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annotate superdsm.xml @ 0:1b0fc671187f draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
author imgteam
date Sun, 25 Jun 2023 21:48:40 +0000
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children 700ae37e5c69
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1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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1 <tool id="ip_superdsm" name="SuperDSM" version="0.1.2-1" profile="20.05">
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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2 <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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3 <requirements>
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4 <requirement type="package" version="0.1.2">superdsm</requirement>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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5 <requirement type="package" version="1.6.0">ray-core</requirement>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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6 <requirement type="package" version="0.18.1">scikit-image</requirement>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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7 </requirements>
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8 <command detect_errors="aggressive">
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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9 <![CDATA[
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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10 python '$__tool_directory__/run-superdsm.py'
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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11 '${dataset}'
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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12 'cfg.json'
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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13 'masks.png'
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14 'overlay.png'
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15 $seg_border
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16 \${GALAXY_SLOTS:-4}
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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17 > stdout.txt
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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22 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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23 <!--
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24 <section name="config" title="Hyperparameters" expanded="false">
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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25 </section>
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26 -->
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27 </inputs>
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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28 <outputs>
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29 <data format="txt" name="stdout" from_work_dir="stdout.txt" label="${tool.name} on ${on_string}: stdout" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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30 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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31 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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32 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="dataset" value="BBBC033_C2_z28.png" />
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37 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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38 </test>
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39 </tests>
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40 <help>
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41 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
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42
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43 You can either use an individual input image (PNG, TIF) or a collection of such images.
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44 </help>
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45 <citations>
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46 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
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47 </citations>
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48 </tool>