Mercurial > repos > goeckslab > vitessce_spatial
comparison vitessce_spatial.xml @ 1:4bf852448b5d draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
| author | goeckslab |
|---|---|
| date | Wed, 28 Feb 2024 20:52:55 +0000 |
| parents | 9f60ef2d586e |
| children |
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| 0:9f60ef2d586e | 1:4bf852448b5d |
|---|---|
| 1 <tool id="vitessce_spatial" name="Vitessce Visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="vitessce_spatial" name="Run multi-modal single-cell visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>integrative visualization of multi-modal, spatial single-cell data</description> | 2 <description>with Vitessce</description> |
| 3 | 3 |
| 4 <macros> | 4 <macros> |
| 5 <import>main_macros.xml</import> | 5 <import>main_macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 | |
| 8 <edam_operations> | |
| 9 <edam_operation>operation_3443</edam_operation> | |
| 10 </edam_operations> | |
| 7 | 11 |
| 8 <expand macro="vitessce_requirements"/> | 12 <expand macro="vitessce_requirements"/> |
| 9 <expand macro="macro_stdio" /> | 13 <expand macro="macro_stdio" /> |
| 10 <version_command> "@VERSION@"</version_command> | 14 <version_command> "@VERSION@"</version_command> |
| 11 <expand macro="vitessce_cmd" /> | 15 <expand macro="vitessce_cmd" /> |
| 16 | 20 |
| 17 <inputs> | 21 <inputs> |
| 18 <param name="image" type="data" format="ome.tiff" label="Select the OME Tiff image" /> | 22 <param name="image" type="data" format="ome.tiff" label="Select the OME Tiff image" /> |
| 19 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" /> | 23 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" /> |
| 20 <conditional name="do_phenotyping"> | 24 <conditional name="do_phenotyping"> |
| 21 <param name="phenotyping_choice" type="boolean" checked="true" label="Whether to do phenotyping"> | 25 <param name="phenotyping_choice" type="select" label="Add annotations or visualizations from Anndata file"> |
| 26 <option value="no_h5ad" selected="true">Do not add elements from Anndata file</option> | |
| 27 <option value="add_h5ad">Add elements from Anndata file</option> | |
| 22 </param> | 28 </param> |
| 23 <when value="true"> | 29 <when value="no_h5ad"> |
| 24 <param name="anndata" type="data" format="h5ad" label="Select the anndata contaning phenotyping info" /> | 30 </when> |
| 31 <when value="add_h5ad"> | |
| 32 <param name="anndata" type="data" format="h5ad" label="Select the anndata file" /> | |
| 25 <conditional name="scatterplot_embeddings"> | 33 <conditional name="scatterplot_embeddings"> |
| 26 <param name="embedding" type="select" label="Select an embedding algorithm for scatterplot"> | 34 <param name="embedding" type="select" label="Select an embedding algorithm for scatterplot"> |
| 27 <option value="umap" selected="true">UMAP</option> | 35 <option value="umap" selected="true">UMAP</option> |
| 28 <option value="tsne">tSNE</option> | 36 <option value="tsne">tSNE</option> |
| 29 <option value="pca">PCA</option> | 37 <option value="pca">PCA</option> |
| 56 <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" /> | 64 <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" /> |
| 57 </section> | 65 </section> |
| 58 </when> | 66 </when> |
| 59 </conditional> | 67 </conditional> |
| 60 <conditional name="phenotype_factory"> | 68 <conditional name="phenotype_factory"> |
| 61 <param name="phenotype_mode" type="select" label="Input phenotyping keys"> | 69 <param name="phenotype_mode" type="select" label="Input the anndata key to display"> |
| 62 <option value="choices" selected="true">Multiple choices</option> | 70 <option value="choices" selected="true">Multiple choices</option> |
| 63 <option value="type_in">Type in</option> | 71 <option value="type_in">Type in</option> |
| 64 </param> | 72 </param> |
| 65 <when value="choices"> | 73 <when value="choices"> |
| 66 <param name="phenotypes" type="select" multiple="true" display="checkboxes" label="Select the key(s)" > | 74 <param name="phenotypes" type="select" multiple="true" display="checkboxes" label="Select the key(s)" > |
| 74 <when value="type_in"> | 82 <when value="type_in"> |
| 75 <param name="phenotypes" type="text" value="" label="Type in the keys storing phenotypes" help="Comma delimited for multiple keys."/> | 83 <param name="phenotypes" type="text" value="" label="Type in the keys storing phenotypes" help="Comma delimited for multiple keys."/> |
| 76 </when> | 84 </when> |
| 77 </conditional> | 85 </conditional> |
| 78 </when> | 86 </when> |
| 79 <when value="false"> | |
| 80 </when> | |
| 81 </conditional> | 87 </conditional> |
| 82 </inputs> | 88 </inputs> |
| 83 <outputs> | 89 <outputs> |
| 84 <data format="html" name="output" /> | 90 <data format="html" name="output" /> |
| 85 </outputs> | 91 </outputs> |
| 86 <tests> | 92 <tests> |
| 87 <test> | 93 <test> |
| 88 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> | 94 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> |
| 89 <conditional name="do_phenotyping"> | 95 <conditional name="do_phenotyping"> |
| 90 <param name="phenotyping_choice" value="yes" /> | 96 <param name="phenotyping_choice" value="add_h5ad" /> |
| 91 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> | 97 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> |
| 92 <conditional name="phenotype_factory"> | 98 <conditional name="phenotype_factory"> |
| 93 <param name="phenotype_mode" value="type_in" /> | 99 <param name="phenotype_mode" value="type_in" /> |
| 94 <param name="phenotypes" value="leiden" /> | 100 <param name="phenotypes" value="leiden" /> |
| 95 </conditional> | 101 </conditional> |
| 97 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> | 103 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> |
| 98 </test> | 104 </test> |
| 99 <test> | 105 <test> |
| 100 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> | 106 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> |
| 101 <conditional name="do_phenotyping"> | 107 <conditional name="do_phenotyping"> |
| 102 <param name="phenotyping_choice" value="yes" /> | 108 <param name="phenotyping_choice" value="add_h5ad" /> |
| 103 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> | 109 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> |
| 104 <conditional name="scatterplot_embeddings"> | 110 <conditional name="scatterplot_embeddings"> |
| 105 <param name="embedding" value="pca" /> | 111 <param name="embedding" value="pca" /> |
| 106 </conditional> | 112 </conditional> |
| 107 <conditional name="phenotype_factory"> | 113 <conditional name="phenotype_factory"> |
| 112 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> | 118 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> |
| 113 </test> | 119 </test> |
| 114 <test> | 120 <test> |
| 115 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> | 121 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> |
| 116 <conditional name="do_phenotyping"> | 122 <conditional name="do_phenotyping"> |
| 117 <param name="phenotyping_choice" value="no" /> | 123 <param name="phenotyping_choice" value="no_h5ad" /> |
| 118 </conditional> | 124 </conditional> |
| 119 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> | 125 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> |
| 120 </test> | 126 </test> |
| 121 </tests> | 127 </tests> |
| 122 <help> | 128 <help> |