Mercurial > repos > ebi-gxa > decoupler_pseudobulk
changeset 11:70a5c6f2408d draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f6c6b8e014c99101232dc75aa972a12fc640a4de
| author | ebi-gxa |
|---|---|
| date | Fri, 25 Oct 2024 15:12:24 +0000 |
| parents | f6040492b499 |
| children | a559be56720c |
| files | decoupler_pseudobulk.py decoupler_pseudobulk.xml |
| diffstat | 2 files changed, 11 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/decoupler_pseudobulk.py Wed Oct 02 08:26:56 2024 +0000 +++ b/decoupler_pseudobulk.py Fri Oct 25 15:12:24 2024 +0000 @@ -503,6 +503,14 @@ for condition in conditions: # remove any starting or trailing whitespaces from condition condition = condition.strip() + if condition not in adata.obs[obs_field].unique(): + raise ValueError( + f"Condition '{condition}' from contrast {contrast}" + f" is not present in the " + f"obs_field '{obs_field}' from the AnnData object." + f"Possible values are: " + f"{', '.join(adata.obs[obs_field].unique())}." + ) # check the percentage of cells that express each gene # Filter the AnnData object based on the obs_field value adata_filtered = adata[adata.obs[obs_field] == condition]
--- a/decoupler_pseudobulk.xml Wed Oct 02 08:26:56 2024 +0000 +++ b/decoupler_pseudobulk.xml Fri Oct 25 15:12:24 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy5" profile="20.05"> +<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy6" profile="20.05"> <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description> <requirements> <requirement type="package" version="1.4.0">decoupler</requirement> @@ -103,10 +103,10 @@ <data name="filter_by_expr_plot" format="png" label="${tool.name} on ${on_string}: Filter by Expression plot" from_work_dir="plots_output_dir/filter_by_expr.png"> <filter>produce_plots</filter> </data> - <data name="genes_ignore_per_contrast_field" format="tabular" label="{tool.name} on ${on_string}: Genes to ignore by contrast field" from_work_dir="deseq_output_dir/genes_to_ignore_per_contrast_field.tsv"> + <data name="genes_ignore_per_contrast_field" format="tabular" label="${tool.name} on ${on_string}: Genes to ignore by contrast field" from_work_dir="deseq_output_dir/genes_to_ignore_per_contrast_field.tsv"> <filter>factor_fields</filter> </data> - <data name="genes_ignore_per_contrast" format="tabular" label="{tool.name} on ${on_string}: Genes to ignore by contrast" from_work_dir="plots_output_dir/genes_to_filter_by_contrast.tsv"> + <data name="genes_ignore_per_contrast" format="tabular" label="${tool.name} on ${on_string}: Genes to ignore by contrast" from_work_dir="plots_output_dir/genes_to_filter_by_contrast.tsv"> <filter>filter_per_contrast['filter'] == 'yes'</filter> </data> </outputs>