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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:35:29 -0500
parents 66f7e94db2e6
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3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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1 <tool id="mergeneighboursinlabelimage" name="Merge Neighbours in Label" version="0.2">
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66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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2 <description>Merge Neighbours in Label Image</description>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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3 <requirements>
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3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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4 <requirement type="package" version="0.14.0">scikit-image</requirement>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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5 <requirement type="package" version="1.15.4">numpy</requirement>
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66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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6 </requirements>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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7 <command>
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8 <![CDATA[
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3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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9 python '$__tool_directory__/mergeneighboursinlabelimage.py' '$input' ./tmp.tiff -c $c
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
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10 && mv ./tmp.tiff '$output'
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66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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11 ]]>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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12 </command>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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13 <inputs>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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14 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Label Image File"/>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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15 <param label="Distance in pixel of objects which are merged" name="c" type="integer" value="50"/>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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16 </inputs>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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17 <outputs>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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18 <data format="tiff" name="output"/>
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3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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19 </outputs>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
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20 <tests>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
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21 <test>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
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22 <param name="input" value="galaxyIcon_noText.tif"/>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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23 <param name="c" value="10"/>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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24 <output name="output" file="out.tiff" ftype="tiff" compare="sim_size"/>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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25 </test>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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26 </tests>
3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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27 <help>This tools merges nearby objects in a label image using the minimum pixel distance.</help>
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66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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28 <citations>
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3536648d0a93 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
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29 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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30 </citations>
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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31 </tool>