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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:49:03 -0500
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a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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1 <tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.1">
a1d02d2e814a 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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imgteam
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3 <requirements>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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5 <requirement type="package" version="1.15.4">numpy</requirement>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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6 <requirement type="package" version="1.1.1">openslide-python</requirement>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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7 <requirement type="package" version="0.5">glob2</requirement>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8 </requirements>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9 <command>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <![CDATA[
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output'
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 ]]>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 </command>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <inputs>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <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/-->
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 </inputs>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 <outputs>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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18 <data name="output" format="tiff"/>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 </outputs>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <tests>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <test>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <param name="input" value="CMU-1-Small-Region.svs"/>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 </test>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 </tests>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <help>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 **What it does**
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 </help>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <citations>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 </citations>
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 </tool>