# HG changeset patch
# User ebi-gxa
# Date 1599656252 0
# Node ID aaf4a7a3dd964fa8ae3795409d4eb5aa10fc69d9
# Parent  2472523c0c50d2197999d81bc5be2f1ee3619f6c
"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 2472523c0c50 -r aaf4a7a3dd96 scanpy-integrate-combat.xml
--- a/scanpy-integrate-combat.xml	Mon Sep 07 13:06:34 2020 +0000
+++ b/scanpy-integrate-combat.xml	Wed Sep 09 12:57:32 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
   <description>adjust expression for variables that might introduce batch effect</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -22,8 +22,7 @@
   @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>
 
@@ -61,6 +60,12 @@
       <param name="batch_key" value="louvain"/>
       <output name="output_h5" file="combat.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="combat_copy.h5" ftype="h5" compare="sim_size"/>
+    </test>
   </tests>
 
   <help><![CDATA[