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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
author thomaswollmann
date Mon, 07 Jan 2019 08:38:08 -0500
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children 257397c40c25
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9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
thomaswollmann
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1 <tool id="wsi_extract_top_view" name="Extract Top View from WSI" version="0.1">
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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2 <description>Extracts top view from WSI</description>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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3 <requirements>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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4 <requirement type="package" version="0.14.0" >scikit-image</requirement>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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5 <requirement type="package" version="1.15.4">numpy</requirement>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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6 <requirement type="package" version="1.1.1">openslide-python</requirement>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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7 <requirement type="package" version="0.5">glob2</requirement>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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8 </requirements>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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9 <command>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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10 <![CDATA[
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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11 python "$__tool_directory__/wsi_extract_top_view.py" '$input' '$output'
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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12 ]]>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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13 </command>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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14 <inputs>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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15 <param name="input" type="data" format="svs,tif,ndpi,vms,vmu,scn,mrxs,tiff,svslide,bif" label="Whole Slice Image"/><!--formats taken as listed on https://openslide.org/api/python/-->
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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16 </inputs>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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17 <outputs>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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18 <data name="output" format="tiff"/>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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19 </outputs>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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20 <tests>
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21 <test>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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22 <param name="input" value="CMU-1-Small-Region.svs"/>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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23 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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24 </test>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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25 </tests>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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26 <help>Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.</help>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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27 <citations>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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28 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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29 </citations>
9f01fd145af4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
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30 </tool>