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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 10:00:07 +0000
parents 413c02625317
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c0a1bffb9783 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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1 <tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.2">
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413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>from whole-slice image</description>
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c0a1bffb9783 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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3 <requirements>
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="1.15.4">numpy</requirement>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 <requirement type="package" version="1.1.1">openslide-python</requirement>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7 <requirement type="package" version="0.5">glob2</requirement>
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c0a1bffb9783 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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8 <requirement type="package" version="0.15.1">tifffile</requirement>
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413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 </requirements>
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c0a1bffb9783 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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10 <command detect_errors="aggressive">
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413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <![CDATA[
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output'
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 ]]>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 </command>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <inputs>
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16 <param name="input" type="data" format="svs,svslide,vms,mrxs,tif,tiff" label="Whole Slice Image"/><!--formats taken as listed on https://openslide.org/api/python/-->
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 </inputs>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 <outputs>
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19 <data name="output" format="tiff"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="CMU-1-Small-Region.svs"/>
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24 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 </test>
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26 </tests>
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <help>
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28 **What it does**
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29
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.
413c02625317 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 </help>
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32 <citations>
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33 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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34 </citations>
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35 </tool>