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annotate detection_viz.xml @ 0:629d9e8ca64c draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
author thomaswollmann
date Wed, 12 Dec 2018 04:37:59 -0500
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629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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1 <tool id="detection_viz" name="Detection Visualization" version="0.1">
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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2 <description>Detection Visualization</description>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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3 <requirements>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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4 <requirement type="package" version="0.14.1" >scikit-image</requirement>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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5 <requirement type="package" version="3.0.2" >matplotlib</requirement>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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6 </requirements>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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7 <command>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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8 <![CDATA[
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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9 python '$__tool_directory__/detection_viz.py' '$input' '$output' --stroke_size $thickness --circle_radius $circle_radius $tp $fn $fp
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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10 ]]>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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11 </command>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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12 <inputs>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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13 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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14 <param name="tp" type="boolean" checked="false" falsevalue="" truevalue="--tp"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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15 <param name="fn" type="boolean" checked="false" falsevalue="" truevalue="--fn"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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16 <param name="fp" type="boolean" checked="false" falsevalue="" truevalue="--fp"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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17 <param name="thickness" type="float" value="3.0" label="Stroke thickness"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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18 <param name="circle_radius" type="float" value="50.0" label="Circle radius"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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19 </inputs>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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20 <outputs>
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21 <data format="png" name="output"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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22 </outputs>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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23 <tests>
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24 <test>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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25 <param name="input" value="sample.png"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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26 <output name="output" value="out.png" ftype="png"/>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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27 </test>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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28 </tests>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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29 <help>Draws circles of different colors around detected true positives, false negatives and false positives.</help>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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30 <citations>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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31 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
629d9e8ca64c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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32 </citations>
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33 </tool>