# HG changeset patch
# User ebi-gxa
# Date 1601388689 0
# Node ID a57b128ea4f60eba56d064f75c4088d213fe8945
# Parent  e6c989a9211cb50fa2baeda8b46a72726d5de4b2
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"

diff -r e6c989a9211c -r a57b128ea4f6 scanpy-neighbours.xml
--- a/scanpy-neighbours.xml	Thu Sep 24 13:26:39 2020 +0000
+++ b/scanpy-neighbours.xml	Tue Sep 29 14:11:29 2020 +0000
@@ -1,14 +1,15 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
   <description>to derive kNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
-#from pathlib import Path
 #if $settings.n_neighbors_file
-    #set n_neighbors = Path($settings.n_neighbors_file.__str__).read_text().strip()
+    #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
@@ -106,6 +107,18 @@
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="default" value="false"/>
+      <param name="n_neighbors_file" value="n_neighbors.txt"/>
+      <param name="n_pcs" value="50"/>
+      <param name="knn" value="true"/>
+      <param name="random_seed" value="0"/>
+      <param name="method" value="umap"/>
+      <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>
+    </test>
+    <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_neighbors" value="15"/>
       <param name="n_pcs" value="50"/>
       <param name="knn" value="true"/>