| Previous changeset 2:4bfb75bb7c8e (2019-12-05) Next changeset 4:cb18f2388815 (2019-12-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" |
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modified:
macros.xml plot.xml test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad |
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added:
test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png |
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| diff -r 4bfb75bb7c8e -r a8f865950ac4 macros.xml --- a/macros.xml Thu Dec 05 07:10:37 2019 -0500 +++ b/macros.xml Thu Dec 12 09:24:59 2019 -0500 |
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| b'@@ -1,7 +1,7 @@\n <macros>\n <token name="@version@">1.4.4.post1</token>\n <token name="@profile@">19.01</token>\n- <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>\n+ <token name="@galaxy_version@"><![CDATA[@version@+galaxy1]]></token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@version@">scanpy</requirement>\n@@ -351,10 +351,10 @@\n <option value="gist_ncar">gist_ncar (Miscellaneous)</option>\n </xml>\n <xml name="param_groupby">\n- <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the heatmap is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into `num_categories`."/>\n+ <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into \'num_categories\'."/>\n </xml>\n <xml name="param_use_raw">\n- <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/>\n+ <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use \'raw\' attribute of input if present" help=""/>\n </xml>\n <xml name="param_log">\n <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>\n@@ -378,12 +378,12 @@\n <xml name="pl_var_names">\n <conditional name="var_names">\n <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >\n- <option value="all">All variables in `adata.var_names`</option>\n- <option value="custom">Subset of variables in `adata.var_names`</option>\n+ <option value="all">All variables in \'adata.var_names\'</option>\n+ <option value="custom">Subset of variables in \'adata.var_names\'</option>\n </param>\n <when value="all"/>\n <when value="custom">\n- <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of `adata.var_names`, and separated by comma"/>\n+ <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of \'adata.var_names\', and separated by comma"/>\n </when>\n </conditional>\n </xml>\n@@ -404,27 +404,20 @@\n <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>\n </xml>\n <xml name="param_layer">\n- <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/>\n+ <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default \'adata.raw.X\' is plotted. If \'use_raw=False\' is set, then \'adata.X\' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over \'use_raw\'."/>\n </xml>\n <token name="@CMD_param_plot_inputs@"><![CDATA[\n adata,\n save=\'.$format\',\n show=False,\n ]]></token>\n- <xml name="params_plots">\n+ <xml name="params_inputs">\n <expand macro="pl_var_names"/>\n <expand macro="param_groupby"/>\n- <expand macro="param_log"/>'..b'_pl_heatmap@"><![CDATA[\n+ swap_axes=$method.swap_axes,\n+ show_gene_labels=$method.show_gene_labels,\n+ cmap=\'$method.matplotlib_pyplot_imshow.cmap\',\n+ #if str($method.matplotlib_pyplot_imshow.interpolation) != \'None\'\n+ interpolation=\'$method.matplotlib_pyplot_imshow.interpolation\',\n+ #end if\n+ #if $method.matplotlib_pyplot_imshow.alpha\n+ alpha=$method.matplotlib_pyplot_imshow.alpha,\n+ #end if\n+ #if $method.matplotlib_pyplot_imshow.vmin\n+ vmin=$method.matplotlib_pyplot_imshow.vmin,\n+ #end if\n+ #if $method.matplotlib_pyplot_imshow.vmax\n+ vmax=$method.matplotlib_pyplot_imshow.vmax,\n+ #end if\n+ origin=\'$method.matplotlib_pyplot_imshow.origin\'\n+ ]]>\n+ </token>\n+ <xml name="pl_rank_genes_groups_ext">\n+ <expand macro="param_groups"/>\n+ <expand macro="param_n_genes"/>\n+ <expand macro="param_key"/>\n+ </xml>\n+ <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[\n+ @CMD_params_groups@\n+ #if str($method.n_genes) != \'\'\n+ n_genes=$method.n_genes,\n+ #end if\n+ #if str($method.key) != \'\'\n+ key=\'$method.key\',\n+ #end if\n+ ]]>\n+ </token>\n+ <xml name="pl_matrixplot">\n+ <expand macro="param_swap_axes"/>\n+ <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">\n+ <param argument="cmap" type="select" label="Color palette">\n+ <expand macro="seaborn_color_palette_options"/>\n+ </param>\n+ <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>\n+ <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>\n+ <expand macro="param_matplotlib_pyplot_edgecolors"/>\n+ <expand macro="param_alpha"/>\n+ <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>\n+ </section>\n+ </xml>\n+ <token name="@CMD_pl_matrixplot@"><![CDATA[\n+ swap_axes=$method.swap_axes,\n+ cmap=\'$method.matplotlib_pyplot_pcolor.cmap\',\n+ #if $method.matplotlib_pyplot_pcolor.vmin\n+ vmin=$method.matplotlib_pyplot_pcolor.vmin,\n+ #end if\n+ #if $method.matplotlib_pyplot_pcolor.vmax\n+ vmax=$method.matplotlib_pyplot_pcolor.vmax,\n+ #end if\n+ edgecolors=\'$method.matplotlib_pyplot_pcolor.edgecolors\',\n+ #if $method.matplotlib_pyplot_pcolor.alpha\n+ alpha=$method.matplotlib_pyplot_pcolor.alpha,\n+ #end if\n+ snap=$method.matplotlib_pyplot_pcolor.snap\n+ ]]>\n+ </token>\n+ <xml name="pl_stacked_violin">\n+ <expand macro="param_swap_axes"/>\n+ <section name="violin_plot" title="Violin plot attributes">\n+ <expand macro="conditional_stripplot"/>\n+ <expand macro="param_scale"/>\n+ </section>\n+ <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">\n+ <option value="muted">muted</option>\n+ <expand macro="seaborn_color_palette_options"/>\n+ </param>\n+ <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">\n+ <option value="None">No standardization</option>\n+ <option value="var">Standardization on variable</option>\n+ <option value="obs">Standardization on observation</option>\n+ </param>\n+ <expand macro="seaborn_violinplot"/>\n+ </xml>\n+ <token name="@CMD_pl_stacked_violin@"><![CDATA[\n+ swap_axes=$method.swap_axes,\n+ @CMD_conditional_stripplot@\n+ scale=\'$method.violin_plot.scale\',\n+ row_palette=\'$method.row_palette\',\n+ #if str($method.standard_scale) != \'None\'\n+ standard_scale=\'$method.standard_scale\',\n+ #end if\n+ @CMD_params_seaborn_violinplot@\n+ ]]>\n+ </token>\n </macros>\n' |
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| diff -r 4bfb75bb7c8e -r a8f865950ac4 plot.xml --- a/plot.xml Thu Dec 05 07:10:37 2019 -0500 +++ b/plot.xml Thu Dec 12 09:24:59 2019 -0500 |
| [ |
| b"@@ -37,53 +37,33 @@\n #end if\n use_raw=$method.use_raw,\n sort_order=$method.sort_order,\n- @CMD_params_pl_groups@\n+ @CMD_params_groups@\n @CMD_params_pl_components@\n projection='$method.plot.projection',\n legend_loc='$method.plot.legend_loc',\n- legend_fontsize=$method.plot.legend_fontsize,\n+ @CMD_param_legend_fontsize@\n legend_fontweight='$method.plot.legend_fontweight',\n color_map='$method.plot.color_map',\n+ #if str($method.plot.palette) != ''\n palette='$method.plot.palette',\n+ #end if\n frameon=$method.plot.frameon,\n- #if $method.plot.title\n- title='$method.plot.title',\n- #end if\n- size=$method.plot.size)\n+ @CMD_param_title@\n+ @CMD_param_size@)\n \n #else if $method.method == 'pl.heatmap'\n sc.pl.heatmap(\n @CMD_param_plot_inputs@\n+ @CMD_params_inputs@\n @CMD_params_plots@\n- swap_axes=$method.swap_axes,\n- show_gene_labels=$method.show_gene_labels,\n- cmap='$method.matplotlib_pyplot_imshow.cmap',\n- #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'\n- interpolation='$method.matplotlib_pyplot_imshow.interpolation',\n- #end if\n- #if $method.matplotlib_pyplot_imshow.alpha\n- alpha=$method.matplotlib_pyplot_imshow.alpha,\n- #end if\n- #if $method.matplotlib_pyplot_imshow.vmin\n- vmin=$method.matplotlib_pyplot_imshow.vmin,\n- #end if\n- #if $method.matplotlib_pyplot_imshow.vmax\n- vmax=$method.matplotlib_pyplot_imshow.vmax,\n- #end if\n- origin='$method.matplotlib_pyplot_imshow.origin')\n+ @CMD_pl_heatmap@)\n \n #else if $method.method == 'pl.dotplot'\n sc.pl.dotplot(\n @CMD_param_plot_inputs@\n+ @CMD_params_inputs@\n @CMD_params_plots@\n- color_map='$method.color_map',\n- #if $method.dot_max\n- dot_max=$method.dot_max,\n- #end if\n- #if $method.dot_min\n- dot_min=$method.dot_min,\n- #end if\n- @CMD_params_matplotlib_pyplot_scatter@)\n+ @CMD_pl_dotplot@)\n \n #else if $method.method == 'pl.violin'\n sc.pl.violin(\n@@ -118,33 +98,16 @@\n #else if $method.method == 'pl.stacked_violin'\n sc.pl.stacked_violin(\n @CMD_param_plot_inputs@\n+ @CMD_params_inputs@\n @CMD_params_plots@\n- swap_axes=$method.swap_axes,\n- @CMD_conditional_stripplot@\n- scale='$method.violin_plot.scale',\n- row_palette='$method.row_palette',\n- #if str($method.standard_scale) != 'None'\n- standard_scale='$method.standard_scale',\n- #end if\n- @CMD_params_seaborn_violinplot@)\n+ @CMD_pl_stacked_violin@)\n \n #else if $method.method == 'pl.matrixplot'\n sc.pl.matrixplot(\n @CMD_param_plot_inputs@\n+ @CMD_params_inputs@\n @CMD_params_plots@\n- swap_axes=$method.swap_axes,\n- cmap='$method.matplotlib_pyplot_pcolor.cmap',\n- #if $method.matplotlib_pyplot_pcolor.vmin\n- vmin=$method.matplotlib_pyplot_pcolor.vmin,\n- #end if\n- #if $method.matplotlib_pyplot_pcolor.vmax\n- vmax=$method.matplotlib_pyplot_pcolor.vmax,\n- #end if\n- edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',\n- #if $method.matplotlib_pyplot_pcolor.alpha\n- alpha=$method.matplotlib_pyplot_pcolor.alpha,\n- #end if\n- snap=$method.matplotlib_pyplot_pcolor.snap)\n+ @CMD_pl_matrixplot@)\n \n #else if $method.method == 'pl.clustermap'\n sc.pl.clustermap(\n@@ -190,8 +153,7 @@\n log=$method.log,\n save='.$format',\n show=False,\n- highly_variable_genes=$method.highly_variable_genes\n- )\n+ highly_variable_genes=$method.highly_variable_genes)\n \n #else if $method.method == 'pl.pca'\n sc.pl.pca(\n@@ -199,7 +161,7 @@\n @CMD_param_color@\n use_raw=$method.use_raw,\n sort_order=$method.sort_order,\n- @CMD_params_pl_groups@\n+ @CMD_params_groups@\n @CMD_params_pl_components@\n @CMD_pl_attribute_section@\n @CMD_params_matplotlib_pyplot_scatter@)\n@@ -222,7 +184,7 @@\n @CMD_param_color@\n use_raw=$method.use_raw,\n sort_order=$method.sort_order,\n- @CMD_params_pl_groups@\n+ @CMD_params_groups@\n @CMD_params_pl_components@\n @CMD_pl_attribute_section@\n "..b' </section>\n+ <param name="row_palette" value="muted"/>\n+ <param name="standard_scale" value="None"/>\n+ <section name="seaborn_violinplot">\n+ <param name="bw" value="scott"/>\n+ <param name="linewidth" value="0"/>\n+ <param name="color" value="AliceBlue"/>\n+ <param name="palette" value="viridis"/>\n+ <param name="saturation" value="0.75"/>\n+ </section>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>\n+ <has_text_matching expression="n_genes=10"/>\n+ <has_text_matching expression="log=False"/>\n+ <has_text_matching expression="use_raw=False"/>\n+ <has_text_matching expression="dendrogram=True"/>\n+ <has_text_matching expression="swap_axes=True"/>\n+ <has_text_matching expression="stripplot=True"/>\n+ <has_text_matching expression="jitter=True"/>\n+ <has_text_matching expression="size=1"/>\n+ <has_text_matching expression="scale=\'width\'"/>\n+ <has_text_matching expression="bw=\'scott\'"/>\n+ <has_text_matching expression="scale=\'width\'"/>\n+ <has_text_matching expression="linewidth=0.0"/>\n+ <has_text_matching expression="color=\'AliceBlue\'"/>\n+ <has_text_matching expression="palette=\'viridis\'"/>\n+ <has_text_matching expression="saturation=0.75"/>\n+ </assert_stdout>\n+ <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n Generic: Scatter plot along observations or variables axes (`pl.scatter`)\n@@ -1813,11 +1907,35 @@\n More details on the `scanpy documentation\n <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__\n \n-Marker genes: Plot ranking of genes for all tested comparisons (`pl.rank_genes_groups_violin`)\n-==============================================================================================\n+Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)\n+==================================================================================\n \n More details on the `scanpy documentation\n <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__\n+\n+Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)\n+====================================================================================\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__\n+\n+Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)\n+====================================================================================\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__\n+\n+Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)\n+==========================================================================================\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__\n+\n+Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)\n+==================================================================================================\n+\n+More details on the `scanpy documentation\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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