comparison decoupler_pseudobulk.xml @ 1:046d8ff974ff draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 45145f380b27c3092e1fa2249adc36d7d6fdf5fe

0:59a7f3f83aec

<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy0" 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>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    </inputs>
    <outputs>
        <data name="pbulk_anndata" format="h5ad" label="${tool.name} on ${on_string}: Pseudo-bulk AnnData">
            <filter>produce_anndata</filter>
        </data>
        <data name="count_matrix" format="csv" label="${tool.name} on ${on_string}: Count Matrix" from_work_dir="deseq_output_dir/counts_matrix.csv"/>
        <data name="samples_metadata" format="csv" label="${tool.name} on ${on_string}: Samples Metadata (factors file)" from_work_dir="deseq_output_dir/col_metadata.csv"/>
        <data name="genes_metadata" format="csv" label="${tool.name} on ${on_string}: Genes Metadata" from_work_dir="deseq_output_dir/gene_metadata.csv"/>
        <data name="plot_output" format="png" label="${tool.name} on ${on_string}: Pseudobulk plot" from_work_dir="plots_output_dir/pseudobulk_samples.png">
            <filter>produce_plots</filter>
        </data>
        <data name="filter_by_expr_plot" format="png" label="${tool.name} on ${on_string}: Filter by Expression plot" from_work_dir="plots_output_dir/filter_by_expr.png">
            <filter>produce_plots</filter>

            <output name="pbulk_anndata" ftype="h5ad">
                <assert_contents>
                    <has_h5_keys keys="obs/psbulk_n_cells"/>
                </assert_contents>
            </output>
            <output name="count_matrix" ftype="csv">
                <assert_contents>
                    <has_n_lines n="3620"/>
                </assert_contents>
            </output>
            <output name="samples_metadata" ftype="csv">
                <assert_contents>
                    <has_n_lines n="8"/>
                </assert_contents>
            </output>
            <output name="genes_metadata" ftype="csv">
                <assert_contents>
                    <has_n_lines n="3620"/>
                </assert_contents>
            </output>
            <output name="plot_output" ftype="png">
                <assert_contents>
                    <has_size value="31853" delta="3000"/>

        - Plot Samples Figsize: Size of the samples plot as a tuple (two arguments).
        - Plot Filtering Figsize: Size of the filtering plot as a tuple (two arguments).

        The tool will output the filtered AnnData, count matrix, samples metadata, genes metadata (in DESeq2 format), and the pseudobulk plot and filter by expression plot (if enabled).

        ]]>
    </help>
    <citations>
        <citation type="doi">doi.org/10.1093/bioadv/vbac016</citation>
    </citations>
</tool>

1:046d8ff974ff

<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy1" 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>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    </inputs>
    <outputs>
        <data name="pbulk_anndata" format="h5ad" label="${tool.name} on ${on_string}: Pseudo-bulk AnnData">
            <filter>produce_anndata</filter>
        </data>
        <data name="count_matrix" format="tabular" label="${tool.name} on ${on_string}: Count Matrix" from_work_dir="deseq_output_dir/counts_matrix.tsv"/>
        <data name="samples_metadata" format="tabular" label="${tool.name} on ${on_string}: Samples Metadata (factors file)" from_work_dir="deseq_output_dir/col_metadata.tsv"/>
        <data name="genes_metadata" format="tabular" label="${tool.name} on ${on_string}: Genes Metadata" from_work_dir="deseq_output_dir/gene_metadata.tsv"/>
        <data name="plot_output" format="png" label="${tool.name} on ${on_string}: Pseudobulk plot" from_work_dir="plots_output_dir/pseudobulk_samples.png">
            <filter>produce_plots</filter>
        </data>
        <data name="filter_by_expr_plot" format="png" label="${tool.name} on ${on_string}: Filter by Expression plot" from_work_dir="plots_output_dir/filter_by_expr.png">
            <filter>produce_plots</filter>

            <output name="pbulk_anndata" ftype="h5ad">
                <assert_contents>
                    <has_h5_keys keys="obs/psbulk_n_cells"/>
                </assert_contents>
            </output>
            <output name="count_matrix" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="3620"/>
                    <has_n_columns n="8"/>
                </assert_contents>
            </output>
            <output name="samples_metadata" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="8"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output name="genes_metadata" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="3620"/>
                    <has_n_columns n="13"/>
                </assert_contents>
            </output>
            <output name="plot_output" ftype="png">
                <assert_contents>
                    <has_size value="31853" delta="3000"/>

        - Plot Samples Figsize: Size of the samples plot as a tuple (two arguments).
        - Plot Filtering Figsize: Size of the filtering plot as a tuple (two arguments).

        The tool will output the filtered AnnData, count matrix, samples metadata, genes metadata (in DESeq2 format), and the pseudobulk plot and filter by expression plot (if enabled).

        You can obtain more information about Decoupler pseudobulk at the developers documentation `here <https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html>`_ .

        ]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioadv/vbac016</citation>
    </citations>
</tool>