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