Mercurial > repos > imgteam > 2d_feature_extraction

comparison 2d_feature_extraction.xml @ 6:8e3a52b74876 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 5bf032c4908e344099fba24e914bd26367d24a90
author imgteam
date Mon, 05 Jan 2026 14:35:43 +0000
parents 5530132d500e
children 048545339ced
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5:5530132d500e 6:8e3a52b74876
35 <conditional name="setup"> 35 <conditional name="setup">
36 <param name="mode" value="with-intensities"/> 36 <param name="mode" value="with-intensities"/>
37 <param name="intensities" value="input/input1_uint8.tiff"/> 37 <param name="intensities" value="input/input1_uint8.tiff"/>
38 <param name="features" value="@FEATURE@"/> 38 <param name="features" value="@FEATURE@"/>
39 </conditional> 39 </conditional>
40 <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv"/> 40 <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv" compare="re_match"/>
41 </test> 41 </test>
42 </xml> 42 </xml>
43 </macros> 43 </macros>
44 <creator> 44 <creator>
45 <expand macro="creators/bmcv"/> 45 <expand macro="creators/bmcv"/>
130 <param name="labels" value="input/input12.png"/> 130 <param name="labels" value="input/input12.png"/>
131 <conditional name="setup"> 131 <conditional name="setup">
132 <param name="mode" value="without-intensities"/> 132 <param name="mode" value="without-intensities"/>
133 <param name="features" value="label,area,area_convex,solidity"/> 133 <param name="features" value="label,area,area_convex,solidity"/>
134 </conditional> 134 </conditional>
135 <output name="output" ftype="tabular" value="output/input12.tsv"/> 135 <output name="output" ftype="tabular" value="output/input12.tsv" compare="re_match"/>
136 </test> 136 </test>
137 <test> 137 <test>
138 <param name="labels" value="input/input11.tiff"/> 138 <param name="labels" value="input/input11.tiff"/>
139 <conditional name="setup"> 139 <conditional name="setup">
140 <param name="mode" value="with-intensities"/> 140 <param name="mode" value="with-intensities"/>
141 <param name="intensities" value="input/input1_uint8.tiff"/> 141 <param name="intensities" value="input/input1_uint8.tiff"/>
142 <param name="features" value="area,mean_intensity,perimeter"/> 142 <param name="features" value="area,mean_intensity,perimeter"/>
143 </conditional> 143 </conditional>
144 <output name="output" ftype="tabular" value="output/input11.tsv"/> 144 <output name="output" ftype="tabular" value="output/input11.tsv" compare="re_match"/>
145 </test> 145 </test>
146 <!-- Single-channel 2-D Zarr (isolated features, verify that Dask arrays are converted to NumPy arrays whenever necessary) --> 146 <!-- Single-channel 2-D Zarr (isolated features, verify that Dask arrays are converted to NumPy arrays whenever necessary) -->
147 <expand macro="zarr-isolated-feature-test" feature="area"/> 147 <expand macro="zarr-isolated-feature-test" feature="area"/>
148 <expand macro="zarr-isolated-feature-test" feature="area_convex"/> 148 <expand macro="zarr-isolated-feature-test" feature="area_convex"/>
149 <expand macro="zarr-isolated-feature-test" feature="area_filled"/> 149 <expand macro="zarr-isolated-feature-test" feature="area_filled"/>
170 <conditional name="setup"> 170 <conditional name="setup">
171 <param name="mode" value="with-intensities"/> 171 <param name="mode" value="with-intensities"/>
172 <param name="intensities" value="input/input8_zyx.zarr"/> 172 <param name="intensities" value="input/input8_zyx.zarr"/>
173 <param name="features" value="area,area_convex,area_filled,axis_major_length,axis_minor_length,bbox,centroid,eccentricity,equivalent_diameter_area,euler_number,extent,inertia_tensor_eigvals,moments,moments_hu,orientation,perimeter,solidity,max_intensity,mean_intensity,min_intensity"/> 173 <param name="features" value="area,area_convex,area_filled,axis_major_length,axis_minor_length,bbox,centroid,eccentricity,equivalent_diameter_area,euler_number,extent,inertia_tensor_eigvals,moments,moments_hu,orientation,perimeter,solidity,max_intensity,mean_intensity,min_intensity"/>
174 </conditional> 174 </conditional>
175 <output name="output" ftype="tabular" value="output/input9.tsv"/> 175 <output name="output" ftype="tabular" value="output/input9.tsv" compare="re_match"/>
176 <assert_stdout> 176 <assert_stdout>
177 <has_line line='Skip feature that is not available for 3-D images: "eccentricity"'/> 177 <has_line line='Skip feature that is not available for 3-D images: "eccentricity"'/>
178 <has_line line='Skip feature that is not available for 3-D images: "moments_hu"'/> 178 <has_line line='Skip feature that is not available for 3-D images: "moments_hu"'/>
179 <has_line line='Skip feature that is not available for 3-D images: "orientation"'/> 179 <has_line line='Skip feature that is not available for 3-D images: "orientation"'/>
180 </assert_stdout> 180 </assert_stdout>