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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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<tool id="wsi_extract_top_view" name="Extract Top View from WSI" version="0.1"> 
  <description>Extracts top view from WSI</description>
  <requirements> 
    <requirement type="package" version="0.14.0" >scikit-image</requirement>
    <requirement type="package" version="1.15.4">numpy</requirement>
    <requirement type="package" version="1.1.1">openslide-python</requirement>
    <requirement type="package" version="0.5">glob2</requirement>
  </requirements>
  <command> 
        <![CDATA[
        python "$__tool_directory__/wsi_extract_top_view.py" '$input' '$output'
        ]]>
  </command>
  <inputs> 
    <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/-->
  </inputs>
  <outputs>
    <data name="output" format="tiff"/>
  </outputs>
  <tests>
    <test>
	    <param name="input" value="CMU-1-Small-Region.svs"/>
      <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
    </test>
  </tests>
  <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>
  <citations>
      <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
  </citations>
</tool>