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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:27 +0000
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9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_merge_neighbours_in_label" name="Merge neighbors in label map" version="0.3-2">
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations>
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation>
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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5 </edam_operations>
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
9cbddb13fb9e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <requirements>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <requirement type="package" version="0.14.2">scikit-image</requirement>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <requirement type="package" version="1.15.4">numpy</requirement>
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c6a6ab7c9940 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit b2acc1845a25828181597fe5b6982fe116a7796d
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12 <requirement type="package" version="0.15.1">tifffile</requirement>
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07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 </requirements>
1
c6a6ab7c9940 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit b2acc1845a25828181597fe5b6982fe116a7796d
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14 <command detect_errors="aggressive">
0
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <![CDATA[
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 python '$__tool_directory__/mergeneighboursinlabelimage.py' '$input' ./tmp.tiff -c $c
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 ]]>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 </command>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 <inputs>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Label Image File"/>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <param label="Distance in pixel of objects which are merged" name="c" type="integer" value="50"/>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 </inputs>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <outputs>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <data format="tiff" name="output" from_work_dir="tmp.tiff"/>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 </outputs>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <tests>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <test>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <param name="input" value="galaxyIcon_noText.tif"/>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <param name="c" value="10"/>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <output name="output" file="out.tiff" ftype="tiff" compare="sim_size"/>
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c6a6ab7c9940 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit b2acc1845a25828181597fe5b6982fe116a7796d
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31 </test>
0
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 </tests>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 <help>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 **What it does**
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 This tools merges nearby objects in a label image using the minimum pixel distance.
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 </help>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <citations>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 </citations>
07ac39c0e949 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 </tool>