comparison inspect.xml @ 15:ca086f24422f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0

14:f54f0f0598ad

        #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
    qc_vars=$qc_vars,
    #end if
    #if $method.percent_top
        #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
        percent_top=$method.percent_top,
    #end if
    inplace=True)

#else if $method.method == "tl.score_genes"
sc.tl.score_genes(

                    <has_text_matching expression="sc.pp.sqrt"/>
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Calculate quality control metrics., using `pp.calculate_qc_metrics`
===================================================================

15:ca086f24422f

        #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
    qc_vars=$qc_vars,
    #end if
    #if $method.percent_top
        #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
        percent_top=$percent_top,
    #end if
    inplace=True)

#else if $method.method == "tl.score_genes"
sc.tl.score_genes(

                    <has_text_matching expression="sc.pp.sqrt"/>
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test 13 -->
            <param name="adata" value="sparce_csr_matrix.h5ad" />
            <conditional name="method">
                <param name="method" value="pp.calculate_qc_metrics"/>
                <param name="expr_type" value="counts"/>
                <param name="var_type" value="genes"/>
                <param name="qc_vars" value="mito,negative"/>
                <param name="percent_top" value="50,100,200,300"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pp.calculate_qc_metrics" />
                    <has_text_matching expression="expr_type='counts'" />
                    <has_text_matching expression="var_type='genes'" />
                    <has_text_matching expression="qc_vars=\['mito', 'negative'\]" />
                    <has_text_matching expression="percent_top=\[50, 100, 200, 300\]" />
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Calculate quality control metrics., using `pp.calculate_qc_metrics`
===================================================================