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

2:c700f0381e84

<?xml version="1.0"?>
<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy1" profile="20.05">
    <description>
        scores cells using the AUCell method for gene sets.
    </description>
    <requirements>
        <requirement type="package" version="1.4.0">decoupler</requirement>

            --gene_lists_to_score '$gene_lists_source.gene_lists_to_score'
            --score_names '$gene_lists_source.score_names'
            #end if
            --gene_symbols_field '$gene_symbols_field'
            $use_raw
            #if $write_anndata:
            --write_anndata
            --output_file anndata_aucell.h5ad
            #else:
            --output_file anndata_aucell_per_cell.tsv

            <when value="enumerated">
                <param name="gene_lists_to_score" type="text" label="Genes to score" />
                <param name="score_names" type="text" label="Score names" />
            </when>
        </conditional>
        <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."/>
    </inputs>
    <outputs>

3:e887a7e8c5b4

<?xml version="1.0"?>
<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>
    <requirements>
        <requirement type="package" version="1.4.0">decoupler</requirement>

            --gene_lists_to_score '$gene_lists_source.gene_lists_to_score'
            --score_names '$gene_lists_source.score_names'
            #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
            #else:
            --output_file anndata_aucell_per_cell.tsv

            <when value="enumerated">
                <param name="gene_lists_to_score" type="text" label="Genes to score" />
                <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."/>
    </inputs>
    <outputs>