| Previous changeset 8:6adf98e782f3 (2021-03-16) Next changeset 10:aa0c474463c2 (2021-09-22) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" |
|
modified:
plot.xml test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad |
| b |
| diff -r 6adf98e782f3 -r 9a169729c9f9 plot.xml --- a/plot.xml Tue Mar 16 13:01:04 2021 +0000 +++ b/plot.xml Mon Apr 12 18:15:46 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">\n+<tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@">\n <description> with scanpy</description>\n <macros>\n <import>macros.xml</import>\n@@ -59,6 +59,9 @@\n #else if $method.method == \'pl.heatmap\'\n sc.pl.heatmap(\n @CMD_param_plot_inputs@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_params_inputs@\n @CMD_params_plots@\n @CMD_pl_heatmap@)\n@@ -66,6 +69,9 @@\n #else if $method.method == \'pl.dotplot\'\n sc.pl.dotplot(\n @CMD_param_plot_inputs@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_params_inputs@\n @CMD_params_plots@\n @CMD_pl_dotplot@)\n@@ -103,6 +109,9 @@\n #else if $method.method == \'pl.stacked_violin\'\n sc.pl.stacked_violin(\n @CMD_param_plot_inputs@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_params_inputs@\n @CMD_params_plots@\n @CMD_pl_stacked_violin@)\n@@ -110,6 +119,9 @@\n #else if $method.method == \'pl.matrixplot\'\n sc.pl.matrixplot(\n @CMD_param_plot_inputs@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_params_inputs@\n @CMD_params_plots@\n @CMD_pl_matrixplot@)\n@@ -474,11 +486,13 @@\n </when>\n <when value="pl.heatmap">\n <expand macro="params_inputs"/>\n+ <expand macro="gene_symbols"/>\n <expand macro="params_plots"/>\n <expand macro="pl_heatmap"/>\n </when>\n <when value="pl.dotplot">\n <expand macro="params_inputs"/>\n+ <expand macro="gene_symbols"/>\n <expand macro="params_plots"/>\n <expand macro="pl_dotplot"/>\n </when>\n@@ -523,11 +537,13 @@\n </when>\n <when value="pl.stacked_violin">\n <expand macro="params_inputs"/>\n+ <expand macro="gene_symbols"/>\n <expand macro="params_plots"/>\n <expand macro="pl_stacked_violin"/>\n </when>\n <when value="pl.matrixplot">\n <expand macro="params_inputs"/>\n+ <expand macro="gene_symbols"/>\n <expand macro="params_plots"/>\n <expand macro="pl_matrixplot"/>\n </when>\n@@ -917,6 +933,56 @@\n <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>\n </test>\n <test>\n+ <!-- test 2.1: pl.heatmap with symbols !-->\n+ <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />\n+ <param name="format" value="png"/>\n+ <conditional name="method">\n+ <param name="method" value="pl.heatmap"/>\n+ <conditional name="var_names">\n+ <param name="type" value="custom"/>\n+ <param name="var_names" value="Fog1,EKLF,SCL"/>\n+ </conditional>\n+ <param name="groupby" value="cell_type"/>\n+ <param name="gene_symbols" value="symbol"/>\n+ <param name="num_categories" value="7"/>\n+ <param name="log" value="False"/>\n+ <param name="use_raw" value="False"/>\n+ <conditional name="figsize">\n+ <param name="test" value="yes"/>\n+ <param name="width" value="10" />\n+ <param name="height" value="3"/>\n+ </conditional>\n+ <param name="dendrogram" value="True"/>\n+ <param name="swap_axes" value="True"/>\n+ <param name="show_gene_labels" value="True"/>\n+ <section name="matplotlib_pyplot_imshow">\n+ <param name="cmap" value="YlGnBu"/>\n+ <param name="interpolation" value="None"/'..b'ram name="type" value="custom"/>\n+ <param name="var_names" value="Fog1,EKLF,SCL"/>\n+ </conditional>\n+ <param name="groupby" value="cell_type"/>\n+ <param name="gene_symbols" value="symbol"/>\n+ <param name="num_categories" value="7"/>\n+ <param name="log" value="False"/>\n+ <param name="use_raw" value="False"/>\n+ <param name="dendrogram" value="True"/>\n+ <param name="swap_axes" value="True"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pl.stacked_violin"/>\n+ <has_text_matching expression="gene_symbols=\'symbol\'"/>\n+ <has_text_matching expression="var_names=\\[\'Fog1\', \'EKLF\', \'SCL\'\\]" />\n+ <has_text_matching expression="groupby=\'cell_type\'"/>\n+ <has_text_matching expression="log=False"/>\n+ <has_text_matching expression="use_raw=False"/>\n+ <has_text_matching expression="num_categories=7"/>\n+ <has_text_matching expression="dendrogram=True"/>\n+ <has_text_matching expression="swap_axes=True"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n <!-- test 6: pl.matrixplot !-->\n <param name="adata" value="krumsiek11.h5ad" />\n <param name="format" value="png"/>\n@@ -1137,6 +1276,46 @@\n <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>\n </test>\n <test>\n+ <!-- test 6.1: pl.matrixplot with symbols !-->\n+ <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />\n+ <param name="format" value="png"/>\n+ <conditional name="method">\n+ <param name="method" value="pl.matrixplot"/>\n+ <conditional name="var_names">\n+ <param name="type" value="custom"/>\n+ <param name="var_names" value="Fog1,EKLF,SCL"/>\n+ </conditional>\n+ <param name="groupby" value="cell_type"/>\n+ <param name="gene_symbols" value="symbol"/>\n+ <param name="num_categories" value="7"/>\n+ <param name="log" value="False"/>\n+ <param name="use_raw" value="False"/>\n+ <conditional name="figsize">\n+ <param name="test" value="yes"/>\n+ <param name="width" value="10" />\n+ <param name="height" value="3"/>\n+ </conditional>\n+ <param name="dendrogram" value="True"/>\n+ <param name="swap_axes" value="False"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true" />\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pl.matrixplot"/>\n+ <has_text_matching expression="gene_symbols=\'symbol\'"/>\n+ <has_text_matching expression="var_names=\\[\'Fog1\', \'EKLF\', \'SCL\'\\]" />\n+ <has_text_matching expression="groupby=\'cell_type\'"/>\n+ <has_text_matching expression="log=False"/>\n+ <has_text_matching expression="use_raw=False"/>\n+ <has_text_matching expression="num_categories=7"/>\n+ <has_text_matching expression="dendrogram=True"/>\n+ <has_text_matching expression="swap_axes=False"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n <!-- test 7: pl.clustermap !-->\n <param name="adata" value="krumsiek11.h5ad" />\n <param name="format" value="png"/>\n' |
| b |
| diff -r 6adf98e782f3 -r 9a169729c9f9 test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad |
| b |
| Binary file test-data/pp.filter_genes_dispersion.krumsiek11-seurat.h5ad has changed |