scanpy_plot: plot.xml comparison

comparison plot.xml @ 16:ff6da5117343 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f

author	iuc
date	Thu, 03 Oct 2024 22:41:00 +0000
parents	aa8abbf399b3
children	413ffec60330

comparison

equal deleted inserted replaced

-:8b2c8dcd9519
+:ff6da5117343
 #end if
 @CMD_PARAM_LEGEND_FONTSIZE@
 legend_fontweight='$method.plot.legend_fontweight',
 #if $method.plot.color_map:
 color_map='$method.plot.color_map',
 #end if
 #if $method.plot.palette:
 palette=['$method.plot.palette'],
 #end if
 frameon=$method.plot.frameon,
 @CMD_PARAM_SIZE@
 #else if str($method.method) == 'pl.dotplot':
 @CMD_VAR_NAMES_HEADER_CHECK@
 sc.pl.dotplot(
 @CMD_PARAM_PLOT_INPUTS@
 @CMD_PARAMS_INPUTS@
 @CMD_PARAM_GENE_SYMBOLS@
 @CMD_PARAMS_PLOTS@
 @CMD_PL_DOTPLOT@
 @CMD_SHOW_NONE@)
 use_raw=$method.use_raw,
 sort_order=$method.sort_order,
 @CMD_PARAM_GROUPS@
 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
 @CMD_SCATTER_OUTINE@
 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
 @CMD_SHOW_NONE@)
 #else if str($method.method) == 'pl.tsne':
 sc.pl.tsne(
 @CMD_PARAM_PLOT_INPUTS@
 arrows=$method.arrows,
 sort_order=$method.sort_order,
 @CMD_PARAM_GROUPS@
 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
 @CMD_SCATTER_OUTINE@
 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
 @CMD_PARAM_LAYER@
 @CMD_SHOW_NONE@)
 #else if str($method.method) == 'pl.umap':
 sc.pl.umap(
 sc.pl.paga(
 @CMD_PARAM_PLOT_INPUTS@
 @CMD_PARAMS_PL_PAGA@
 @CMD_SHOW_NONE@)
+@CMD_ANNDATA_WRITE_OUTPUTS@
 #else if str($method.method) == 'pl.paga_compare':
 sc.pl.paga_compare(
 @CMD_PARAM_PLOT_INPUTS@
 @CMD_PARAMS_PL_PAGA@
 @CMD_PARAM_PL_COMPONENTS@
 #end if
 @CMD_PARAM_LEGEND_FONTSIZE@
 legend_fontweight='$method.plot.legend_fontweight',
 #if $method.plot.color_map:
 color_map='$method.plot.color_map',
 #end if
 #if $method.plot.palette:
 palette=['$method.plot.palette'],
 #end if
 @CMD_PARAM_SIZE@
 @CMD_PARAM_TITLE@
 <expand macro="param_use_raw" falsevalue="None"/>
 <section name="violin_plot" title="Violin plot attributes">
 <expand macro="conditional_stripplot"/>
 <conditional name="multi_panel">
 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
 <option value="None" selected="true">No</option>
 <option value="True">Yes</option>
 </param>
 <when value="None"/>
 <when value="True">
 <!-- <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure"/>
 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
 </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">
 <param name="adata" value="pbmc68k_reduced.h5ad"/>
 <has_text_matching expression="size=1.0"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 2 -->
 <test expect_num_outputs="2">
 <param name="adata" value="krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="title='A title'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 3 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pbmc68k_reduced.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="origin='upper'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 5 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="cmap='YlGnBu'"/>
 <has_text_matching expression="origin='upper'"/>
 </assert_contents>
 </output>
 </test>
 <!-- test 6 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pbmc68k_reduced.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="dot_min=0.1"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 7 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <conditional name="var_names">
 <param name="type" value="custom"/>
 <param name="var_names" value="Fog1,EKLF,SCL"/>
 </conditional>
 <param name="gene_symbols" value="symbol"/>
 <param name="groupby" value="cell_type"/>
 <param name="dendrogram" value="True"/>
 <section name="matplotlib_pyplot_imshow">
 <param name="cmap" value="YlGnBu"/>
 </section>
 </conditional>
 <has_text_matching expression="num_categories=7"/>
 <has_text_matching expression="dendrogram=True"/>
 </assert_contents>
 </output>
 </test>
 <!-- test 8 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.tracksplot"/>
 <param name="gene_symbols" value="symbol"/>
 <param name="groupby" value="cell_type"/>
 <param name="dendrogram" value="True"/>
 <section name="matplotlib_pyplot_imshow">
 <param name="cmap" value="YlGnBu"/>
 </section>
 </conditional>
 <conditional name="method">
 <param name="method" value="pl.violin"/>
 <conditional name="key_variables">
 <param name="type" value="custom"/>
 <param name="keys" value="n_genes, percent_mito, n_counts"/>
 </conditional>
 <section name="violin_plot">
 <conditional name="multi_panel">
 <param name="multi_panel" value="True"/>
 </conditional>
 </section>
 <has_text_matching expression="saturation=0.75"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="image_diff" eps="0.4"/>
 </test>
 <!-- test 10 -->
 <test expect_num_outputs="2">
 <param name="adata" value="krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="saturation=0.75"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="image_diff" eps="1.1"/>
 </test>
 <!-- test 11 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="swap_axes=True"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png" compare="image_diff" eps="0.6"/>
 </test>
 <!-- test 12 -->
 <test expect_num_outputs="2">
 <param name="adata" value="krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="snap=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 13 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="dendrogram=True"/>
 <has_text_matching expression="swap_axes=False"/>
 </assert_contents>
 </output>
 </test>
 <!-- test 14 -->
 <test expect_num_outputs="2">
 <param name="adata" value="krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="row_cluster=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 15 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="saturation=0.5"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 16 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.highly_variable_genes"/>
 </conditional>
 <section name="advanced_common">
 <param name="show_log" value="true"/>
 </section>
 <output name="hidden_output">
 <has_text_matching expression="highly_variable_genes=True"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 17 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.scrublet.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.scrublet_score_distribution"/>
 </conditional>
 <section name="advanced_common">
 <param name="show_log" value="true"/>
 </section>
 <output name="hidden_output">
 <has_text_matching expression="hspace=0.25"/>
 </assert_contents>
 </output>
 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
 </test>
 <!-- test 19 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="components=\[1, 2, 3\]"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="image_diff"/>
 </test>
 <!-- test 20 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="log=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="image_diff"/>
 </test>
 <!-- test 21 -->
 <test expect_num_outputs="2">
 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="hspace=0.25"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="image_diff"/>
 </test>
 <!-- test 22 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.tsne.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="hspace=0.25"/>
 </assert_contents>
 </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">
 <has_text_matching expression="size=1.0"/>
 <has_text_matching expression="frameon=True"/>
 <has_text_matching expression="ncols=4"/>
 <has_text_matching expression="wspace=0.1"/>
 <has_text_matching expression="hspace=0.25"/>
 </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="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="size=1.0"/>
 <has_text_matching expression="frameon=True"/>
 <has_text_matching expression="ncols=4"/>
 <has_text_matching expression="wspace=0.1"/>
 <has_text_matching expression="hspace=0.25"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 25 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="hspace=0.25"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 26 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="key='umap_density_bulk_labels'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
 <!-- test 27 -->
 <!-- <test expect_num_outputs="2">
 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.dpt_groups_pseudotime"/>
 </conditional>
 <section name="advanced_common">
 <param name="show_log" value="true"/>
 </section>
 <output name="hidden_output">
 <has_text_matching expression="color_map='viridis'"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
 </test> -->
 <!-- test 28 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="as_heatmap=True"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 29 -->
-<test expect_num_outputs="1">
+<test expect_num_outputs="2">
 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.paga"/>
 <param name="threshold" value="0.01"/>
 <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"/>
-</test>
+<output name="anndata_out" ftype="h5ad">
+<assert_contents>
+<has_h5_keys keys="uns/paga"/>
+</assert_contents>
+</output>
+</test>
 <!-- test 30 -->
 <test expect_num_outputs="1">
 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <!-- test 31 -->
 <!-- <test expect_num_outputs="2">
 test pl.paga_path
 </test> -->
 <!-- test 32 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <param name="method" value="pl.rank_genes_groups"/>
 <param name="n_genes" value="10"/>
 </conditional>
 <section name="advanced_common">
 <param name="show_log" value="true"/>
 </section>
 <output name="hidden_output">
 <has_text_matching expression="ncols=4"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 33 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="image_diff" eps="3.5"/>
 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/>
 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/>
 </output_collection>
 </test>
 <!-- test 34 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="saturation=0.75"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/>
 </test>
 <!-- test 35 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="dendrogram=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 37 -->
 <test expect_num_outputs="2">
 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="snap=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 38 pl.rank_genes_groups_dotplot with marker list-->
 <test expect_num_outputs="2">
 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">
 <has_text_matching expression="dendrogram=False"/>
 </assert_contents>
 </output>
 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/>
 </test>
 <!-- test 39: pl.rank_genes_groups_dotplot with marker list -->
 <test expect_num_outputs="2">
 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
 <param name="format" value="png"/>
 <conditional name="method">

Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 16:ff6da5117343 draft