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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:33:42 -0500
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9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
thomaswollmann
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1 <?xml version="1.0"?>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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2 <tool name="Colocalization" id="ip_colocalization" version="0.0.6">
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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3 <description>Colocalization of two segmentation maps</description>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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4 <requirements>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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5 <requirement type="package" version="0.14.0">scikit-image</requirement>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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6 <requirement type="package" version="1.15.4">numpy</requirement>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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7 </requirements>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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8 <command>
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9 <![CDATA[
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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10 python '$__tool_directory__/colocalization_viz.py' '$input_mask1' '$input_mask2' ./tmp.png
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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11 && mv ./tmp.png '$output'
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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12 ]]>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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13 </command>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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14 <inputs>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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15 <param name="input_mask1" type="data" format="tiff" label="Mask1 Source File" />
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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16 <param name="input_mask2" type="data" format="tiff" label="Mask2 Source File" />
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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17 </inputs>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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18 <outputs>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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19 <data format="png" name="output" />
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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20 </outputs>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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21 <tests>
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22 <test>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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23 <param name="input_mask1" value="sample1.tiff"/>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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24 <param name="input_mask2" value="sample2.tiff"/>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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25 <output name="output" value="out.png" ftype="png" compare="sim_size"/>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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26 </test>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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27 </tests>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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28 <help>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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29 This tool overlays two segmentation maps and displays the colocalization results.
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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30 </help>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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31 <citations>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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32 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
9174e8eaa1e1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit d93e1dd276027cfc3fb518236110395a23d96f66
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33 </citations>
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34 </tool>