| Previous changeset 15:70fa84e99463 (2024-07-31) Next changeset 17:2dfb2227a16c (2024-09-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 |
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modified:
macros.xml plot.xml test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad |
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added:
test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png |
| b |
| diff -r 70fa84e99463 -r 1072ce66b426 macros.xml --- a/macros.xml Wed Jul 31 18:11:37 2024 +0000 +++ b/macros.xml Tue Aug 20 09:53:51 2024 +0000 |
| [ |
| @@ -435,6 +435,10 @@ </when> <when value="customfile"> <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param> + <param name="header" type="select" label="Header in the list of markers?"> + <option value="included">Header incldued</option> + <option value="not_included">Header not included</option> + </param> </when> </conditional> </xml> @@ -471,6 +475,12 @@ <expand macro="param_groupby"/> <expand macro="param_num_categories"/> </xml> + <token name="@CMD_var_names_header_check@"><![CDATA[ +header='infer' +#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' : +header=None +#end if + ]]></token> <token name="@CMD_params_inputs@"><![CDATA[ #if $method.var_names.type == 'custom' #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) |
| b |
| diff -r 70fa84e99463 -r 1072ce66b426 plot.xml --- a/plot.xml Wed Jul 31 18:11:37 2024 +0000 +++ b/plot.xml Tue Aug 20 09:53:51 2024 +0000 |
| [ |
| @@ -79,6 +79,7 @@ frameon=$method.plot.frameon) #else if $method.method == 'pl.heatmap' +@CMD_var_names_header_check@ sc.pl.heatmap( @CMD_param_plot_inputs@ #if $method.gene_symbols @@ -89,6 +90,7 @@ @CMD_pl_heatmap@) #else if $method.method == 'pl.dotplot' +@CMD_var_names_header_check@ sc.pl.dotplot( @CMD_param_plot_inputs@ #if $method.gene_symbols @@ -129,6 +131,7 @@ @CMD_params_seaborn_violinplot@) #else if $method.method == 'pl.stacked_violin' +@CMD_var_names_header_check@ sc.pl.stacked_violin( @CMD_param_plot_inputs@ #if $method.gene_symbols @@ -139,6 +142,7 @@ @CMD_pl_stacked_violin@) #else if $method.method == 'pl.matrixplot' +@CMD_var_names_header_check@ sc.pl.matrixplot( @CMD_param_plot_inputs@ #if $method.gene_symbols @@ -399,9 +403,26 @@ scale='$method.violin_plot.scale') #else if $method.method == 'pl.rank_genes_groups_dotplot' + +@CMD_var_names_header_check@ + sc.pl.rank_genes_groups_dotplot( @CMD_param_plot_inputs@ - @CMD_pl_rank_genes_groups_ext@ + #if $method.var_names.type == 'custom' + #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) + var_names=$var_names, + #else if $method.var_names.type == 'customfile' + var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0, header=header).to_dict(orient='index').items()}, + #else + n_genes=$method.n_genes, + #end if + #if $method.groupby != '' + groupby='$method.groupby', + #end if + num_categories=$method.num_categories, + #if $method.key != '' + key='$method.key', + #end if #if $method.gene_symbols gene_symbols='$method.gene_symbols', #end if @@ -819,6 +840,7 @@ </section> </when> <when value="pl.rank_genes_groups_dotplot"> + <expand macro="params_inputs"/> <expand macro="pl_rank_genes_groups_ext"/> <expand macro="params_plots"/> <expand macro="gene_symbols"/> @@ -2033,6 +2055,9 @@ <param name="method" value="pl.rank_genes_groups_dotplot"/> <param name="gene_symbols" value="symbol"/> <param name="n_genes" value="10"/> + <conditional name="var_names"> + <param name="type" value="all"/> + </conditional> <param name="log" value="False"/> <param name="use_raw" value="False"/> <param name="dendrogram" value="False"/> @@ -2233,6 +2258,80 @@ </output> <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> </test> + <test expect_num_outputs="2"> + <!-- test 35: pl.rank_genes_groups_dotplot with marker list --> + <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> + <param name="format" value="png"/> + <conditional name="method"> + <param name="method" value="pl.rank_genes_groups_dotplot"/> + <conditional name="var_names"> + <param name="type" value="customfile"/> + <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/> + </conditional> + <param name="groupby" value="bulk_labels"/> + <param name="log" value="False"/> + <param name="use_raw" value="False"/> + <param name="dendrogram" value="False"/> + <param name="color_map" value="viridis"/> + <section name="matplotlib_pyplot_scatter"> + <param name="linewidths" value="0" /> + <param name="edgecolors" value="face"/> + </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.rank_genes_groups_dotplot"/> + <has_text_matching expression="groupby='bulk_labels'"/> + <has_text_matching expression="log=False"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="dendrogram=False"/> + <has_text_matching expression="color_map='viridis'"/> + <has_text_matching expression="lw=0.0"/> + <has_text_matching expression="ec='face'"/> + </assert_contents> + </output> + <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="sim_size"/> + </test> + <test expect_num_outputs="2"> + <!-- test 36: pl.rank_genes_groups_dotplot with marker list --> + <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> + <param name="format" value="png"/> + <conditional name="method"> + <param name="method" value="pl.rank_genes_groups_dotplot"/> + <conditional name="var_names"> + <param name="type" value="customfile"/> + <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/> + </conditional> + <param name="groupby" value="bulk_labels"/> + <param name="log" value="False"/> + <param name="use_raw" value="False"/> + <param name="dendrogram" value="False"/> + <param name="color_map" value="viridis"/> + <section name="matplotlib_pyplot_scatter"> + <param name="linewidths" value="0" /> + <param name="edgecolors" value="face"/> + </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.rank_genes_groups_dotplot"/> + <has_text_matching expression="groupby='bulk_labels'"/> + <has_text_matching expression="log=False"/> + <has_text_matching expression="use_raw=False"/> + <has_text_matching expression="dendrogram=False"/> + <has_text_matching expression="color_map='viridis'"/> + <has_text_matching expression="lw=0.0"/> + <has_text_matching expression="ec='face'"/> + </assert_contents> + </output> + <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="sim_size"/> + </test> </tests> <help><
