Mercurial > repos > thomaswollmann > wsi_extract_top_view

comparison wsi_extract_top_view.xml @ 1:257397c40c25 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:36:04 -0500
parents 9f01fd145af4
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0:9f01fd145af4 1:257397c40c25
6 <requirement type="package" version="1.1.1">openslide-python</requirement> 6 <requirement type="package" version="1.1.1">openslide-python</requirement>
7 <requirement type="package" version="0.5">glob2</requirement> 7 <requirement type="package" version="0.5">glob2</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 python "$__tool_directory__/wsi_extract_top_view.py" '$input' '$output' 11 python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output'
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <inputs> 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/--> 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> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data name="output" format="tiff"/> 18 <data name="output" format="tiff"/>
19 </outputs> 19 </outputs>
20 <tests> 20 <tests>
23 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> 23 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
24 </test> 24 </test>
25 </tests> 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> 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> 27 <citations>
28 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 28 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
29 </citations> 29 </citations>
30 </tool> 30 </tool>