 <requirement type="package" version="0.14.2">scikit-image</requirement>
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6c92ac9ce868 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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15 <requirement type="package" version="0.15.1">tifffile</requirement>
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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16 <requirement type="package" version="1.15.4">numpy</requirement>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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17 <requirement type="package" version="5.3.0">pillow</requirement>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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18 <requirement type="package" version="1.2.1">scipy</requirement>
0
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 </requirements>
1
6c92ac9ce868 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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20 <command detect_errors="aggressive">
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <![CDATA[
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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22 #if str($mode.mode_selector) == 'cca':
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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23 python '$__tool_directory__/binary2label.py' '$input' '$output'
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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24 #elif str($mode.mode_selector) == 'watershed':
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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25 python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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26 #end if
0
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 ]]>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </command>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <inputs>
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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30 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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31 <conditional name="mode">
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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32 <param name="mode_selector" type="select" label="Mode">
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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33 <option value="cca">Connected component analysis</option>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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34 <option value="watershed">Watershed transform</option>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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35 </param>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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36 <when value="cca">
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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37 </when>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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38 <when value="watershed">
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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39 <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" />
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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40 </when>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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41 </conditional>
0
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42 </inputs>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 <outputs>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 <data format="tiff" name="output"/>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 </outputs>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 <tests>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 <test>
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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48 <param name="input" value="galaxyIcon_noText.tif" />
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49 <conditional name="mode">
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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50 <param name="mode_selector" value="cca" />
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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51 </conditional>
1
6c92ac9ce868 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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52 <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/>
0
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53 </test>
4
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54 <test>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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55 <param name="input" value="in.tif"/>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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56 <conditional name="mode">
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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57 <param name="mode_selector" value="watershed" />
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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58 <param name="min_distance" value="10" />
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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59 </conditional>
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60 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
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61 </test>
0
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62 </tests>
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63 <help>
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64 This tool assigns each object a unique label.
0
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65
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66 Individual objects are determined using connected component analysis, or distance transform and watershed.
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67 </help>
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68 <citations>
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69 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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70 </citations>
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71 </tool>