--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-run-paga.xml	Mon Sep 16 08:25:36 2019 -0400
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy0">
+  <description>trajectory inference</description>
+  <macros>
+    <import>scanpy_macros2.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-cli paga
+    --groups '${groups}'
+#if $use_graph
+    --use-graph '${use_graph}'
+#end if
+#if $key_added
+    --key-added '${key_added}'
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+
+    <param name="groups" argument="--groups" type="text" label="Name of the clustering"/>
+    <param name="use_graph" argument="--use-graph" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/>
+    <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated trajectory"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: PAGA object"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="compute_graph.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="groups" value="leiden"/>
+      <param name="use_graph" value="neighbors"/>
+      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+===================================================================
+Perform PAGA (partition-based graph abstraction) (`scanpy.tl.paga`)
+===================================================================
+
+Infer trajectories by mapping out the coarse-grained connectivity structures of
+complex manifolds of single cell KNN graphs (Wolf et al, 2019).
+
+This requires to run `Scanpy FindCluster`, first.
+
+It yields `paga`, connectivity graph between clusters.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations">
+    <citation type="doi">10.1186/s13059-019-1663-x</citation>
+  </expand>
+</tool>