| Previous changeset 11:95777145cb92 (2023-11-08) Next changeset 13:6f5349dd5c49 (2024-03-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 |
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modified:
macros.xml plot.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
| b |
| diff -r 95777145cb92 -r 9b0cdb8cf6be macros.xml --- a/macros.xml Wed Nov 08 14:47:20 2023 +0000 +++ b/macros.xml Fri Nov 17 09:14:28 2023 +0000 |
| [ |
| b'@@ -1,10 +1,10 @@\n <macros>\n- <token name="@version@">1.9.6</token>\n+ <token name="@TOOL_VERSION@">1.9.6</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n <token name="@profile@">22.05</token>\n- <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="@version@">scanpy</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>\n <requirement type="package" version="3.0.6">loompy</requirement>\n <requirement type="package" version="0.10.1">leidenalg</requirement>\n <requirement type="package" version="0.8.1">louvain</requirement>\n@@ -469,13 +469,13 @@\n <token name="@CMD_params_inputs@"><![CDATA[\n #if $method.var_names.type == \'all\'\n var_names=adata.var_names,\n-#else\n+ #else\n #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(\',\')])\n var_names=$var_names,\n-#end if\n-#if str($method.groupby) != \'\'\n+ #end if\n+ #if $method.groupby\n groupby=\'$method.groupby\',\n-#end if\n+ #end if\n num_categories=$method.num_categories,\n ]]></token>\n <xml name="params_plots">\n@@ -501,15 +501,15 @@\n var_group_positions=$var_group_positions,\n var_group_labels=$var_group_labels,\n #end if\n-#if $method.var_group_rotation\n- var_group_rotation=$method.var_group_rotation,\n-#end if\n-#if $method.figsize.test == \'yes\'\n- figsize=($method.figsize.width, $method.figsize.height),\n-#end if\n-#if $method.layer != \'\'\n- layer=\'$method.layer\',\n-#end if\n+ #if str($method.var_group_rotation) != \'\'\n+ var_group_rotation=$method.var_group_rotation,\n+ #end if\n+ #if $method.figsize.test == \'yes\'\n+ figsize=($method.figsize.width, $method.figsize.height),\n+ #end if\n+ #if $method.layer\n+ layer=\'$method.layer\',\n+ #end if\n ]]></token>\n <xml name="matplotlib_color">\n <option value="AliceBlue">AliceBlue</option>\n@@ -662,9 +662,8 @@\n <option value="YellowGreen">YellowGreen</option>\n </xml>\n <xml name="param_matplotlib_pyplot_edgecolors">\n- <param argument="edgecolors" type="select" label="Edge color of the marker" help="">\n+ <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">\n <option value="face">The edge color will always be the same as the face color</option>\n- <option value="none">No patch boundary will be drawn</option>\n <expand macro="matplotlib_color"/>\n </param>\n </xml>\n@@ -702,17 +701,19 @@\n </section>\n </xml>\n <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[\n- #if $method.matplotlib_pyplot_scatter.vmin\n+ #if str($method.matplotlib_pyplot_scatter.vmin) != \'\'\n vmin=$method.matplotlib_pyplot_scatter.vmin,\n #end if\n- #if $method.matplotlib_pyplot_scatter.vmax\n+ #if str($method.matplotlib_pyplot_scatter.vmax) != \'\'\n vmax=$method.matplotlib_pyplot_scatter.vmax,\n #end if\n- #if $method.matplotlib_pyplot_scatter.alpha\n+ #if str($method.matplotlib_pyplot_scatter.alpha) != \'\'\n alpha=$method.matplotlib_pyplot_scatter.alpha,\n #end if\n- linewidths=$method.matplotlib_pyplot_scatter.linewidths,\n- edgecolors=\'$method.matplotlib_pyplot_scatter.edgecolors\'\n+ lw=$method.matplotlib_pyplot_scatter.linewidths,\n+ #if $method.matplotlib_pyplot_scatter.edgecolors\n+ ec=\'$method.matplotlib_pyplot_scatter.edgecolors\'\n+ #end if\n ]]></token>\n <xml name="conditional_stripplot">\n <conditional name="stripplot">\n@@ -752,13 +753,7 @@\n </param>\n </xml>\n <token name="@CMD_params_violin_plots@"><![CDATA[\n- stripplot=$method.violin_plot.stripplot.stripplot,\n-#if $method.violin_plot.stripplot.stripplot == "True"\n- jitter=$method.violin_plot.stripplot.jitter.jitter,\n- #if $method.violin_plot.stripplot.jitter.jitt'..b' All fractions larger than dot_max are clipped to this value."/>\n@@ -1133,7 +1132,9 @@\n <expand macro="section_matplotlib_pyplot_scatter"/>\n </xml>\n <token name="@CMD_pl_dotplot@"><![CDATA[\n+ #if $method.color_map\n color_map=\'$method.color_map\',\n+ #end if\n #if str($method.dot_max) != \'\'\n dot_max=$method.dot_max,\n #end if\n@@ -1184,17 +1185,19 @@\n <token name="@CMD_pl_heatmap@"><![CDATA[\n swap_axes=$method.swap_axes,\n show_gene_labels=$method.show_gene_labels,\n+ #if $method.matplotlib_pyplot_imshow.cmap\n cmap=\'$method.matplotlib_pyplot_imshow.cmap\',\n+ #end if\n #if str($method.matplotlib_pyplot_imshow.interpolation) != \'None\'\n interpolation=\'$method.matplotlib_pyplot_imshow.interpolation\',\n #end if\n- #if $method.matplotlib_pyplot_imshow.alpha\n+ #if str($method.matplotlib_pyplot_imshow.alpha) != \'\'\n alpha=$method.matplotlib_pyplot_imshow.alpha,\n #end if\n- #if $method.matplotlib_pyplot_imshow.vmin\n+ #if str($method.matplotlib_pyplot_imshow.vmin) != \'\'\n vmin=$method.matplotlib_pyplot_imshow.vmin,\n #end if\n- #if $method.matplotlib_pyplot_imshow.vmax\n+ #if str($method.matplotlib_pyplot_imshow.vmax) != \'\'\n vmax=$method.matplotlib_pyplot_imshow.vmax,\n #end if\n origin=\'$method.matplotlib_pyplot_imshow.origin\'\n@@ -1207,10 +1210,8 @@\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+ #if $method.key\n key=\'$method.key\',\n #end if\n ]]>\n@@ -1218,7 +1219,7 @@\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+ <param argument="cmap" type="select" optional="true" 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@@ -1230,15 +1231,19 @@\n </xml>\n <token name="@CMD_pl_matrixplot@"><![CDATA[\n swap_axes=$method.swap_axes,\n+ #if $method.matplotlib_pyplot_pcolor.cmap\n cmap=\'$method.matplotlib_pyplot_pcolor.cmap\',\n- #if $method.matplotlib_pyplot_pcolor.vmin\n+ #end if\n+ #if str($method.matplotlib_pyplot_pcolor.vmin) != \'\'\n vmin=$method.matplotlib_pyplot_pcolor.vmin,\n #end if\n- #if $method.matplotlib_pyplot_pcolor.vmax\n+ #if str($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+ #if $method.matplotlib_pyplot_pcolor.edgecolors\n+ ec=\'$method.matplotlib_pyplot_pcolor.edgecolors\',\n+ #end if\n+ #if str($method.matplotlib_pyplot_pcolor.alpha) != \'\'\n alpha=$method.matplotlib_pyplot_pcolor.alpha,\n #end if\n snap=$method.matplotlib_pyplot_pcolor.snap\n@@ -1250,7 +1255,7 @@\n <expand macro="conditional_stripplot"/>\n <expand macro="param_scale"/>\n </section>\n- <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">\n+ <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">\n <option value="muted">muted</option>\n <expand macro="seaborn_color_palette_options"/>\n </param>\n@@ -1265,7 +1270,9 @@\n swap_axes=$method.swap_axes,\n @CMD_conditional_stripplot@\n scale=\'$method.violin_plot.scale\',\n+ #if $method.row_palette\n row_palette=\'$method.row_palette\',\n+ #end if\n #if str($method.standard_scale) != \'None\'\n standard_scale=\'$method.standard_scale\',\n #end if\n' |
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| diff -r 95777145cb92 -r 9b0cdb8cf6be plot.xml --- a/plot.xml Wed Nov 08 14:47:20 2023 +0000 +++ b/plot.xml Fri Nov 17 09:14:28 2023 +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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">\n <description> with scanpy</description>\n <macros>\n <import>macros.xml</import>\n@@ -47,18 +47,18 @@\n #if $method.type.type == \'xy\':\n x=x_field,\n y=y_field,\n- #if str($method.type.color) != \'\'\n+ #if $method.type.color\n color=\'$method.type.color\',\n-\t #end if\n- #if str(\'$method.type.layers.use_layers\') == \'true\'\n+ #end if\n+ #if str(\'$method.type.layers.use_layers\') == \'true\'\n layers=(\'$method.type.layers.layer_x\', \'$method.type.layers.layer_y\', \'$method.type.layers.layer_color\'),\n- #end if\n+ #end if\n #else\n basis=\'$method.type.basis\',\n- #if str($method.type.color) != \'\'\n- #set $color = ([x.strip() for x in str($method.type.color).split(\',\')])\n+ #if $method.type.color\n+ #set $color = ([x.strip() for x in str($method.type.color).split(\',\')])\n color=$color,\n- #end if\n+ #end if\n #end if\n use_raw=$method.use_raw,\n sort_order=$method.sort_order,\n@@ -66,10 +66,10 @@\n @CMD_params_pl_components@\n projection=\'$method.plot.projection\',\n legend_loc=\'$method.plot.legend_loc\',\n- #if $method.plot.palette != \'default\'\n+ #if $method.plot.palette\n palette=[\'$method.plot.palette\'],\n #end if\n- #if $method.plot.color_map != \'None\'\n+ #if $method.plot.color_map\n color_map=\'$method.plot.color_map\',\n #end if\n @CMD_param_legend_fontsize@\n@@ -81,7 +81,7 @@\n #else if $method.method == \'pl.heatmap\'\n sc.pl.heatmap(\n @CMD_param_plot_inputs@\n- #if str($method.gene_symbols) != \'\'\n+ #if $method.gene_symbols\n gene_symbols=\'$method.gene_symbols\',\n #end if\n @CMD_params_inputs@\n@@ -91,7 +91,7 @@\n #else if $method.method == \'pl.dotplot\'\n sc.pl.dotplot(\n @CMD_param_plot_inputs@\n- #if str($method.gene_symbols) != \'\'\n+ #if $method.gene_symbols\n gene_symbols=\'$method.gene_symbols\',\n #end if\n @CMD_params_inputs@\n@@ -123,7 +123,7 @@\n #if $method.xlabel\n xlabel=\'$method.xlabel\',\n #end if\n- #if $method.rotation\n+ #if str($method.rotation) != \'\'\n rotation=$method.rotation,\n #end if\n @CMD_params_seaborn_violinplot@)\n@@ -131,7 +131,7 @@\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+ #if $method.gene_symbols\n gene_symbols=\'$method.gene_symbols\',\n #end if\n @CMD_params_inputs@\n@@ -141,7 +141,7 @@\n #else if $method.method == \'pl.matrixplot\'\n sc.pl.matrixplot(\n @CMD_param_plot_inputs@\n- #if str($method.gene_symbols) != \'\'\n+ #if $method.gene_symbols\n gene_symbols=\'$method.gene_symbols\',\n #end if\n @CMD_params_inputs@\n@@ -156,7 +156,7 @@\n adata=adata,\n #end if\n show=False,\n- #if str($method.obs_keys) != \'\'\n+ #if $method.obs_keys\n obs_keys=\'$method.obs_keys\',\n #end if\n use_raw=$method.use_raw,\n@@ -175,13 +175,13 @@\n sc.pl.highest_expr_genes(\n @CMD_param_plot_inputs@\n n_top=$method.n_top,\n- #if str($method.gene_symbols) != \'\'\n+ #if $method.gene_symbols\n gene_symbols=\'$method.gene_symbols\',\n #end if\n- #if str($method.setseaborn_boxplot.color) != \'\'\n+ #if $method.setseaborn_boxplot.color\n color=\'$method.setseaborn_boxplot.color\',\n #end if\n- #if str($method.setseaborn_boxplot.palette) != \'None\'\n+ #if $method.setseaborn_boxplot.palette\n palette=\'$method.setseaborn_boxplot.palette\',\n #end if\n saturation=$method.setseaborn_boxplot.saturation)\n@@ -269,7 +269,7 @@\n sc.pl.draw_graph(\n @CMD_param_plot_inputs@\n @CMD_param_color@\n- #if str($method.gene_symbols) != \'\'\n+ #if $method.gene_symbols\n gene_symbols=\'$method.gene_symbols\',\n #end if\n use_raw=$method.use_raw,\n@@ -290,17 +290,17 @@\n sc.pl.embedding_density(\n @'..b' <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>\n@@ -1670,8 +1670,8 @@\n <has_text_matching expression="ncols=4"/>\n <has_text_matching expression="wspace=0.1"/>\n <has_text_matching expression="hspace=0.25"/>\n- <has_text_matching expression="linewidths=0.0"/>\n- <has_text_matching expression="edgecolors=\'face\'"/>\n+ <has_text_matching expression="lw=0.0"/>\n+ <has_text_matching expression="ec=\'face\'"/>\n </assert_contents>\n </output>\n <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>\n@@ -1730,8 +1730,8 @@\n <has_text_matching expression="ncols=4"/>\n <has_text_matching expression="wspace=0.1"/>\n <has_text_matching expression="hspace=0.25"/>\n- <has_text_matching expression="linewidths=0.0"/>\n- <has_text_matching expression="edgecolors=\'face\'"/>\n+ <has_text_matching expression="lw=0.0"/>\n+ <has_text_matching expression="ec=\'face\'"/>\n </assert_contents>\n </output>\n <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>\n@@ -1781,8 +1781,8 @@\n <has_text_matching expression="ncols=4"/>\n <has_text_matching expression="wspace=0.1"/>\n <has_text_matching expression="hspace=0.25"/>\n- <has_text_matching expression="linewidths=0.0"/>\n- <has_text_matching expression="edgecolors=\'face\'"/>\n+ <has_text_matching expression="lw=0.0"/>\n+ <has_text_matching expression="ec=\'face\'"/>\n </assert_contents>\n </output>\n <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>\n@@ -1837,8 +1837,8 @@\n <has_text_matching expression="ncols=4"/>\n <has_text_matching expression="wspace=0.1"/>\n <has_text_matching expression="hspace=0.25"/>\n- <has_text_matching expression="linewidths=0.0"/>\n- <has_text_matching expression="edgecolors=\'face"/>\n+ <has_text_matching expression="lw=0.0"/>\n+ <has_text_matching expression="ec=\'face"/>\n </assert_contents>\n </output>\n <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>\n@@ -2053,8 +2053,8 @@\n <has_text_matching expression="use_raw=False"/>\n <has_text_matching expression="dendrogram=False"/>\n <has_text_matching expression="color_map=\'viridis\'"/>\n- <has_text_matching expression="linewidths=0.0"/>\n- <has_text_matching expression="edgecolors=\'face\'"/>\n+ <has_text_matching expression="lw=0.0"/>\n+ <has_text_matching expression="ec=\'face\'"/>\n </assert_contents>\n </output>\n <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>\n@@ -2126,7 +2126,7 @@\n <has_text_matching expression="dendrogram=False"/>\n <has_text_matching expression="swap_axes=False"/>\n <has_text_matching expression="cmap=\'viridis\'"/>\n- <has_text_matching expression="edgecolors=\'face\'"/>\n+ <has_text_matching expression="ec=\'face\'"/>\n <has_text_matching expression="snap=False"/>\n </assert_contents>\n </output>\n' |
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| diff -r 95777145cb92 -r 9b0cdb8cf6be test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png |
| b |
| Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed |
