Mercurial > repos > watsocam > palom

comparison palom_svs.xml @ 1:69f8e01b2e17 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit a19fd3bd500b83efe504234f3306b41e0334312d"
author watsocam
date Wed, 18 May 2022 22:55:21 +0000
parents b66b59713319
children e30f622ef2c3
comparison
equal deleted inserted replaced
0:b66b59713319 1:69f8e01b2e17
1 <tool id="palom" name="palom" version="2021.12.0.0"> 1 <tool id="palom" name="palom" version="2021.12.0.1">
2 <description>Piecewise alignment for layers of mosaics. A tool for registering whole-slide images with different IHC stainings</description> 2 <description>Piecewise alignment for layers of mosaics. A tool for registering whole-slide images with different IHC stainings</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
44 modes += list(channel_df['mode']) 44 modes += list(channel_df['mode'])
45 45
46 pixel_size = None 46 pixel_size = None
47 47
48 #if $pixel_size: 48 #if $pixel_size:
49 pixel_size = int($pixel_size) 49 pixel_size = float($pixel_size)
50 #end if 50 #end if
51 51
52 level = 0 52 level = 0
53 53
54 #if $level: 54 #if $level:
74 </configfiles> 74 </configfiles>
75 <inputs> 75 <inputs>
76 <param name="reference_image" type="data" format="tiff" label="Hematoxylin reference image" help="An H+E image in .svs format"/> 76 <param name="reference_image" type="data" format="tiff" label="Hematoxylin reference image" help="An H+E image in .svs format"/>
77 <param name="moving_images" type="data_collection" label="Moving Images (data collection)" help="A collection of svs-format images to align to the reference image"/> 77 <param name="moving_images" type="data_collection" label="Moving Images (data collection)" help="A collection of svs-format images to align to the reference image"/>
78 <param name="channels" type="data" label="Channel and mode dataframe" help="A CSV file with 'channel' and 'mode' columns, with a row corresponding to each moving image"/> 78 <param name="channels" type="data" label="Channel and mode dataframe" help="A CSV file with 'channel' and 'mode' columns, with a row corresponding to each moving image"/>
79 <param name="pixel_size" type="integer" optional="true" label="Pixel Size" help="defaults to px size of reference image"/> 79 <param name="pixel_size" type="float" optional="true" label="Pixel Size" help="defaults to px size of reference image"/>
80 <param name="level" type="integer" optional="true" label="Level" help="pyramid level, defaults to 0 (lowest level)"/> 80 <param name="level" type="integer" optional="true" label="Level" help="pyramid level, defaults to 0 (lowest level)"/>
81 </inputs> 81 </inputs>
82 <outputs> 82 <outputs>
83 <collection name="qc_plots" type="list" label="${tool.name}: qc_plots"> 83 <collection name="qc_plots" type="list" label="${tool.name}: qc_plots">
84 <discover_datasets pattern="__name_and_ext__" directory="qc" ext="png" visible="false"/> 84 <discover_datasets pattern="__name_and_ext__" directory="qc" ext="png" visible="false"/>