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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
author thomaswollmann
date Thu, 16 Feb 2017 05:18:42 -0500
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cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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1 <tool id="visceral_evaluatesegmentation" name="Visceral - Evaluate Segmentation" version="0.4">
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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2 <description>Evaluate Segmentation</description>
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3 <requirements>
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4 <requirement type="package">visceral-evaluatesegmentation</requirement>
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5 </requirements>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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6 <command>
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7 <![CDATA[
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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8 EvaluateSegmentation '$gt_path' '$seg_path' -xml '$output'
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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9 ]]>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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10 </command>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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11 <inputs>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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12 <param name="gt_path" type="data" format="tiff,png,jpg,bmp" label="Ground Truth Image"/>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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13 <param name="seg_path" type="data" format="tiff,png,jpg,bmp" label="Segmented Image"/>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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14 </inputs>
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15 <outputs>
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16 <data format="xml" name="output"/>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="gt_path" value="sample.png" />
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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21 <param name="seg_path" value="sample.png" />
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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22 <output name="output" value="out.xml" ftype="xml" lines_diff="10" />
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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23 </test>
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24 </tests>
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25 <help>Calculates Metrics for Evaluating Image Segmentation</help>
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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26 <citations>
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27 <citation type="bibtex">@article{TA2015,
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28 author = {Abdel Aziz Taha and Allan Hanbury},
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29 title = {Metrics for Evaluating 3{D} Medical Image Segmentation: analysis, selection, and tool},
cc77c9bf7b4a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation commit 84957f4ad2994ba9bf594d835e5ddd6bcb98c59f
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30 journal = {BMC Medical Imaging},
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31 year = {2015},
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32 volume = {15},
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33 pages = {29},
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34 month = {August},
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35 }</citation>
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36 </citations>
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37 </tool>