comparison decoupler_pseudobulk.xml @ 8:93f61ea19336 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567

7:68a2b5445558

<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy2" 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[

    #if $produce_plots:
    --save_path plots_output_dir
    #end if
    #if $min_counts:
    --min_counts $min_counts
    #end if
    #if $min_total_counts:
    --min_total_counts $min_total_counts
    #end if
    #if $produce_anndata:

        <param type="integer" name="min_cells" label="Minimum Cells" optional="true"/>
        <param type="boolean" name="produce_plots" label="Produce plots"/>
        <param type="boolean" name="produce_anndata" label="Produce AnnData with Pseudo-bulk"/>
        <param type="integer" name="min_counts" label="Minimum Counts" optional="true"/>
        <param type="integer" name="min_total_counts" label="Minimum Total Counts" optional="true"/>
        <param type="boolean" name="filter_expr" label="Enable Filtering by Expression"/>
        <param type="text" name="plot_samples_figsize" label="Plot Samples Figsize" value="10 10" help="X and Y sizes in points separated by a space"/>
        <param type="text" name="plot_filtering_figsize" label="Plot Filtering Figsize" value="10 10" help="X and Y sizes in points separated by a space"/>
    </inputs>
    <outputs>

            <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>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="6">
            <param name="input_file" value="mito_counted_anndata.h5ad"/>
            <param name="adata_obs_fields_to_merge" value="batch,sex:batch,genotype"/>
            <param name="groupby" value="batch_sex"/>
            <param name="sample_key" value="genotype"/>
            <param name="factor_fields" value="genotype,batch_sex"/>
            <param name="mode" value="sum"/>
            <param name="min_cells" value="10"/>
            <param name="produce_plots" value="true"/>
            <param name="produce_anndata" value="true"/>
            <param name="min_counts" value="10"/>
            <param name="min_total_counts" value="1000"/>
            <param name="filter_expr" value="true"/>
            <param name="plot_samples_figsize" value="10 10"/>
            <param name="plot_filtering_figsize" value="10 10"/>
            <output name="pbulk_anndata" ftype="h5ad">

                </assert_contents>
            </output>
            <output name="plot_output" ftype="png">
                <assert_contents>
                    <has_size value="31853" delta="3000"/>
                </assert_contents>
            </output>
            <output name="filter_by_expr_plot" ftype="png">
                <assert_contents>
                    <has_size value="21656" delta="2000"/>

8:93f61ea19336

<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy3" 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[

    #if $produce_plots:
    --save_path plots_output_dir
    #end if
    #if $min_counts:
    --min_counts $min_counts
    #end if
    #if $min_counts_per_sample:
    --min_counts_per_sample_marking $min_counts_per_sample
    #end if
    #if $min_total_counts:
    --min_total_counts $min_total_counts
    #end if
    #if $produce_anndata:

        <param type="integer" name="min_cells" label="Minimum Cells" optional="true"/>
        <param type="boolean" name="produce_plots" label="Produce plots"/>
        <param type="boolean" name="produce_anndata" label="Produce AnnData with Pseudo-bulk"/>
        <param type="integer" name="min_counts" label="Minimum Counts" optional="true"/>
        <param type="integer" name="min_total_counts" label="Minimum Total Counts" optional="true"/>
        <param type="integer" name="min_counts_per_sample" value="20" label="Minimum counts per gene per contrast field" help="Used to signal genes that should be excluded per contrast field after DE, to avoid very lowly expressed genes in specific contrasts. Genes are not excluded from the result, but a separate file tagging them is produced."/>
        <param type="boolean" name="filter_expr" label="Enable Filtering by Expression"/>
        <param type="text" name="plot_samples_figsize" label="Plot Samples Figsize" value="10 10" help="X and Y sizes in points separated by a space"/>
        <param type="text" name="plot_filtering_figsize" label="Plot Filtering Figsize" value="10 10" help="X and Y sizes in points separated by a space"/>
    </inputs>
    <outputs>

            <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>
        </data>
        <data name="genes_ignore_per_contrast_field" format="tabular" label="{tool.name} on ${on_string}: Genes to ignore by contrast field" from_work_dir="deseq_output_dir/genes_to_ignore_per_contrast_field.tsv">
            <filter>factor_fields</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="7">
            <param name="input_file" value="mito_counted_anndata.h5ad"/>
            <param name="adata_obs_fields_to_merge" value="batch,sex:batch,genotype"/>
            <param name="groupby" value="batch_sex"/>
            <param name="sample_key" value="genotype"/>
            <param name="factor_fields" value="genotype,batch_sex"/>
            <param name="mode" value="sum"/>
            <param name="min_cells" value="10"/>
            <param name="produce_plots" value="true"/>
            <param name="produce_anndata" value="true"/>
            <param name="min_counts" value="10"/>
            <param name="min_counts_per_sample" value="50"/>
            <param name="min_total_counts" value="1000"/>
            <param name="filter_expr" value="true"/>
            <param name="plot_samples_figsize" value="10 10"/>
            <param name="plot_filtering_figsize" value="10 10"/>
            <output name="pbulk_anndata" ftype="h5ad">

                </assert_contents>
            </output>
            <output name="plot_output" ftype="png">
                <assert_contents>
                    <has_size value="31853" delta="3000"/>
                </assert_contents>
            </output>
            <output name="genes_ignore_per_contrast_field" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="5"/>
                </assert_contents>
            </output>
            <output name="filter_by_expr_plot" ftype="png">
                <assert_contents>
                    <has_size value="21656" delta="2000"/>