# HG changeset patch
# User iuc
# Date 1700212515 0
# Node ID 3081ff5c84a37d92e80e99b4531805083f356088
# Parent  6bd82ed14acdbee46b904cabd227a2346d888a34
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0

diff -r 6bd82ed14acd -r 3081ff5c84a3 inspect.xml
--- a/inspect.xml	Wed Nov 08 14:48:14 2023 +0000
+++ b/inspect.xml	Fri Nov 17 09:15:15 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">
+<tool id="scanpy_inspect" name="Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
     <description> with scanpy</description>
     <macros>
         <import>macros.xml</import>
@@ -66,11 +66,11 @@
     adata=adata,
     expr_type='$method.expr_type',
     var_type='$method.var_type',
-    #if str($method.qc_vars) != ''
+    #if $method.qc_vars
         #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
     qc_vars=$qc_vars,
     #end if
-    #if str($method.percent_top) != ''
+    #if $method.percent_top
         #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
         percent_top=$method.percent_top,
     #end if
@@ -125,7 +125,7 @@
     #if str($method.n_pcs) != ''
     n_pcs=$method.n_pcs,
     #end if
-    #if str($method.use_rep) != ''
+    #if $method.use_rep
     use_rep='$method.use_rep',
     #end if
     knn=$method.knn,
@@ -138,7 +138,7 @@
 sc.tl.rank_genes_groups(
     adata=adata,
     groupby='$method.groupby',
-    #if str($method.groups) != ''
+    #if $method.groups
     #set $group=[x.strip() for x in str($method.groups).split(',')]
     groups=$group,
     #end if
@@ -176,13 +176,13 @@
             #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'
     intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
             #end if
-            #if $method.tl_rank_genes_groups_method.solver.random_state
+            #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
     random_state=$method.tl_rank_genes_groups_method.solver.random_state,
             #end if
         #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'
     penalty='l2',
     fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
-            #if $method.tl_rank_genes_groups_method.solver.random_state
+            #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
     random_state=$method.tl_rank_genes_groups_method.solver.random_state,
             #end if
     max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
@@ -213,7 +213,7 @@
 sc.tl.marker_gene_overlap(
     adata,
     reference_markers,
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
     method='$method.overlap.method',
@@ -226,7 +226,7 @@
     #if str($method.adj_pval_threshold) != ''
     adj_pval_threshold=$method.adj_pval_threshold,
     #end if
-    #if str($method.key_added) != ''
+    #if $method.key_added
     key_added='$method.key_added',
     #end if
     inplace=True)
@@ -240,7 +240,7 @@
 sc.pp.scale(
     adata,
     zero_center=$method.zero_center,
-    #if $method.max_value
+    #if str($method.max_value) != ''
     max_value=$method.max_value,
     #end if
     copy=False)
@@ -368,9 +368,9 @@
                 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
                 <conditional name="tl_rank_genes_groups_method">
                     <param argument="method" type="select" label="Method">
-                        <option value="t-test">t-test</option>
+                        <option value="t-test" selected="true">t-test</option>
                         <option value="wilcoxon">Wilcoxon-Rank-Sum</option>
-                        <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option>
+                        <option value="t-test_overestim_var">t-test with overestimate of variance of each group</option>
                         <option value="logreg">Logistic regression</option>
                     </param>
                     <when value="t-test">
diff -r 6bd82ed14acd -r 3081ff5c84a3 macros.xml
--- a/macros.xml	Wed Nov 08 14:48:14 2023 +0000
+++ b/macros.xml	Fri Nov 17 09:15:15 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
diff -r 6bd82ed14acd -r 3081ff5c84a3 test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png
Binary file test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png has changed