--- a/scanpy-plot-embedding.xml	Fri Jun 05 08:55:24 2020 -0400
+++ b/scanpy-plot-embedding.xml	Mon Sep 07 14:02:08 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>visualise cell embeddings</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -8,31 +8,58 @@
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-cli plot embed
-    @INPUT_OPTS@
-    --basis '${basis}'
+@INPUT_OPTS@
+#if $color_by
     --color '${color_by}'
-    ${use_raw}
+#end if
+${use_raw}
     --legend-loc '${legend_loc}'
     --legend-fontsize '${legend_fontsize}'
+#if $basis
+    --basis '${basis}'
+#end if
+#if $groups
+    --groups $groups
+#end if
+#if $neighbors_key
+    --neighbors-key '${neighbors_key}'
+#end if    
+#if $layer
+    --layer '${layer}'
+#end if
 #if $point_size
     --size ${point_size}
 #end if
 #if $gene_symbols_field
     --gene-symbols ${gene_symbols_field}
+    #end if
+${edges} --edges-width ${edges_width}
+#if $edges_color
+    --edges-color ${edges_color}
 #end if
-    @PLOT_OPTS@
+#if $components
+    --components ${components}
+#end if
+--projection $projection
+$sort_order
+@PLOT_OPTS@
 ]]></command>
 
   <inputs>
     <expand macro="input_object_params"/>
-    <param name="basis" argument="--basis" type="text" label="Name of the embedding to plot"/>
-    <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts">
+    <param name="basis" argument="--basis" type="text" value='umap' label="name of the embedding to plot"/>
+    <param name="color_by" argument="--color" type="text" label="color by attributes, comma separated texts">
       <sanitizer>
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
+    <param name="groups" argument="--groups" type="text" value="" label="Key for categorical in `.obs`" help="You can pass your predefined groups by choosing any categorical annotation of observations."/>
     <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/>
     <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
+    <param name="layer" argument="--layer" value="" type="text"
+        label="Name of the AnnData object layer to plot" help="By default adata.raw.X is plotted. If use_raw=False is set, then adata.X is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over use_raw." />
+    <param name="neighbors_key" argument="--neighbors-key" value="" type="text"
+        label="Where to look for neighbors connectivities." help="If not specified, this looks in .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, this looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities."/>
     <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
       <option value="right margin" selected="true">Right margin</option>
       <option value="on data">On data</option>
@@ -40,6 +67,15 @@
     <param name="legend_fontsize" argument="--legend-fontsize" type="integer" value="15" label="Legend font size"/>
     <param name="point_size" argument="--size" type="integer" optional="true" label="Point size"
            help="Automatically determined if not specified."/>
+    <param name="edges" argument="--edges" type="boolean" checked="False" truevalue="--edges" falsevalue="" label="Show edges?"/>
+    <param name="edges_width" argument="--edges-width" type="float" value="0.1" label="Width of edges"/>
+    <param name="edges_color" argument="--edges-color" type="text" value="" label="Color of edges"/>
+    <param name="sort_order" argument="--no-sort-order" type="boolean" checked="False" truevalue="" falsevalue="--no-sort-order" label="Plot in order?" help="For continuous annotations used as 'color parameter, plot data points with higher values on top of others."/>
+    <param name="components" argument="--components" type="text" value="" label="Components to plot" help="Comma-separated list, e.g. '1,2', '2,3'. To plot all available components use 'all'."/>
+    <param name="projection" argument="--projection" type="select" label="Plot projection">
+      <option value="2d" selected="true">2D</option>
+      <option value="3d">3D</option>
+    </param>
     <expand macro="output_plot_params"/>
   </inputs>
 
@@ -51,8 +87,9 @@
     <test>
       <param name="input_obj_file" value="find_cluster.h5"/>
       <param name="input_format" value="anndata"/>
+      <param name="basis" value="X_pca"/>
       <param name="color_by" value="louvain"/>
-      <output name="output_png" file="run_tsne.png" ftype="png" compare="sim_size"/>
+      <output name="output_png" file="plot_embed.png" ftype="png" compare="sim_size"/>
     </test>
   </tests>