# HG changeset patch
# User ebi-gxa
# Date 1599727510 0
# Node ID 7ae183da3f0709d416f8b632e3f81ac608c1e034
# Parent  873449082a2920ba2f3fef698cfa439cef5b93c6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"

diff -r 873449082a29 -r 7ae183da3f07 pbmc3k_filtered_gene_bc_matrices.tar.gz
Binary file pbmc3k_filtered_gene_bc_matrices.tar.gz has changed
diff -r 873449082a29 -r 7ae183da3f07 scanpy-integrate-mnn.xml
--- a/scanpy-integrate-mnn.xml	Mon Sep 07 13:10:40 2020 +0000
+++ b/scanpy-integrate-mnn.xml	Thu Sep 10 08:45:10 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
   <description>correct batch effects by matching mutual nearest neighbors</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -46,8 +46,7 @@
   @INPUT_OPTS@
   @OUTPUT_OPTS@
 #else
-  echo "No batch variables passed, simply passing original input as output unchanged.";
-  cp '${input_obj_file}' '${output_h5}'
+  echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5
 #end if
 ]]></command>
 
@@ -103,6 +102,12 @@
       <param name="batch_key" value="louvain"/>
       <output name="output_h5" file="mnn.h5" ftype="h5" compare="sim_size"/>
     </test>
+    <test>
+      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <output name="output_h5" file="mnn_copy.h5" ftype="h5" compare="sim_size"/>
+    </test>
   </tests>
 
   <help><![CDATA[