--- a/plot.xml	Thu Feb 20 08:22:46 2020 -0500
+++ b/plot.xml	Wed May 20 16:08:18 2020 -0400
@@ -25,6 +25,9 @@
     #if $method.type.type == 'xy'
     x='$method.type.x',
     y='$method.type.y',
+    #if str($method.type.color) != ''
+    color='$method.type.color',
+	  #end if
         #if str('$method.type.layers.use_layers') == 'true'
     layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
         #end if
@@ -41,15 +44,17 @@
     @CMD_params_pl_components@
     projection='$method.plot.projection',
     legend_loc='$method.plot.legend_loc',
+    #if $method.plot.palette != 'default'
+    palette='$method.plot.palette',
+    #end if
+    #if $method.plot.color_map != 'None'
+    color_map='$method.plot.color_map',
+    #end if
     @CMD_param_legend_fontsize@
     legend_fontweight='$method.plot.legend_fontweight',
-    color_map='$method.plot.color_map',
-    #if str($method.plot.palette) != ''
-    palette='$method.plot.palette',
-    #end if
-    frameon=$method.plot.frameon,
     @CMD_param_title@
-    @CMD_param_size@)
+    @CMD_param_size@
+    frameon=$method.plot.frameon)
 
 #else if $method.method == 'pl.heatmap'
 sc.pl.heatmap(
@@ -412,17 +417,30 @@
                         <option value="basis">Using tool that computes coordinates</option>
                     </param>
                     <when value="xy">
-                        <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'"/>
-                        <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'"/>
+                        <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
+                            <expand macro="sanitize_query" />
+                        </param>
+                        <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
+                            <expand macro="sanitize_query" />
+                        </param>
+                        <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
+                            <expand macro="sanitize_query" />
+                        </param>
                         <conditional name="layers">
                             <param argument="use_layers" type="select" label="Use the layers attribute?">
                                 <option value="true">Yes</option>
                                 <option value="false" selected="true">No</option>
                             </param>
                             <when value="true">
-                                <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present"/>
-                                <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present"/>
-                                <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present"/>
+                                <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present">
+                                    <expand macro="sanitize_query" />
+                                </param>
+                                <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present">
+                                    <expand macro="sanitize_query" />
+                                </param>
+                                <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present">
+                                    <expand macro="sanitize_query" />
+                                </param>
                             </when>
                             <when value="false"/>
                         </conditional>
@@ -474,7 +492,9 @@
                     <when value="var_names"/>
                     <when value="obs"/>
                     <when value="custom">
-                        <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
+                        <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
+                            <expand macro="sanitize_query" />
+                        </param>
                     </when>
                 </conditional>
                 <expand macro="param_groupby"/>
@@ -495,7 +515,9 @@
                     </conditional>
                     <expand macro="param_scale"/>
                 </section>
-                <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None',    otherwise, no label is shown."/>
+                <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None',    otherwise, no label is shown.">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
                 <expand macro="seaborn_violinplot"/>
             </when>
@@ -510,7 +532,9 @@
                 <expand macro="pl_matrixplot"/>
             </when>
             <when value="pl.clustermap">
-                <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/>
+                <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">
+                    <expand macro="sanitize_query" />
+                </param>
                 <expand macro="param_use_raw"/>
                 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
                     <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
@@ -545,9 +569,13 @@
             </when>
             <when value="pl.highest_expr_genes">
                 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
-                <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'."/>
+                <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'.">
+                    <expand macro="sanitize_query" />
+                </param>
                 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
-                    <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
+                    <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help="">
+                        <expand macro="sanitize_query" />
+                    </param>
                     <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
                         <expand macro="seaborn_color_palette_options"/>
                     </param>
@@ -563,7 +591,9 @@
                 <expand macro="section_matplotlib_pyplot_scatter"/>
             </when>
             <when value="pl.pca_loadings">
-                <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components"/>
+                <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components">
+                    <expand macro="sanitize_query" />
+                </param>
             </when>
             <when value="pl.pca_variance_ratio">
                 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
@@ -642,13 +672,21 @@
             </when>
             <when value="pl.paga_path">
                 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
-                    help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>
-                <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
+                       help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated">
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
+                    <expand macro="sanitize_query" />
+                </param>
                 <expand macro="param_use_raw"/>
-                <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
+                <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated">
+                    <expand macro="sanitize_query" />
+                </param>
                 <expand macro="param_color_map"/>
                 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
-                <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups"/>
+                <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups">
+                    <expand macro="sanitize_query" />
+                </param>
                 <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
                 <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
                 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
@@ -674,7 +712,9 @@
                         <expand macro="param_n_genes"/>
                     </when>
                     <when value="gene_names">
-                        <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/>
+                        <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
+                                <expand macro="sanitize_query" />
+                        </param>
                     </when>
                 </conditional>
                 <expand macro="gene_symbols"/>