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annotate detection_viz.xml @ 1:065118c24f2d draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 04:56:47 -0400
parents 4391508d0d82
children 94c60eb4ba3b
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065118c24f2d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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1 <tool id="ip_detection_viz" name="Detection Visualization" version="0.2">
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4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>Detection Visualization</description>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
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065118c24f2d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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5 <requirement type="package" version="3.0.2">matplotlib</requirement>
065118c24f2d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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6 <requirement type="package" version="0.15.1">tifffile</requirement>
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4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7 </requirements>
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065118c24f2d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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8 <command detect_errors="aggressive">
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4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <![CDATA[
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 python '$__tool_directory__/detection_viz.py' '$input' '$output'
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 --stroke_size $thickness --circle_radius $circle_radius $tp $fn $fp
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065118c24f2d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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12 ]]>
0
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 </command>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <inputs>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 <param argument="--tp" type="boolean" checked="false" falsevalue="" truevalue="--tp"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 <param argument="--fn" type="boolean" checked="false" falsevalue="" truevalue="--fn"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 <param argument="--fp" type="boolean" checked="false" falsevalue="" truevalue="--fp"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 <param name="thickness" type="float" value="3.0" label="Stroke thickness"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <param name="circle_radius" type="float" value="50.0" label="Circle radius"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 </inputs>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <outputs>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <data format="png" name="output"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 </outputs>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <tests>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <test>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <param name="input" value="sample.png"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <output name="output" value="out.png" ftype="png"/>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 </test>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 </tests>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <help>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 **What it does**
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 Draws circles of different colors around detected true positives, false negatives and false positives.
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 </help>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <citations>
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37 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 </citations>
4391508d0d82 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 </tool>