Mercurial > repos > iuc > scanpy_plot

diff plot.xml @ 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 f7446fd8d5e7
line wrap: on
line diff
--- 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>