comparison plot.xml @ 9:9a169729c9f9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"

8:6adf98e782f3

<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">
    <description> with scanpy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    frameon=$method.plot.frameon)

#else if $method.method == 'pl.heatmap'
sc.pl.heatmap(
    @CMD_param_plot_inputs@
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_heatmap@)

#else if $method.method == 'pl.dotplot'
sc.pl.dotplot(
    @CMD_param_plot_inputs@
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_dotplot@)

#else if $method.method == 'pl.violin'

    @CMD_params_seaborn_violinplot@)

#else if $method.method == 'pl.stacked_violin'
sc.pl.stacked_violin(
    @CMD_param_plot_inputs@
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_stacked_violin@)

#else if $method.method == 'pl.matrixplot'
sc.pl.matrixplot(
    @CMD_param_plot_inputs@
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_matrixplot@)

#else if $method.method == 'pl.clustermap'

                    <expand macro="param_title"/>
                </section>
            </when>
            <when value="pl.heatmap">
                <expand macro="params_inputs"/>
                <expand macro="params_plots"/>
                <expand macro="pl_heatmap"/>
            </when>
            <when value="pl.dotplot">
                <expand macro="params_inputs"/>
                <expand macro="params_plots"/>
                <expand macro="pl_dotplot"/>
            </when>
            <when value="pl.violin">
                <conditional name="key_variables">

                <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
                <expand macro="seaborn_violinplot"/>
            </when>
            <when value="pl.stacked_violin">
                <expand macro="params_inputs"/>
                <expand macro="params_plots"/>
                <expand macro="pl_stacked_violin"/>
            </when>
            <when value="pl.matrixplot">
                <expand macro="params_inputs"/>
                <expand macro="params_plots"/>
                <expand macro="pl_matrixplot"/>
            </when>
            <when value="pl.clustermap">
                <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">

                </assert_contents>
            </output>
            <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 3: pl.dotplot !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dotplot"/>

                </assert_contents>
            </output>
            <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 4: pl.violin !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.violin"/>

                </assert_contents>
            </output>
            <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 6: pl.matrixplot !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.matrixplot"/>

                    <has_text_matching expression="edgecolors='face'"/>
                    <has_text_matching expression="snap=False"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <!-- test 7: pl.clustermap !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>

9:9a169729c9f9

<tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@">
    <description> with scanpy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    frameon=$method.plot.frameon)

#else if $method.method == 'pl.heatmap'
sc.pl.heatmap(
    @CMD_param_plot_inputs@
    #if str($method.gene_symbols) != ''
    gene_symbols='$method.gene_symbols',
    #end if
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_heatmap@)

#else if $method.method == 'pl.dotplot'
sc.pl.dotplot(
    @CMD_param_plot_inputs@
    #if str($method.gene_symbols) != ''
    gene_symbols='$method.gene_symbols',
    #end if
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_dotplot@)

#else if $method.method == 'pl.violin'

    @CMD_params_seaborn_violinplot@)

#else if $method.method == 'pl.stacked_violin'
sc.pl.stacked_violin(
    @CMD_param_plot_inputs@
    #if str($method.gene_symbols) != ''
    gene_symbols='$method.gene_symbols',
    #end if
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_stacked_violin@)

#else if $method.method == 'pl.matrixplot'
sc.pl.matrixplot(
    @CMD_param_plot_inputs@
    #if str($method.gene_symbols) != ''
    gene_symbols='$method.gene_symbols',
    #end if
    @CMD_params_inputs@
    @CMD_params_plots@
    @CMD_pl_matrixplot@)

#else if $method.method == 'pl.clustermap'

                    <expand macro="param_title"/>
                </section>
            </when>
            <when value="pl.heatmap">
                <expand macro="params_inputs"/>
                <expand macro="gene_symbols"/>
                <expand macro="params_plots"/>
                <expand macro="pl_heatmap"/>
            </when>
            <when value="pl.dotplot">
                <expand macro="params_inputs"/>
                <expand macro="gene_symbols"/>
                <expand macro="params_plots"/>
                <expand macro="pl_dotplot"/>
            </when>
            <when value="pl.violin">
                <conditional name="key_variables">

                <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
                <expand macro="seaborn_violinplot"/>
            </when>
            <when value="pl.stacked_violin">
                <expand macro="params_inputs"/>
                <expand macro="gene_symbols"/>
                <expand macro="params_plots"/>
                <expand macro="pl_stacked_violin"/>
            </when>
            <when value="pl.matrixplot">
                <expand macro="params_inputs"/>
                <expand macro="gene_symbols"/>
                <expand macro="params_plots"/>
                <expand macro="pl_matrixplot"/>
            </when>
            <when value="pl.clustermap">
                <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">

                </assert_contents>
            </output>
            <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
          <!-- test 2.1: pl.heatmap with symbols !-->
          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
          <param name="format" value="png"/>
          <conditional name="method">
              <param name="method" value="pl.heatmap"/>
              <conditional name="var_names">
                  <param name="type" value="custom"/>
                  <param name="var_names" value="Fog1,EKLF,SCL"/>
              </conditional>
              <param name="groupby" value="cell_type"/>
              <param name="gene_symbols" value="symbol"/>
              <param name="num_categories" value="7"/>
              <param name="log" value="False"/>
              <param name="use_raw" value="False"/>
              <conditional name="figsize">
                  <param name="test" value="yes"/>
                  <param name="width" value="10" />
                  <param name="height" value="3"/>
              </conditional>
              <param name="dendrogram" value="True"/>
              <param name="swap_axes" value="True"/>
              <param name="show_gene_labels" value="True"/>
              <section name="matplotlib_pyplot_imshow">
                  <param name="cmap" value="YlGnBu"/>
                  <param name="interpolation" value="None"/>
                  <param name="origin" value="upper"/>
              </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.heatmap"/>
                  <has_text_matching expression="gene_symbols='symbol'"/>
                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
                  <has_text_matching expression="groupby='cell_type'"/>
                  <has_text_matching expression="log=False"/>
                  <has_text_matching expression="use_raw=False"/>
                  <has_text_matching expression="num_categories=7"/>
                  <has_text_matching expression="dendrogram=True"/>
                  <has_text_matching expression="figsize=\(10, 3\)"/>
                  <has_text_matching expression="swap_axes=True"/>
                  <has_text_matching expression="show_gene_labels=True"/>
                  <has_text_matching expression="cmap='YlGnBu'"/>
                  <has_text_matching expression="origin='upper'"/>
              </assert_contents>
          </output>
        </test>
        <test>
            <!-- test 3: pl.dotplot !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.dotplot"/>

                </assert_contents>
            </output>
            <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
          <!-- test 3.1: pl.dotplot with symbols !-->
          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
          <param name="format" value="png"/>
          <conditional name="method">
              <param name="method" value="pl.dotplot"/>
              <conditional name="var_names">
                  <param name="type" value="custom"/>
                  <param name="var_names" value="Fog1,EKLF,SCL"/>
              </conditional>
              <param name="groupby" value="cell_type"/>
              <param name="gene_symbols" value="symbol"/>
              <param name="num_categories" value="7"/>
              <param name="log" value="False"/>
              <param name="use_raw" value="False"/>
              <param name="dendrogram" value="True"/>
              <section name="matplotlib_pyplot_imshow">
                  <param name="cmap" value="YlGnBu"/>
                  <param name="interpolation" value="None"/>
                  <param name="origin" value="upper"/>
              </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.dotplot"/>
                  <has_text_matching expression="gene_symbols='symbol'"/>
                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
                  <has_text_matching expression="groupby='cell_type'"/>
                  <has_text_matching expression="log=False"/>
                  <has_text_matching expression="use_raw=False"/>
                  <has_text_matching expression="num_categories=7"/>
                  <has_text_matching expression="dendrogram=True"/>
              </assert_contents>
          </output>
        </test>
        <test>
            <!-- test 4: pl.violin !-->
            <param name="adata" value="pbmc68k_reduced.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.violin"/>

                </assert_contents>
            </output>
            <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
          <!-- test 5.1: pl.stacked_violin with symbols !-->
          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
          <param name="format" value="png"/>
          <conditional name="method">
              <param name="method" value="pl.stacked_violin"/>
              <conditional name="var_names">
                  <param name="type" value="custom"/>
                  <param name="var_names" value="Fog1,EKLF,SCL"/>
              </conditional>
              <param name="groupby" value="cell_type"/>
              <param name="gene_symbols" value="symbol"/>
              <param name="num_categories" value="7"/>
              <param name="log" value="False"/>
              <param name="use_raw" value="False"/>
              <param name="dendrogram" value="True"/>
              <param name="swap_axes" value="True"/>
          </conditional>
          <section name="advanced_common">
              <param name="show_log" value="true" />
          </section>
          <output name="hidden_output">
              <assert_contents>
                  <has_text_matching expression="sc.pl.stacked_violin"/>
                  <has_text_matching expression="gene_symbols='symbol'"/>
                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
                  <has_text_matching expression="groupby='cell_type'"/>
                  <has_text_matching expression="log=False"/>
                  <has_text_matching expression="use_raw=False"/>
                  <has_text_matching expression="num_categories=7"/>
                  <has_text_matching expression="dendrogram=True"/>
                  <has_text_matching expression="swap_axes=True"/>
              </assert_contents>
          </output>
        </test>
        <test>
            <!-- test 6: pl.matrixplot !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>
            <conditional name="method">
                <param name="method" value="pl.matrixplot"/>

                    <has_text_matching expression="edgecolors='face'"/>
                    <has_text_matching expression="snap=False"/>
                </assert_contents>
            </output>
            <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
          <!-- test 6.1: pl.matrixplot with symbols !-->
          <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
          <param name="format" value="png"/>
          <conditional name="method">
              <param name="method" value="pl.matrixplot"/>
              <conditional name="var_names">
                  <param name="type" value="custom"/>
                  <param name="var_names" value="Fog1,EKLF,SCL"/>
              </conditional>
              <param name="groupby" value="cell_type"/>
              <param name="gene_symbols" value="symbol"/>
              <param name="num_categories" value="7"/>
              <param name="log" value="False"/>
              <param name="use_raw" value="False"/>
              <conditional name="figsize">
                  <param name="test" value="yes"/>
                  <param name="width" value="10" />
                  <param name="height" value="3"/>
              </conditional>
              <param name="dendrogram" value="True"/>
              <param name="swap_axes" value="False"/>
          </conditional>
          <section name="advanced_common">
              <param name="show_log" value="true" />
          </section>
          <output name="hidden_output">
              <assert_contents>
                  <has_text_matching expression="sc.pl.matrixplot"/>
                  <has_text_matching expression="gene_symbols='symbol'"/>
                  <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
                  <has_text_matching expression="groupby='cell_type'"/>
                  <has_text_matching expression="log=False"/>
                  <has_text_matching expression="use_raw=False"/>
                  <has_text_matching expression="num_categories=7"/>
                  <has_text_matching expression="dendrogram=True"/>
                  <has_text_matching expression="swap_axes=False"/>
              </assert_contents>
          </output>
        </test>
        <test>
            <!-- test 7: pl.clustermap !-->
            <param name="adata" value="krumsiek11.h5ad" />
            <param name="format" value="png"/>