Mercurial > repos > iuc > scanpy_plot

changeset 12:9b0cdb8cf6be draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
author iuc
date Fri, 17 Nov 2023 09:14:28 +0000
parents 95777145cb92
children 6f5349dd5c49
files macros.xml plot.xml test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png
diffstat 3 files changed, 118 insertions(+), 111 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Nov 08 14:47:20 2023 +0000
+++ b/macros.xml	Fri Nov 17 09:14:28 2023 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@version@">1.9.6</token>
+    <token name="@TOOL_VERSION@">1.9.6</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@profile@">22.05</token>
-    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@version@">scanpy</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
             <requirement type="package" version="3.0.6">loompy</requirement>
             <requirement type="package" version="0.10.1">leidenalg</requirement>
             <requirement type="package" version="0.8.1">louvain</requirement>
@@ -469,13 +469,13 @@
     <token name="@CMD_params_inputs@"><![CDATA[
     #if $method.var_names.type == 'all'
     var_names=adata.var_names,
-#else
+    #else
     #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
     var_names=$var_names,
-#end if
-#if str($method.groupby) != ''
+    #end if
+    #if $method.groupby
     groupby='$method.groupby',
-#end if
+    #end if
     num_categories=$method.num_categories,
     ]]></token>
     <xml name="params_plots">
@@ -501,15 +501,15 @@
     var_group_positions=$var_group_positions,
     var_group_labels=$var_group_labels,
     #end if
-#if $method.var_group_rotation
-    var_group_rotation=$method.var_group_rotation,
-#end if
-#if $method.figsize.test == 'yes'
-    figsize=($method.figsize.width, $method.figsize.height),
-#end if
-#if $method.layer != ''
-    layer='$method.layer',
-#end if
+    #if str($method.var_group_rotation) != ''
+        var_group_rotation=$method.var_group_rotation,
+    #end if
+    #if $method.figsize.test == 'yes'
+        figsize=($method.figsize.width, $method.figsize.height),
+    #end if
+    #if $method.layer
+        layer='$method.layer',
+    #end if
     ]]></token>
     <xml name="matplotlib_color">
         <option value="AliceBlue">AliceBlue</option>
@@ -662,9 +662,8 @@
         <option value="YellowGreen">YellowGreen</option>
     </xml>
     <xml name="param_matplotlib_pyplot_edgecolors">
-        <param argument="edgecolors" type="select" label="Edge color of the marker" help="">
+        <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">
             <option value="face">The edge color will always be the same as the face color</option>
-            <option value="none">No patch boundary will be drawn</option>
             <expand macro="matplotlib_color"/>
         </param>
     </xml>
@@ -702,17 +701,19 @@
         </section>
     </xml>
     <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
-    #if $method.matplotlib_pyplot_scatter.vmin
+    #if str($method.matplotlib_pyplot_scatter.vmin) != ''
     vmin=$method.matplotlib_pyplot_scatter.vmin,
     #end if
-    #if $method.matplotlib_pyplot_scatter.vmax
+    #if str($method.matplotlib_pyplot_scatter.vmax) != ''
     vmax=$method.matplotlib_pyplot_scatter.vmax,
     #end if
-    #if $method.matplotlib_pyplot_scatter.alpha
+    #if str($method.matplotlib_pyplot_scatter.alpha) != ''
     alpha=$method.matplotlib_pyplot_scatter.alpha,
     #end if
-    linewidths=$method.matplotlib_pyplot_scatter.linewidths,
-    edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
+    lw=$method.matplotlib_pyplot_scatter.linewidths,
+    #if $method.matplotlib_pyplot_scatter.edgecolors
+    ec='$method.matplotlib_pyplot_scatter.edgecolors'
+    #end if
     ]]></token>
     <xml name="conditional_stripplot">
         <conditional name="stripplot">
@@ -752,13 +753,7 @@
         </param>
     </xml>
     <token name="@CMD_params_violin_plots@"><![CDATA[
-    stripplot=$method.violin_plot.stripplot.stripplot,
-#if $method.violin_plot.stripplot.stripplot == "True"
-    jitter=$method.violin_plot.stripplot.jitter.jitter,
-    #if $method.violin_plot.stripplot.jitter.jitter == "True"
-    size=$method.violin_plot.stripplot.jitter.size,
-    #end if
-#end if
+    @CMD_conditional_stripplot@
     multi_panel=$method.violin_plot.multi_panel.multi_panel,
 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
     figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
@@ -776,7 +771,7 @@
                 <option value="h">horizontal</option>
             </param>
             <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
-            <param argument="color" type="select" label="Color for all of the elements" help="">
+            <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
                 <expand macro="matplotlib_color"/>
             </param>
             <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
@@ -788,7 +783,9 @@
     orient='$method.seaborn_violinplot.orient',
 #end if
     linewidth=$method.seaborn_violinplot.linewidth,
+    #if $method.seaborn_violinplot.color
     color='$method.seaborn_violinplot.color',
+    #end if
     saturation=$method.seaborn_violinplot.saturation
     ]]></token>
     <xml name="param_color">
@@ -797,7 +794,7 @@
         </param>
     </xml>
     <token name="@CMD_param_color@"><![CDATA[
-#if str($method.color) != ''
+#if $method.color
     #set $color = ([x.strip() for x in str($method.color).split(',')])
     color=$color,
 #end if
@@ -808,7 +805,7 @@
         </param>
     </xml>
     <token name="@CMD_params_groups@"><![CDATA[
-#if str($method.groups) != ''
+#if $method.groups
     #set $groups=([x.strip() for x in str($method.groups).split(',')])
     groups=$groups,
 #end if
@@ -878,14 +875,12 @@
         </param>
     </xml>
     <xml name="param_palette">
-        <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help="">
-            <option value="default">Default</option>
+        <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
     <xml name="param_color_map">
-        <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
-            <option value="" >Default</option>
+        <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -941,7 +936,7 @@
             </param>
             <when value="True">
                 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
-                <param argument="edges_color" type="select" label="Color of edges">
+                <param argument="edges_color" type="select" optional="true" label="Color of edges">
                     <expand macro="matplotlib_color"/>
                 </param>
             </when>
@@ -952,7 +947,9 @@
 #if str($method.edges.edges) == 'True'
     edges=True,
     edges_width=$method.edges.edges_width,
+    #if $method.edges.edges_color
     edges_color='$method.edges.edges_color',
+    #end if
 #else
     edges=False,
 #end if
@@ -962,7 +959,7 @@
         <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
     </xml>
     <xml name="param_cmap">
-        <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
+        <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -989,10 +986,10 @@
     @CMD_param_legend_fontsize@
     legend_fontweight='$method.plot.legend_fontweight',
     @CMD_param_size@
-    #if str($method.plot.color_map) != ''
+    #if $method.plot.color_map
     color_map='$method.plot.color_map',
     #end if
-    #if str($method.plot.palette) != ''
+    #if $method.plot.palette
     palette='$method.plot.palette',
     #end if
     frameon=$method.plot.frameon,
@@ -1062,18 +1059,18 @@
     </xml>
     <token name="@CMD_params_pl_paga@"><![CDATA[
     threshold=$method.threshold,
-#if str($method.groups) != ''
+#if $method.groups
     #set $groups=([x.strip() for x in str($method.groups).split(',')])
     groups=$groups,
 #end if
-#if str($method.color) != ''
+#if $method.color
     #set $color=([x.strip() for x in str($method.color).split(',')])
     color=$color,
 #end if
 #if $method.pos
     pos=np.fromfile($method.pos, dtype=dt),
 #end if
-#if str($method.labels) != ''
+#if $method.labels
     #set $labels=([x.strip() for x in str($method.labels).split(',')])
     labels=$labels,
 #end if
@@ -1082,7 +1079,7 @@
     init_pos=np.fromfile($method.init_pos, dtype=dt),
 #end if
     random_state=$method.random_state,
-#if str($method.root) != ''
+#if $method.root
     #set $root=([int(x.strip()) for x in str($method.root).split(',')])
     root=$root,
 #end if
@@ -1098,15 +1095,17 @@
     node_size_scale=$method.node_size_scale,
     node_size_power=$method.node_size_power,
     edge_width_scale=$method.edge_width_scale,
-#if $method.min_edge_width
+#if str($method.min_edge_width) != ''
     min_edge_width=$method.min_edge_width,
 #end if
-#if $method.max_edge_width
+#if str($method.max_edge_width) != ''
     max_edge_width=$method.max_edge_width,
 #end if
     arrowsize=$method.arrowsize,
     normalize_to_color=$method.normalize_to_color,
+    #if $method.cmap
     cmap='$method.cmap',
+    #end if
 #if $method.title
     title='$method.title',
 #end if
@@ -1125,7 +1124,7 @@
         <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
     </xml>
     <xml name="pl_dotplot">
-        <param argument="color_map" type="select" label="Color palette">
+        <param argument="color_map" type="select" optional="true" label="Color palette">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
         <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
@@ -1133,7 +1132,9 @@
         <expand macro="section_matplotlib_pyplot_scatter"/>
     </xml>
     <token name="@CMD_pl_dotplot@"><![CDATA[
+    #if $method.color_map
     color_map='$method.color_map',
+    #end if
     #if str($method.dot_max) != ''
     dot_max=$method.dot_max,
     #end if
@@ -1184,17 +1185,19 @@
     <token name="@CMD_pl_heatmap@"><![CDATA[
     swap_axes=$method.swap_axes,
     show_gene_labels=$method.show_gene_labels,
+    #if $method.matplotlib_pyplot_imshow.cmap
     cmap='$method.matplotlib_pyplot_imshow.cmap',
+    #end if
     #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
     interpolation='$method.matplotlib_pyplot_imshow.interpolation',
     #end if
-    #if $method.matplotlib_pyplot_imshow.alpha
+    #if str($method.matplotlib_pyplot_imshow.alpha) != ''
     alpha=$method.matplotlib_pyplot_imshow.alpha,
     #end if
-    #if $method.matplotlib_pyplot_imshow.vmin
+    #if str($method.matplotlib_pyplot_imshow.vmin) != ''
     vmin=$method.matplotlib_pyplot_imshow.vmin,
     #end if
-    #if $method.matplotlib_pyplot_imshow.vmax
+    #if str($method.matplotlib_pyplot_imshow.vmax) != ''
     vmax=$method.matplotlib_pyplot_imshow.vmax,
     #end if
     origin='$method.matplotlib_pyplot_imshow.origin'
@@ -1207,10 +1210,8 @@
     </xml>
     <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
     @CMD_params_groups@
-    #if str($method.n_genes) != ''
     n_genes=$method.n_genes,
-    #end if
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
     ]]>
@@ -1218,7 +1219,7 @@
     <xml name="pl_matrixplot">
         <expand macro="param_swap_axes"/>
         <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
-            <param argument="cmap" type="select" label="Color palette">
+            <param argument="cmap" type="select" optional="true" label="Color palette">
                 <expand macro="seaborn_color_palette_options"/>
             </param>
             <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
@@ -1230,15 +1231,19 @@
     </xml>
     <token name="@CMD_pl_matrixplot@"><![CDATA[
     swap_axes=$method.swap_axes,
+    #if $method.matplotlib_pyplot_pcolor.cmap
     cmap='$method.matplotlib_pyplot_pcolor.cmap',
-    #if $method.matplotlib_pyplot_pcolor.vmin
+    #end if
+    #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
     vmin=$method.matplotlib_pyplot_pcolor.vmin,
     #end if
-    #if $method.matplotlib_pyplot_pcolor.vmax
+    #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
     vmax=$method.matplotlib_pyplot_pcolor.vmax,
     #end if
-    edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
-    #if $method.matplotlib_pyplot_pcolor.alpha
+    #if $method.matplotlib_pyplot_pcolor.edgecolors
+    ec='$method.matplotlib_pyplot_pcolor.edgecolors',
+    #end if
+    #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
     alpha=$method.matplotlib_pyplot_pcolor.alpha,
     #end if
     snap=$method.matplotlib_pyplot_pcolor.snap
@@ -1250,7 +1255,7 @@
             <expand macro="conditional_stripplot"/>
             <expand macro="param_scale"/>
         </section>
-        <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">
+        <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
             <option value="muted">muted</option>
             <expand macro="seaborn_color_palette_options"/>
         </param>
@@ -1265,7 +1270,9 @@
     swap_axes=$method.swap_axes,
     @CMD_conditional_stripplot@
     scale='$method.violin_plot.scale',
+    #if $method.row_palette
     row_palette='$method.row_palette',
+    #end if
     #if str($method.standard_scale) != 'None'
     standard_scale='$method.standard_scale',
     #end if
--- a/plot.xml	Wed Nov 08 14:47:20 2023 +0000
+++ b/plot.xml	Fri Nov 17 09:14:28 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_plot" name="Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description> with scanpy</description>
     <macros>
         <import>macros.xml</import>
@@ -47,18 +47,18 @@
     #if $method.type.type == 'xy':
     x=x_field,
     y=y_field,
-    #if str($method.type.color) != ''
+    #if $method.type.color
     color='$method.type.color',
-	  #end if
-        #if str('$method.type.layers.use_layers') == 'true'
+    #end if
+    #if str('$method.type.layers.use_layers') == 'true'
     layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
-        #end if
+    #end if
     #else
     basis='$method.type.basis',
-        #if str($method.type.color) != ''
-            #set $color = ([x.strip() for x in str($method.type.color).split(',')])
+    #if $method.type.color
+        #set $color = ([x.strip() for x in str($method.type.color).split(',')])
     color=$color,
-        #end if
+    #end if
     #end if
     use_raw=$method.use_raw,
     sort_order=$method.sort_order,
@@ -66,10 +66,10 @@
     @CMD_params_pl_components@
     projection='$method.plot.projection',
     legend_loc='$method.plot.legend_loc',
-    #if $method.plot.palette != 'default'
+    #if $method.plot.palette
     palette=['$method.plot.palette'],
     #end if
-    #if $method.plot.color_map != 'None'
+    #if $method.plot.color_map
     color_map='$method.plot.color_map',
     #end if
     @CMD_param_legend_fontsize@
@@ -81,7 +81,7 @@
 #else if $method.method == 'pl.heatmap'
 sc.pl.heatmap(
     @CMD_param_plot_inputs@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_params_inputs@
@@ -91,7 +91,7 @@
 #else if $method.method == 'pl.dotplot'
 sc.pl.dotplot(
     @CMD_param_plot_inputs@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_params_inputs@
@@ -123,7 +123,7 @@
     #if $method.xlabel
     xlabel='$method.xlabel',
     #end if
-    #if $method.rotation
+    #if str($method.rotation) != ''
     rotation=$method.rotation,
     #end if
     @CMD_params_seaborn_violinplot@)
@@ -131,7 +131,7 @@
 #else if $method.method == 'pl.stacked_violin'
 sc.pl.stacked_violin(
     @CMD_param_plot_inputs@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_params_inputs@
@@ -141,7 +141,7 @@
 #else if $method.method == 'pl.matrixplot'
 sc.pl.matrixplot(
     @CMD_param_plot_inputs@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_params_inputs@
@@ -156,7 +156,7 @@
     adata=adata,
     #end if
     show=False,
-    #if str($method.obs_keys) != ''
+    #if $method.obs_keys
     obs_keys='$method.obs_keys',
     #end if
     use_raw=$method.use_raw,
@@ -175,13 +175,13 @@
 sc.pl.highest_expr_genes(
     @CMD_param_plot_inputs@
     n_top=$method.n_top,
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
-    #if str($method.setseaborn_boxplot.color) != ''
+    #if $method.setseaborn_boxplot.color
     color='$method.setseaborn_boxplot.color',
     #end if
-    #if str($method.setseaborn_boxplot.palette) != 'None'
+    #if $method.setseaborn_boxplot.palette
     palette='$method.setseaborn_boxplot.palette',
     #end if
     saturation=$method.setseaborn_boxplot.saturation)
@@ -269,7 +269,7 @@
 sc.pl.draw_graph(
     @CMD_param_plot_inputs@
     @CMD_param_color@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     use_raw=$method.use_raw,
@@ -290,17 +290,17 @@
 sc.pl.embedding_density(
     @CMD_param_plot_inputs@
     basis='$method.basis',
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
-    #if str($method.groupby) != ''
+    #if $method.groupby
     groupby='$method.groupby',
     #end if
-    #if str($method.group) != ''
+    #if $method.group
     #set $group = ([x.strip() for x in str($method.group).split(',')])
     group=$group,
     #end if
-    #if str($method.color_map) != ''
+    #if $method.color_map
     color_map='$method.color_map',
     #end if
     bg_dotsize=$method.bg_dotsize,
@@ -312,7 +312,7 @@
 #else if $method.method == 'pl.dpt_groups_pseudotime'
 sc.pl.dpt_groups_pseudotime(
     @CMD_param_plot_inputs@
-    #if str($method.color_map) != ''
+    #if $method.color_map
     color_map='$method.color_map'
     #end if
     )
@@ -321,7 +321,7 @@
 sc.pl.dpt_timeseries(
     @CMD_param_plot_inputs@
     #if $method.heatmap.as_heatmap == "True"
-        #if str($method.heatmap.color_map) != ''
+        #if $method.heatmap.color_map
     color_map='$method.heatmap.color_map',
         #end if
     #end if
@@ -345,15 +345,15 @@
     #set $keys=([x.strip() for x in str($method.keys).split(',')])
     keys=$keys,
     use_raw=$method.use_raw,
-    #if str($method.annotations) != ''
+    #if $method.annotations
         #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
     annotations=$annotations,
     #end if
-    #if str($method.color_map) != 'None'
+    #if $method.color_map
     color_map='$method.color_map',
     #end if
     n_avg=$method.n_avg,
-    #if str($method.annotations) != ''
+    #if $method.annotations
     groups_key='$method.groups_key',
     #end if
     as_heatmap=$method.as_heatmap,
@@ -367,7 +367,7 @@
     @CMD_param_plot_inputs@
     @CMD_params_groups@
     n_genes=$method.n_genes,
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     fontsize=$method.fontsize,
@@ -384,7 +384,7 @@
         #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
     gene_names=$gene_names,
     #end if
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     use_raw=$method.use_raw,
@@ -402,7 +402,7 @@
 sc.pl.rank_genes_groups_dotplot(
     @CMD_param_plot_inputs@
     @CMD_pl_rank_genes_groups_ext@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_params_plots@
@@ -413,7 +413,7 @@
     @CMD_param_plot_inputs@
     @CMD_pl_rank_genes_groups_ext@
     @CMD_params_plots@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_pl_heatmap@)
@@ -423,7 +423,7 @@
     @CMD_param_plot_inputs@
     @CMD_pl_rank_genes_groups_ext@
     @CMD_params_plots@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_pl_matrixplot@)
@@ -433,7 +433,7 @@
     @CMD_param_plot_inputs@
     @CMD_pl_rank_genes_groups_ext@
     @CMD_params_plots@
-    #if str($method.gene_symbols) != ''
+    #if $method.gene_symbols
     gene_symbols='$method.gene_symbols',
     #end if
     @CMD_pl_stacked_violin@)
@@ -1116,8 +1116,8 @@
                     <has_text_matching expression="color_map='hot'"/>
                     <has_text_matching expression="dot_max=0.7"/>
                     <has_text_matching expression="dot_min=0.1"/>
-                    <has_text_matching expression="linewidths=0.0"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <has_text_matching expression="lw=0.0"/>
+                    <has_text_matching expression="ec='face'"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
@@ -1350,7 +1350,7 @@
                     <has_text_matching expression="dendrogram=True"/>
                     <has_text_matching expression="swap_axes=True"/>
                     <has_text_matching expression="cmap='viridis'"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <has_text_matching expression="ec='face'"/>
                     <has_text_matching expression="snap=False"/>
                 </assert_contents>
             </output>
@@ -1532,8 +1532,8 @@
                     <has_text_matching expression="ncols=2" />
                     <has_text_matching expression="wspace=0.1" />
                     <has_text_matching expression="hspace=0.25" />
-                    <has_text_matching expression="linewidths=0.0" />
-                    <has_text_matching expression="edgecolors='face'" />
+                    <has_text_matching expression="lw=0.0" />
+                    <has_text_matching expression="ec='face'" />
                 </assert_contents>
             </output>
             <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
@@ -1670,8 +1670,8 @@
                     <has_text_matching expression="ncols=4"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
-                    <has_text_matching expression="linewidths=0.0"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <has_text_matching expression="lw=0.0"/>
+                    <has_text_matching expression="ec='face'"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
@@ -1730,8 +1730,8 @@
                     <has_text_matching expression="ncols=4"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
-                    <has_text_matching expression="linewidths=0.0"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <has_text_matching expression="lw=0.0"/>
+                    <has_text_matching expression="ec='face'"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
@@ -1781,8 +1781,8 @@
                     <has_text_matching expression="ncols=4"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
-                    <has_text_matching expression="linewidths=0.0"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <has_text_matching expression="lw=0.0"/>
+                    <has_text_matching expression="ec='face'"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
@@ -1837,8 +1837,8 @@
                     <has_text_matching expression="ncols=4"/>
                     <has_text_matching expression="wspace=0.1"/>
                     <has_text_matching expression="hspace=0.25"/>
-                    <has_text_matching expression="linewidths=0.0"/>
-                    <has_text_matching expression="edgecolors='face"/>
+                    <has_text_matching expression="lw=0.0"/>
+                    <has_text_matching expression="ec='face"/>
                 </assert_contents>
             </output>
             <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
@@ -2053,8 +2053,8 @@
                     <has_text_matching expression="use_raw=False"/>
                     <has_text_matching expression="dendrogram=False"/>
                     <has_text_matching expression="color_map='viridis'"/>
-                    <has_text_matching expression="linewidths=0.0"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <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_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
@@ -2126,7 +2126,7 @@
                     <has_text_matching expression="dendrogram=False"/>
                     <has_text_matching expression="swap_axes=False"/>
                     <has_text_matching expression="cmap='viridis'"/>
-                    <has_text_matching expression="edgecolors='face'"/>
+                    <has_text_matching expression="ec='face'"/>
                     <has_text_matching expression="snap=False"/>
                 </assert_contents>
             </output>
Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed