Mercurial > repos > thomaswollmann > wsi_extract_top_view
comparison wsi_extract_top_view.xml @ 0:9f01fd145af4 draft
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 |
| parents | |
| children | 257397c40c25 |
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| -1:000000000000 | 0:9f01fd145af4 |
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| 1 <tool id="wsi_extract_top_view" name="Extract Top View from WSI" version="0.1"> | |
| 2 <description>Extracts top view from WSI</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.14.0" >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,tif,ndpi,vms,vmu,scn,mrxs,tiff,svslide,bif" 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>Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.</help> | |
| 27 <citations> | |
| 28 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | |
| 29 </citations> | |
| 30 </tool> |