comparison plot.xml @ 19:fc222791d03c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy commit a6bd86a67a159906ff55e8b2dedda71d019d3caf

18:6a2f9865e303

sc.pl.paga(
    @CMD_PARAM_PLOT_INPUTS@
    @CMD_PARAMS_PL_PAGA@
    @CMD_SHOW_NONE@)

@CMD_ANNDATA_WRITE_OUTPUTS@

#else if str($method.method) == 'pl.paga_compare':
sc.pl.paga_compare(
    @CMD_PARAM_PLOT_INPUTS@
    @CMD_PARAMS_PL_PAGA@
    @CMD_PARAM_PL_COMPONENTS@

    @CMD_PARAM_GENE_SYMBOLS@
    @CMD_PARAMS_PL_HEATMAP@
    @CMD_SHOW_NONE@)

#end if
]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="inputs_anndata"/>
        <expand macro="param_plot_format"/>

                <expand macro="params_plots"/>
                <expand macro="param_gene_symbols"/>
                <expand macro="params_pl_heatmap"/>
            </when>
        </conditional>
        <expand macro="inputs_common_advanced"/>
    </inputs>
    <outputs>
        <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
            <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
        </data>

        </collection>
        <data name="hidden_output" format="txt" label="Log file" hidden="true" >
            <filter>advanced_common['show_log']</filter>
        </data>
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
            <filter>method['method'] == 'pl.paga'</filter>
        </data>
    </outputs>
    <tests>
        <!-- test 1 -->
        <test expect_num_outputs="2">

            </output>
            <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="image_diff"/>
        </test>

        <!-- test 23 -->
        <test expect_num_outputs="2">
            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.umap"/>
                <param name="color" value="paul15_clusters"/>

                    <param name="size" value="1"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.umap"/>
                    <has_text_matching expression="color=\['paul15_clusters'\]"/>

                    <has_text_matching expression="hspace=0.25"/>
                    <has_text_matching expression="gene_symbols='symbol'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
        </test>

        <!-- test 24 -->
        <test expect_num_outputs="2">
            <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>

                <param name="color" value="louvain"/>
                <param name="layout" value="fr"/>
                <param name="fontsize" value="1"/>
                <param name="edge_width_scale" value="5"/>
            </conditional>
            <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
            <output name="anndata_out" ftype="h5ad">
                <assert_contents>
                    <has_h5_keys keys="uns/paga"/>
                </assert_contents>

19:fc222791d03c

sc.pl.paga(
    @CMD_PARAM_PLOT_INPUTS@
    @CMD_PARAMS_PL_PAGA@
    @CMD_SHOW_NONE@)

#else if str($method.method) == 'pl.paga_compare':
sc.pl.paga_compare(
    @CMD_PARAM_PLOT_INPUTS@
    @CMD_PARAMS_PL_PAGA@
    @CMD_PARAM_PL_COMPONENTS@

    @CMD_PARAM_GENE_SYMBOLS@
    @CMD_PARAMS_PL_HEATMAP@
    @CMD_SHOW_NONE@)

#end if

#if $advanced_common.output_anndata:
@CMD_ANNDATA_WRITE_OUTPUTS@
#end if

]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="inputs_anndata"/>
        <expand macro="param_plot_format"/>

                <expand macro="params_plots"/>
                <expand macro="param_gene_symbols"/>
                <expand macro="params_pl_heatmap"/>
            </when>
        </conditional>
        <expand macro="inputs_common_advanced">
            <param name="output_anndata" type="boolean" checked="false" label="Output annotated data matrix?"/>
        </expand>
    </inputs>
    <outputs>
        <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
            <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
        </data>

        </collection>
        <data name="hidden_output" format="txt" label="Log file" hidden="true" >
            <filter>advanced_common['show_log']</filter>
        </data>
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
            <filter>advanced_common['output_anndata']</filter>
        </data>
    </outputs>
    <tests>
        <!-- test 1 -->
        <test expect_num_outputs="2">

            </output>
            <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="image_diff"/>
        </test>

        <!-- test 23 -->
        <test expect_num_outputs="3">
            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.umap"/>
                <param name="color" value="paul15_clusters"/>

                    <param name="size" value="1"/>
                </section>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
                <param name="output_anndata" value="true"/>
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sc.pl.umap"/>
                    <has_text_matching expression="color=\['paul15_clusters'\]"/>

                    <has_text_matching expression="hspace=0.25"/>
                    <has_text_matching expression="gene_symbols='symbol'"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
            <output name="anndata_out">
                <assert_contents>
                    <has_h5_keys keys="uns/paul15_clusters_colors"/>
                </assert_contents>
            </output>
        </test>

        <!-- test 24 -->
        <test expect_num_outputs="2">
            <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>

                <param name="color" value="louvain"/>
                <param name="layout" value="fr"/>
                <param name="fontsize" value="1"/>
                <param name="edge_width_scale" value="5"/>
            </conditional>
            <section name="advanced_common">
                <param name="output_anndata" value="true"/>
            </section>
            <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
            <output name="anndata_out" ftype="h5ad">
                <assert_contents>
                    <has_h5_keys keys="uns/paga"/>
                </assert_contents>