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annotate detection_viz.xml @ 1:245a1cde4cd5 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
author thomaswollmann
date Wed, 12 Dec 2018 04:50:23 -0500
parents f5f85c63737c
children 69218d7300e5
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f5f85c63737c 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">
f5f85c63737c 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>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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3 <requirements>
f5f85c63737c 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>
f5f85c63737c 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>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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6 </requirements>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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7 <command>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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8 <![CDATA[
f5f85c63737c 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
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245a1cde4cd5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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10 ]]>
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f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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11 </command>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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12 <inputs>
f5f85c63737c 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"/>
f5f85c63737c 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"/>
f5f85c63737c 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"/>
f5f85c63737c 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"/>
f5f85c63737c 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"/>
f5f85c63737c 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"/>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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19 </inputs>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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20 <outputs>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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21 <data format="png" name="output"/>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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22 </outputs>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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23 <tests>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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24 <test>
f5f85c63737c 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"/>
f5f85c63737c 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"/>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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27 </test>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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28 </tests>
f5f85c63737c 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>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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30 <citations>
f5f85c63737c 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>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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32 </citations>
f5f85c63737c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
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33 </tool>