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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 05:36:05 -0500
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9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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1 <tool id="split_labelmap" name="Split Labelmap" version="0.1">
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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2 <description>Split Labelmap</description>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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3 <requirements>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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4 <requirement type="package" version="0.14.1" >scikit-image</requirement>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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5 <requirement type="package" version="1.15.4">numpy</requirement>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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6 <requirement type="package" version="0.15.1">tifffile</requirement> <!--not sure if this is required-->
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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7 </requirements>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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8 <command>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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9 <![CDATA[
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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10 python "$__tool_directory__/split_labelmap.py" '$input' '$output'
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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11 ]]>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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12 </command>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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13 <inputs>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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14 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image containing labels"/>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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15 </inputs>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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16 <outputs>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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17 <data name="output" format="tiff"/>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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18 </outputs>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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19 <tests>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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20 <test>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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21 <param name="input" value="sample_seg.tif"/>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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22 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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23 </test>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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24 </tests>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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25 <help>Takes a label image and outputs a similar file with the given name where the labeled parts of the image that touch (or overlap) are separated by at least 1 pixel (at most 2).</help>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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26 <citations>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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27 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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28 </citations>
9e15e70bb22b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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29 </tool>