Mercurial > repos > ebi-gxa > score_genes_aucell
comparison 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 |
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date | Mon, 15 Apr 2024 13:20:21 +0000 |
parents | e024d8280886 |
children | 515ac51db6e5 |
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2:c700f0381e84 | 3:e887a7e8c5b4 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy1" profile="20.05"> | 2 <tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy2" profile="20.05"> |
3 <description> | 3 <description> |
4 scores cells using the AUCell method for gene sets. | 4 scores cells using the AUCell method for gene sets. |
5 </description> | 5 </description> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="1.4.0">decoupler</requirement> | 7 <requirement type="package" version="1.4.0">decoupler</requirement> |
18 --gene_lists_to_score '$gene_lists_source.gene_lists_to_score' | 18 --gene_lists_to_score '$gene_lists_source.gene_lists_to_score' |
19 --score_names '$gene_lists_source.score_names' | 19 --score_names '$gene_lists_source.score_names' |
20 #end if | 20 #end if |
21 --gene_symbols_field '$gene_symbols_field' | 21 --gene_symbols_field '$gene_symbols_field' |
22 $use_raw | 22 $use_raw |
23 #if $min_n_genes: | |
24 --min_n '$min_n_genes' | |
25 #end if | |
23 #if $write_anndata: | 26 #if $write_anndata: |
24 --write_anndata | 27 --write_anndata |
25 --output_file anndata_aucell.h5ad | 28 --output_file anndata_aucell.h5ad |
26 #else: | 29 #else: |
27 --output_file anndata_aucell_per_cell.tsv | 30 --output_file anndata_aucell_per_cell.tsv |
41 <when value="enumerated"> | 44 <when value="enumerated"> |
42 <param name="gene_lists_to_score" type="text" label="Genes to score" /> | 45 <param name="gene_lists_to_score" type="text" label="Genes to score" /> |
43 <param name="score_names" type="text" label="Score names" /> | 46 <param name="score_names" type="text" label="Score names" /> |
44 </when> | 47 </when> |
45 </conditional> | 48 </conditional> |
49 <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"/> | |
46 <param name="gene_symbols_field" type="text" label="Gene symbols field" help="The field in the AnnData var table where gene symbols are stored."/> | 50 <param name="gene_symbols_field" type="text" label="Gene symbols field" help="The field in the AnnData var table where gene symbols are stored."/> |
47 <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."/> | 51 <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."/> |
48 <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."/> | 52 <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."/> |
49 </inputs> | 53 </inputs> |
50 <outputs> | 54 <outputs> |