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comparison mesmer.xml @ 3:c60b810d570d draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit caf99c99d5698c3524e6eb7fd43c0197c2a3b3cb
author goeckslab
date Tue, 28 Nov 2023 19:46:58 +0000
parents 187918c47051
children 2675ff99a53b
comparison
equal deleted inserted replaced
2:187918c47051 3:c60b810d570d
44 #if $compartment_select.compartment != 'whole-cell': 44 #if $compartment_select.compartment != 'whole-cell':
45 nuc_kwargs = { 45 nuc_kwargs = {
46 #if $compartment_select.nuclear_options.pixel_expansion != '': 46 #if $compartment_select.nuclear_options.pixel_expansion != '':
47 'pixel_expansion': $compartment_select.nuclear_options.pixel_expansion, 47 'pixel_expansion': $compartment_select.nuclear_options.pixel_expansion,
48 #end if 48 #end if
49 #for $key, $value in $dict.items($compartment_select.nuclear_options.adv_options) 49 #for $key, $value in $compartment_select.nuclear_options.adv_options.items():
50 '$key': $value, 50 '$key': $value,
51 #end for 51 #end for
52 'maxima_threshold': $compartment_select.nuclear_options.maxima_threshold 52 'maxima_threshold': $compartment_select.nuclear_options.maxima_threshold
53 } 53 }
54 #end if 54 #end if
57 nuclear_channels = level_array.oindex[nuclear_indices, :, :] 57 nuclear_channels = level_array.oindex[nuclear_indices, :, :]
58 nuclear_channels = np.sum(nuclear_channels, axis = 0) 58 nuclear_channels = np.sum(nuclear_channels, axis = 0)
59 59
60 #if $compartment_select.compartment != 'nuclear': 60 #if $compartment_select.compartment != 'nuclear':
61 wc_kwargs = { 61 wc_kwargs = {
62 #for $key, $value in $dict.items($compartment_select.wc_options.adv_options) 62 #for $key, $value in $compartment_select.wc_options.adv_options.items():
63 '$key': $value, 63 '$key': $value,
64 #end for 64 #end for
65 'maxima_threshold': $compartment_select.wc_options.maxima_threshold 65 'maxima_threshold': $compartment_select.wc_options.maxima_threshold
66 } 66 }
67 67
145 <data format="tiff" name="mask" from_work_dir="mask.tif" label="${tool.name} on ${on_string}: Mask"> 145 <data format="tiff" name="mask" from_work_dir="mask.tif" label="${tool.name} on ${on_string}: Mask">
146 <filter>compartment_select['compartment'] != 'both'</filter> 146 <filter>compartment_select['compartment'] != 'both'</filter>
147 </data> 147 </data>
148 </outputs> 148 </outputs>
149 <tests> 149 <tests>
150 <test> 150 <test expect_num_outputs="1">
151 <param name="image" value="deepcell_test.tiff" ftype="tiff"/> 151 <param name="image" value="deepcell_test.tiff" ftype="tiff"/>
152 <param name="compartment" value="nuclear" /> 152 <param name="compartment" value="nuclear" />
153 <param name="image_mpp" value="0.65" /> 153 <param name="image_mpp" value="0.65" />
154 <param name="squeeze" value="True" /> 154 <param name="squeeze" value="True" />
155 <output name="mask" ftype="tiff"> 155 <output name="mask" ftype="tiff">
156 <assert_contents> 156 <assert_contents>
157 <has_size value="1049000" delta="1000" /> 157 <has_size value="1049000" delta="1000" />
158 </assert_contents> 158 </assert_contents>
159 </output> 159 </output>
160 </test> 160 </test>
161 <test> 161 <test expect_num_outputs="1">
162 <param name="image" value="deepcell_test.tiff" ftype="tiff"/> 162 <param name="image" value="deepcell_test.tiff" ftype="tiff"/>
163 <param name="compartment" value="whole-cell" /> 163 <param name="compartment" value="whole-cell" />
164 <param name="wc_channels" value="0, 1" /> 164 <param name="wc_channels" value="0, 1" />
165 <param name="maxima_threshold" value="0.075" /> 165 <param name="maxima_threshold" value="0.075" />
166 <param name="image_mpp" value="0.65" /> 166 <param name="image_mpp" value="0.65" />
169 <assert_contents> 169 <assert_contents>
170 <has_size value="1049000" delta="1000" /> 170 <has_size value="1049000" delta="1000" />
171 </assert_contents> 171 </assert_contents>
172 </output> 172 </output>
173 </test> 173 </test>
174 <test> 174 <test expect_num_outputs="2">
175 <param name="image" value="deepcell_test.tiff" ftype="tiff"/> 175 <param name="image" value="deepcell_test.tiff" ftype="tiff"/>
176 <param name="compartment" value="both" /> 176 <param name="compartment" value="both" />
177 <param name="image_mpp" value="0.65" /> 177 <param name="image_mpp" value="0.65" />
178 <param name="wc_channels" value="1" /> 178 <param name="wc_channels" value="1" />
179 <param name="nuclear_channels" value="0" /> 179 <param name="nuclear_channels" value="0" />