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comparison superdsm.xml @ 5:9b4830300f3a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:50 +0000
parents dc5f72f6b1e9
children 79ec3263686a
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4:dc5f72f6b1e9 5:9b4830300f3a
1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with SuperDSM</description> 2 <description>with SuperDSM</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
4 <token name="@TOOL_VERSION@">0.2.0</token> 6 <token name="@TOOL_VERSION@">0.2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 </creator>
7 <edam_operations> 12 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 13 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 14 </edam_operations>
10 <xrefs> 15 <xrefs>
11 <xref type="bio.tools">superdsm</xref> 16 <xref type="bio.tools">superdsm</xref>
12 <xref type="biii">superdsm</xref> 17 <xref type="biii">superdsm</xref>
13 </xrefs> 18 </xrefs>
14 <requirements> 19 <requirements>
15 20
16 <requirement type="package" version="0.2.0">superdsm</requirement> 21 <requirement type="package" version="@TOOL_VERSION@">superdsm</requirement>
17 22
18 <!-- 23 <!--
19 Pin the dependencies to specific versions for reproducibility: 24 Pin the dependencies to specific versions for reproducibility:
20 https://github.com/BMCV/SuperDSM#dependency-version-considerations 25 https://github.com/BMCV/SuperDSM#dependency-version-considerations
21 --> 26 -->
157 <tests> 162 <tests>
158 <test expect_num_outputs="3"> 163 <test expect_num_outputs="3">
159 <param name="dataset" value="BBBC033_C2_z28.png" /> 164 <param name="dataset" value="BBBC033_C2_z28.png" />
160 <param name="global_energy_minimization_pruning" value="exact" /> 165 <param name="global_energy_minimization_pruning" value="exact" />
161 <param name="outputs" value="overlay,masks,cfg" /> 166 <param name="outputs" value="overlay,masks,cfg" />
162 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" /> 167 <expand macro="tests/intensity_image_diff" name="overlay" value="overlay.png" ftype="png"/>
163 <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" /> 168 <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" />
169 <output name="masks" ftype="png">
170 <assert_contents>
171
172 <has_image_width width="1024"/>
173 <has_image_height height="1344"/>
174 <has_image_channels channels="1"/>
175 <has_image_n_labels n="16"/><!-- 15 objects plus the background -->
176
177 </assert_contents>
178 </output>
164 </test> 179 </test>
165 <test expect_num_outputs="1"> 180 <test expect_num_outputs="1">
166 <param name="dataset" value="BBBC033_C2_z28.png" /> 181 <param name="dataset" value="BBBC033_C2_z28.png" />
167 <param name="global_energy_minimization_pruning" value="exact" /> 182 <param name="global_energy_minimization_pruning" value="exact" />
168 <param name="outputs" value="cfg" /> 183 <param name="outputs" value="cfg" />
169 <output name="cfg" value="cfg.tsv" ftype="tsv" compare="diff" /> 184 <output name="cfg" value="cfg.tsv" ftype="tsv" compare="diff" />
170 </test> 185 </test>
171 </tests> 186 </tests>
172 <help> 187 <help>
173 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images. 188
189 **Performs segmentation of 2-D fluorescence microscopy images using deformable shape models and superadditivity.**
190
191 SuperDSM is a globally optimal method for cell nuclei segmentation using deformable shape models and their inherent law of superadditivity.
174 192
175 You can either use an individual input image (PNG, TIF) or a collection of such images. 193 You can either use an individual input image (PNG, TIF) or a collection of such images.
194
176 </help> 195 </help>
177 <citations> 196 <citations>
178 <citation type="bibtex"> 197 <citation type="bibtex">
179 @inproceedings{kostrykin2024, 198 @inproceedings{kostrykin2024,
180 author = {Kostrykin, L. and Rohr, K.}, 199 author = {Kostrykin, L. and Rohr, K.},