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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:56 +0000
parents 5bf8eb50b280
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b58447a2eed2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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1 <tool id="ip_count_objects" name="Count objects in label map" version="0.0.5-2">
b58447a2eed2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
b58447a2eed2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations>
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4 <edam_operation>operation_3443</edam_operation>
b58447a2eed2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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5 </edam_operations>
b58447a2eed2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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6 <xrefs>
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
b58447a2eed2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <requirements>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <requirement type="package" version="0.14.2">scikit-image</requirement>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <requirement type="package" version="1.15.4">numpy</requirement>
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664232d2a3f7 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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12 <requirement type="package" version="0.15.1">tifffile</requirement>
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895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 </requirements>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <command>
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15 <![CDATA[
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 python '$__tool_directory__/count_objects.py' '$input' '$output'
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 ]]>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 </command>
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664232d2a3f7 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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19 <inputs>
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20 <param name="input" type="data" format="tiff,png" label="Source file" />
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895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 </inputs>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <outputs>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <data format="tabular" name="output" />
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 </outputs>
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25 <tests>
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26 <test>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <param name="input" value="input.tiff"/>
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28 <output name="output" value="table.tsv" ftype="tabular"/>
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29 </test>
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30 </tests>
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <help>
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32 **What it does**
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33
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34 This tool counts objects in a labeled image.
895a29ebd0c7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 </help>
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36 <citations>
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37 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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38 </citations>
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39 </tool>