Mercurial > repos > goeckslab > vitessce_spatial
comparison vitessce_spatial.xml @ 4:068da7f7cd83 draft
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 | 97be83fc3677 |
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| 3:7cc457aa78b1 | 4:068da7f7cd83 |
|---|---|
| 1 <tool id="vitessce_spatial" name="Run multi-modal single-cell visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="vitessce_spatial" name="Vitessce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>with Vitessce</description> | 2 <description>Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments</description> |
| 3 | 3 |
| 4 <macros> | 4 <macros> |
| 5 <import>main_macros.xml</import> | 5 <import>main_macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 | 7 |
| 9 <edam_operation>operation_3443</edam_operation> | 9 <edam_operation>operation_3443</edam_operation> |
| 10 </edam_operations> | 10 </edam_operations> |
| 11 | 11 |
| 12 <expand macro="vitessce_requirements"/> | 12 <expand macro="vitessce_requirements"/> |
| 13 <expand macro="macro_stdio" /> | 13 <expand macro="macro_stdio" /> |
| 14 <version_command> "@VERSION@"</version_command> | 14 <version_command>echo "@TOOL_VERSION@"</version_command> |
| 15 <expand macro="vitessce_cmd" /> | 15 <expand macro="vitessce_cmd" /> |
| 16 | 16 |
| 17 <configfiles> | 17 <configfiles> |
| 18 <inputs name="inputs" /> | 18 <inputs name="inputs" /> |
| 19 </configfiles> | 19 </configfiles> |
| 86 </when> | 86 </when> |
| 87 </conditional> | 87 </conditional> |
| 88 </inputs> | 88 </inputs> |
| 89 <outputs> | 89 <outputs> |
| 90 <data format="html" name="output" /> | 90 <data format="html" name="output" /> |
| 91 <data format="json" name="vitessce_config" from_work_dir="config.json" hidden="true" label="Vitessce config file on ${on_string}" /> | |
| 91 </outputs> | 92 </outputs> |
| 92 <tests> | 93 <tests> |
| 93 <test> | 94 <test> |
| 94 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> | 95 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" /> |
| 95 <conditional name="do_phenotyping"> | 96 <conditional name="do_phenotyping"> |
| 96 <param name="phenotyping_choice" value="add_h5ad" /> | 97 <param name="phenotyping_choice" value="add_h5ad" /> |
| 97 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> | 98 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" /> |
| 98 <conditional name="phenotype_factory"> | |
| 99 <param name="phenotype_mode" value="type_in" /> | |
| 100 <param name="phenotypes" value="leiden" /> | |
| 101 </conditional> | |
| 102 </conditional> | 99 </conditional> |
| 103 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> | 100 <output name="vitessce_config"> |
| 101 <assert_contents> | |
| 102 <has_json_property_with_text property="name" text="OMETIFF" /> | |
| 103 <has_json_property_with_text property="path" text="obs/phenotype" /> | |
| 104 </assert_contents> | |
| 105 </output> | |
| 104 </test> | 106 </test> |
| 105 <test> | 107 <test> |
| 106 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> | 108 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" /> |
| 109 <param name="masks" value="vitessce_mask.tiff" ftype="tiff" /> | |
| 107 <conditional name="do_phenotyping"> | 110 <conditional name="do_phenotyping"> |
| 108 <param name="phenotyping_choice" value="add_h5ad" /> | 111 <param name="phenotyping_choice" value="add_h5ad" /> |
| 109 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> | 112 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" /> |
| 110 <conditional name="scatterplot_embeddings"> | |
| 111 <param name="embedding" value="pca" /> | |
| 112 </conditional> | |
| 113 <conditional name="phenotype_factory"> | |
| 114 <param name="phenotype_mode" value="type_in" /> | |
| 115 <param name="phenotypes" value="leiden" /> | |
| 116 </conditional> | |
| 117 </conditional> | 113 </conditional> |
| 118 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> | 114 <output name="vitessce_config"> |
| 119 </test> | 115 <assert_contents> |
| 120 <test> | 116 <has_json_property_with_text property="name" text="OMETIFF" /> |
| 121 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> | 117 <has_json_property_with_text property="name" text="MASKS" /> |
| 122 <conditional name="do_phenotyping"> | 118 <has_json_property_with_text property="path" text="obs/phenotype" /> |
| 123 <param name="phenotyping_choice" value="no_h5ad" /> | 119 </assert_contents> |
| 124 </conditional> | 120 </output> |
| 125 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> | |
| 126 </test> | 121 </test> |
| 127 </tests> | 122 </tests> |
| 128 <help> | 123 <help> |
| 129 <![CDATA[ | 124 <![CDATA[ |
| 130 **What it does** | 125 **What it does** |