Mercurial > repos > goeckslab > vitessce_spatial
diff vitessce_spatial.xml @ 4:068da7f7cd83 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
| author | goeckslab |
|---|---|
| date | Thu, 20 Feb 2025 19:47:16 +0000 |
| parents | 4bf852448b5d |
| children |
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--- a/vitessce_spatial.xml Thu May 30 17:24:44 2024 +0000 +++ b/vitessce_spatial.xml Thu Feb 20 19:47:16 2025 +0000 @@ -1,5 +1,5 @@ -<tool id="vitessce_spatial" name="Run multi-modal single-cell visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>with Vitessce</description> +<tool id="vitessce_spatial" name="Vitessce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments</description> <macros> <import>main_macros.xml</import> @@ -11,7 +11,7 @@ <expand macro="vitessce_requirements"/> <expand macro="macro_stdio" /> - <version_command> "@VERSION@"</version_command> + <version_command>echo "@TOOL_VERSION@"</version_command> <expand macro="vitessce_cmd" /> <configfiles> @@ -88,41 +88,36 @@ </inputs> <outputs> <data format="html" name="output" /> + <data format="json" name="vitessce_config" from_work_dir="config.json" hidden="true" label="Vitessce config file on ${on_string}" /> </outputs> <tests> <test> - <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> - <conditional name="do_phenotyping"> - <param name="phenotyping_choice" value="add_h5ad" /> - <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> - <conditional name="phenotype_factory"> - <param name="phenotype_mode" value="type_in" /> - <param name="phenotypes" value="leiden" /> - </conditional> - </conditional> - <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> - </test> - <test> - <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> + <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" /> <conditional name="do_phenotyping"> <param name="phenotyping_choice" value="add_h5ad" /> - <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> - <conditional name="scatterplot_embeddings"> - <param name="embedding" value="pca" /> - </conditional> - <conditional name="phenotype_factory"> - <param name="phenotype_mode" value="type_in" /> - <param name="phenotypes" value="leiden" /> - </conditional> + <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" /> </conditional> - <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> + <output name="vitessce_config"> + <assert_contents> + <has_json_property_with_text property="name" text="OMETIFF" /> + <has_json_property_with_text property="path" text="obs/phenotype" /> + </assert_contents> + </output> </test> <test> - <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> + <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" /> + <param name="masks" value="vitessce_mask.tiff" ftype="tiff" /> <conditional name="do_phenotyping"> - <param name="phenotyping_choice" value="no_h5ad" /> + <param name="phenotyping_choice" value="add_h5ad" /> + <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" /> </conditional> - <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> + <output name="vitessce_config"> + <assert_contents> + <has_json_property_with_text property="name" text="OMETIFF" /> + <has_json_property_with_text property="name" text="MASKS" /> + <has_json_property_with_text property="path" text="obs/phenotype" /> + </assert_contents> + </output> </test> </tests> <help>