Mercurial > repos > ebi-gxa > score_genes_aucell
diff decoupler_aucell_score.xml @ 3:e887a7e8c5b4 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 11fb36a94b8262ef8e78f1c6dd46c4146eb59341
author | ebi-gxa |
---|---|
date | Mon, 15 Apr 2024 13:20:21 +0000 |
parents | e024d8280886 |
children | 515ac51db6e5 |
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--- a/decoupler_aucell_score.xml Fri Mar 15 12:18:05 2024 +0000 +++ b/decoupler_aucell_score.xml Mon Apr 15 13:20:21 2024 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy1" profile="20.05"> +<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy2" profile="20.05"> <description> scores cells using the AUCell method for gene sets. </description> @@ -20,6 +20,9 @@ #end if --gene_symbols_field '$gene_symbols_field' $use_raw + #if $min_n_genes: + --min_n '$min_n_genes' + #end if #if $write_anndata: --write_anndata --output_file anndata_aucell.h5ad @@ -43,6 +46,7 @@ <param name="score_names" type="text" label="Score names" /> </when> </conditional> + <param name="min_n_genes" type="integer" label="Minimum number of genes" help="Minimum number of genes to match in each gene set" optional="true" value="5"/> <param name="gene_symbols_field" type="text" label="Gene symbols field" help="The field in the AnnData var table where gene symbols are stored."/> <param name="use_raw" type="boolean" value="false" truevalue="--use_raw" falsevalue="" label="Use raw data" help="Use RAW data in the AnnData instead of the X matrix."/> <param name="write_anndata" type="boolean" value="false" truevalue="--write_anndata" falsevalue="" label="Write the modified AnnData object" help="Whether to write or not the same AnnData file again with the signatures on it. If unselected, a text files of cells in rows and signatures in columns (as in Obs) is produced."/>