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Add CellTypist tool for automated celltype annotation #7415

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Add CellTypist tool for automated celltype annotation #7415

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@pavanvidem pavanvidem commented Oct 30, 2025 •
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FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

@bernt-matthias bernt-matthias changed the title Add CellTypist tool for automated celltye annotation Add CellTypist tool for automated celltype annotation Oct 30, 2025
bernt-matthias
bernt-matthias reviewed Oct 30, 2025
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tools/celltypist/celltypist.xml
<param name="prediction" type="text" label="Prediction column in AnnData.obs for dotplot" value="predicted_labels" />
</inputs>
<outputs>
<data name="anndata_out" format="h5ad" label="${tool.name} on ${on_string}: AnnData with celltype annotations" />
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No label needed if there is only one output.

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Intially, I implemented an option to create a dotplot of probabilities per predicted type over some existing annotation. But this is not very useful. Removed it.

tools/celltypist/celltypist.xml Outdated
<requirement type="package" version="@TOOL_VERSION@">celltypist</requirement>
</requirements>
<command><![CDATA[
cp '$adata' 'anndata.h5ad' &&
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Is the copy needed?

tools/celltypist/celltypist.xml Outdated
import celltypist
from celltypist import models

adata = sc.read_h5ad('anndata.h5ad') models.download_models(models='$model_name', cache_dir='./celltypist_models_cache')
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Suggested change
adata = sc.read_h5ad('anndata.h5ad') models.download_models(models='$model_name', cache_dir='./celltypist_models_cache')
adata = sc.read_h5ad('$adata')
models.download_models(models='$model_name', cache_dir='./celltypist_models_cache')

tools/celltypist/celltypist.xml Outdated
<option value="prob match">Enable a multi-label classification utilising a probability threshold</option>
</param>
<param name="p_thres" type="float" label="Probability threshold" value="0.5" />
<param name="min_prop" type="float" label="Minimum proportion for cell type assignment" value="0.05" />
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min/max

tools/celltypist/celltypist.xml Outdated
<param name="p_thres" type="float" label="Probability threshold" value="0.5" />
<param name="min_prop" type="float" label="Minimum proportion for cell type assignment" value="0.05" />
<param name="reference" type="text" label="Reference column in AnnData.obs for dotplot" value="cell_type" />
<param name="prediction" type="text" label="Prediction column in AnnData.obs for dotplot" value="predicted_labels" />
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are empty_field validators needed for the text inputs?

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@pavanvidem @bernt-matthias