Mercurial > repos > imgteam > superdsm
diff superdsm.xml @ 5:9b4830300f3a draft
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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--- a/superdsm.xml Mon Feb 12 14:58:45 2024 +0000 +++ b/superdsm.xml Thu Apr 04 15:26:50 2024 +0000 @@ -1,9 +1,14 @@ <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>with SuperDSM</description> <macros> + <import>creators.xml</import> + <import>tests.xml</import> <token name="@TOOL_VERSION@">0.2.0</token> <token name="@VERSION_SUFFIX@">0</token> </macros> + <creator> + <expand macro="creators/bmcv"/> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -13,7 +18,7 @@ </xrefs> <requirements> - <requirement type="package" version="0.2.0">superdsm</requirement> + <requirement type="package" version="@TOOL_VERSION@">superdsm</requirement> <!-- Pin the dependencies to specific versions for reproducibility: @@ -159,8 +164,18 @@ <param name="dataset" value="BBBC033_C2_z28.png" /> <param name="global_energy_minimization_pruning" value="exact" /> <param name="outputs" value="overlay,masks,cfg" /> - <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" /> + <expand macro="tests/intensity_image_diff" name="overlay" value="overlay.png" ftype="png"/> <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" /> + <output name="masks" ftype="png"> + <assert_contents> + + <has_image_width width="1024"/> + <has_image_height height="1344"/> + <has_image_channels channels="1"/> + <has_image_n_labels n="16"/><!-- 15 objects plus the background --> + + </assert_contents> + </output> </test> <test expect_num_outputs="1"> <param name="dataset" value="BBBC033_C2_z28.png" /> @@ -170,9 +185,13 @@ </test> </tests> <help> - This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images. + + **Performs segmentation of 2-D fluorescence microscopy images using deformable shape models and superadditivity.** + + SuperDSM is a globally optimal method for cell nuclei segmentation using deformable shape models and their inherent law of superadditivity. You can either use an individual input image (PNG, TIF) or a collection of such images. + </help> <citations> <citation type="bibtex">