# HG changeset patch
# User ebi-gxa
# Date 1602086830 0
# Node ID 087a7edb099585cd88992d8134a6eadea332c842
# Parent  3cf0177ed87e5f0feaed71b20323fdcdffab6f6f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"

diff -r 3cf0177ed87e -r 087a7edb0995 scanpy-neighbours.xml
--- a/scanpy-neighbours.xml	Wed Sep 30 11:16:35 2020 +0000
+++ b/scanpy-neighbours.xml	Wed Oct 07 16:07:10 2020 +0000
@@ -1,22 +1,22 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
   <description>to derive kNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
-#if $settings.n_neighbors_file
-    #set f = open($settings.n_neighbors_file.__str__)
-    #set n_neighbors = f.read().strip()
-    #silent f.close
-#elif $settings.n_neighbors
-    #set n_neighbors = $settings.n_neighbors.__str__.strip()
-#end if
-
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-neighbors
 #if $settings.default == "false"
+    #if $settings.n_neighbors_file
+        #set f = open($settings.n_neighbors_file.__str__)
+        #set n_neighbors = f.read().strip()
+        #silent f.close
+    #elif $settings.n_neighbors
+        #set n_neighbors = $settings.n_neighbors.__str__.strip()
+    #end if
+
     #if $n_neighbors
         --n-neighbors $n_neighbors
     #end if