--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-neighbours.xml	Wed Apr 03 11:11:14 2019 -0400
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1">
+  <description>to derive kNN graph</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-neighbours.py
+    -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    #if $settings.default == "false"
+        -N '${settings.n_neighbours}'
+        -m '${settings.method}'
+        -s '${settings.random_seed}'
+        #if $settings.use_rep != "auto"
+            -r '${settings.use_rep}'
+        #end if
+        #if $settings.n_pcs
+            -n '${settings.n_pcs}'
+        #end if
+        #if $settings.knn
+            --knn
+        #end if
+        #if $settings.metric
+            -M '${settings.metric}'
+        #end if
+    #end if
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <conditional name="settings">
+      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
+      <when value="true"/>
+      <when value="false">
+        <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/>
+        <param name="use_rep" type="select" label="Use the indicated representation">
+          <option value="X_pca">X_pca, use PCs</option>
+          <option value="X">X, use normalised expression values</option>
+          <option value="auto" selected="true">Automatically chosen based on problem size</option>
+        </param>
+        <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
+        <param name="knn" argument="--knn/--no-knn" type="boolean" checked="true" label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/>
+        <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
+          <option value="umap" selected="true">UMAP</option>
+          <option value="gauss">Gaussian</option>
+        </param>
+        <param name="metric" argument="--metric" type="text" value="euclidean" label="Distance metric"/>
+        <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Graph object"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="run_pca.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="default" value="false"/>
+      <param name="n_neighbours" value="15"/>
+      <param name="n_pcs" value="50"/>
+      <param name="knn" value="true"/>
+      <param name="random_seed" value="0"/>
+      <param name="method" value="umap"/>
+      <param name="metric" value="euclidean"/>
+      <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=============================================================
+Compute a neighborhood graph of observations (`pp.neighbors`)
+=============================================================
+
+The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
+which also provides a method for estimating connectivities of data points -
+the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`,
+connectivities are computed according to Coifman et al (2005), in the adaption of
+Haghverdi et al (2016).
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>