comparison decoupler_aucell_score.xml @ 4:515ac51db6e5 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b01245159f9cb67101497bb974b2c13bcee019b7

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>

            --write_anndata
            --output_file anndata_aucell.h5ad
            #else:
            --output_file anndata_aucell_per_cell.tsv
            #end if
    </command>
    <inputs>
        <param name="input_file" type="data" format="h5ad" label="Input AnnData file" />
        <conditional name="gene_lists_source">
            <param name="source" type="select" label="Source of gene lists to score" help="Choose between using a GMT file and specified gene sets or enumerated genes and gene set names.">

                    <has_n_columns n="3"/>
                    <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**Description**

This tool scores cells using the AUCell method for gene sets.

4:515ac51db6e5

<?xml version="1.0"?>
<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy3" profile="20.05">
    <description>
        scores cells using the AUCell method for gene sets.
    </description>
    <requirements>
        <requirement type="package" version="1.4.0">decoupler</requirement>

            --write_anndata
            --output_file anndata_aucell.h5ad
            #else:
            --output_file anndata_aucell_per_cell.tsv
            #end if
            --max_threads "\${GALAXY_SLOTS:-4}"
    </command>
    <inputs>
        <param name="input_file" type="data" format="h5ad" label="Input AnnData file" />
        <conditional name="gene_lists_source">
            <param name="source" type="select" label="Source of gene lists to score" help="Choose between using a GMT file and specified gene sets or enumerated genes and gene set names.">

                    <has_n_columns n="3"/>
                    <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_file" value="mito_counted_anndata.h5ad"/>
            <param name="gene_symbols_field" value="Symbol"/>
            <param name="write_anndata" value="False"/>
            <param name="min_n_genes" value="33"/>
            <conditional name="gene_lists_source">
                <param name="source" value="gmt"/>
                <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/>
                <param name="gmt_file" value="mouse_hallmark_ss.gmt"/>
            </conditional>
            <output name="output_table">
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_text_matching expression="AUCell_HALLMARK_APICAL_SURFACE"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**Description**

This tool scores cells using the AUCell method for gene sets.