--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-plot-embedding.xml	Mon Sep 16 08:26:08 2019 -0400
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy0">
+  <description>visualise cell embeddings</description>
+  <macros>
+    <import>scanpy_macros2.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-cli plot embed
+    @INPUT_OPTS@
+    --basis '${basis}'
+    --color '${color_by}'
+    ${use_raw}
+    --legend-loc '${legend_loc}'
+    --legend-fontsize '${legend_fontsize}'
+#if $point_size
+    --size ${point_size}
+#end if
+    @PLOT_OPTS@
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <param name="basis" argument="--basis" type="text" label="Name of the embedding to plot"/>
+    <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts"/>
+    <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
+    <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
+      <option value="right margin" selected="true">Right margin</option>
+      <option value="on data">On data</option>
+    </param>
+    <param name="legend_fontsize" argument="--legend-fontsize" type="integer" value="15" label="Legend font size"/>
+    <param name="point_size" argument="--size" type="integer" optional="true" label="Point size"
+           help="Automatically determined if not specified."/>
+    <expand macro="output_plot_params"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: embedding plot"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="color_by" value="louvain"/>
+      <output name="output_png" file="run_tsne.png" ftype="png" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=============================================================
+Plot embeddings of a given method of dimensionality reduction
+=============================================================
+
+It yields a scatter plot in png format, wherein cells are placed in space of
+reduced dimensionality and coloured by attribute of choice.
+
+Requires calculating the specified embeddings first. For example, to make
+UMAP/TSNE plots, run `Scanpy RunUMAP`/`Scanpy RunTSNE` first, then enter
+"umap"/"tsne" as the name of the embedding to plot here.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>