--- a/scanpy-neighbours.xml	Wed Apr 03 11:11:14 2019 -0400
+++ b/scanpy-neighbours.xml	Mon Sep 16 08:18:53 2019 -0400
@@ -1,34 +1,27 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0">
   <description>to derive kNN graph</description>
   <macros>
-    <import>scanpy_macros.xml</import>
+    <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-neighbours.py
-    -i input.h5
-    -f '${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
+PYTHONIOENCODING=utf-8 scanpy-neighbors
+#if $settings.default == "false"
+    --n-neighbors '${settings.n_neighbours}'
+    --method '${settings.method}'
+    --random-state '${settings.random_seed}'
+    #if $settings.use_rep != "auto"
+        --use-rep '${settings.use_rep}'
     #end if
+    #if $settings.n_pcs
+        --n-pcs '${settings.n_pcs}'
+    #end if
+    ${settings.knn}
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
 ]]></command>
 
   <inputs>
@@ -39,18 +32,17 @@
       <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>
+        <param name="use_rep" type="text" label="Use the indicated representation">
+          <option value="X_pca" selected="true">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="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" 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>
@@ -71,7 +63,6 @@
       <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>