Mercurial > repos > thomaswollmann > wsi_extract_top_view
comparison wsi_extract_top_view.xml @ 1:257397c40c25 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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date | Wed, 16 Jan 2019 15:36:04 -0500 |
parents | 9f01fd145af4 |
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0:9f01fd145af4 | 1:257397c40c25 |
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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> |