| Previous changeset 0:9f60ef2d586e (2022-09-08) Next changeset 2:4f43e11fb3c9 (2024-05-10) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a |
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modified:
main_macros.xml vitessce_spatial.xml |
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| diff -r 9f60ef2d586e -r 4bf852448b5d main_macros.xml --- a/main_macros.xml Thu Sep 08 17:23:33 2022 +0000 +++ b/main_macros.xml Wed Feb 28 20:52:55 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.0.4</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.01</token> <xml name="vitessce_requirements"> @@ -16,7 +16,7 @@ </xml> <xml name="vitessce_cmd" token_tool_id="vitessce_spatial"> - <command> + <command detect_errors="aggressive"> <![CDATA[ export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" && mkdir -p '${output.files_path}/A/0' && @@ -70,7 +70,7 @@ #if $masks --masks '${output.files_path}/A/0/masks01.ome.tiff' #end if - #if $do_phenotyping.phenotyping_choice + #if $do_phenotyping.phenotyping_choice == 'add_h5ad' --anndata '$anndata' #end if && |
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| diff -r 9f60ef2d586e -r 4bf852448b5d vitessce_spatial.xml --- a/vitessce_spatial.xml Thu Sep 08 17:23:33 2022 +0000 +++ b/vitessce_spatial.xml Wed Feb 28 20:52:55 2024 +0000 |
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| @@ -1,10 +1,14 @@ -<tool id="vitessce_spatial" name="Vitessce Visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>integrative visualization of multi-modal, spatial single-cell data</description> +<tool id="vitessce_spatial" name="Run multi-modal single-cell visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>with Vitessce</description> <macros> <import>main_macros.xml</import> </macros> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <expand macro="vitessce_requirements"/> <expand macro="macro_stdio" /> <version_command> "@VERSION@"</version_command> @@ -18,10 +22,14 @@ <param name="image" type="data" format="ome.tiff" label="Select the OME Tiff image" /> <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" /> <conditional name="do_phenotyping"> - <param name="phenotyping_choice" type="boolean" checked="true" label="Whether to do phenotyping"> + <param name="phenotyping_choice" type="select" label="Add annotations or visualizations from Anndata file"> + <option value="no_h5ad" selected="true">Do not add elements from Anndata file</option> + <option value="add_h5ad">Add elements from Anndata file</option> </param> - <when value="true"> - <param name="anndata" type="data" format="h5ad" label="Select the anndata contaning phenotyping info" /> + <when value="no_h5ad"> + </when> + <when value="add_h5ad"> + <param name="anndata" type="data" format="h5ad" label="Select the anndata file" /> <conditional name="scatterplot_embeddings"> <param name="embedding" type="select" label="Select an embedding algorithm for scatterplot"> <option value="umap" selected="true">UMAP</option> @@ -58,7 +66,7 @@ </when> </conditional> <conditional name="phenotype_factory"> - <param name="phenotype_mode" type="select" label="Input phenotyping keys"> + <param name="phenotype_mode" type="select" label="Input the anndata key to display"> <option value="choices" selected="true">Multiple choices</option> <option value="type_in">Type in</option> </param> @@ -76,8 +84,6 @@ </when> </conditional> </when> - <when value="false"> - </when> </conditional> </inputs> <outputs> @@ -87,7 +93,7 @@ <test> <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> <conditional name="do_phenotyping"> - <param name="phenotyping_choice" value="yes" /> + <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" /> @@ -99,7 +105,7 @@ <test> <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> <conditional name="do_phenotyping"> - <param name="phenotyping_choice" value="yes" /> + <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" /> @@ -114,7 +120,7 @@ <test> <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> <conditional name="do_phenotyping"> - <param name="phenotyping_choice" value="no" /> + <param name="phenotyping_choice" value="no_h5ad" /> </conditional> <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> </test> |