--- a/scanpy-find-markers.xml	Fri Sep 11 11:05:29 2020 +0000
+++ b/scanpy-find-markers.xml	Wed Sep 30 11:16:08 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -9,10 +9,15 @@
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-find-markers
 #if $output_markers
-    --save output.csv
+    --save diffexp.tsv
 #end if
     --n-genes '${n_genes}'
+#set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
     --groupby '${groupby}'
+#if $settings.key_added
+    #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__)
+    --key-added '${key_added}'
+#end if
 #if $settings.default == "false"
     --method '${settings.method}'
     ${settings.use_raw}
@@ -31,13 +36,15 @@
   <inputs>
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
-    <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/>
+    <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/>
     <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
     <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
     <conditional name="settings">
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>
       <when value="false">
+        <param name="key_added" argument="--key-added" type="text" optional="true"
+               label="The key in adata.uns information is saved to. If included, the keyword 'GROUPBY' will be substituted with the value of the groupby setting."/>
         <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
           <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
           <option value="t-test">t-test</option>
@@ -64,24 +71,26 @@
 
   <outputs>
     <expand macro="output_data_obj" description="Marker genes"/>
-    <data name="output_csv" format="csv" from_work_dir="output.csv" label="${tool.name} on ${on_string}: Marker table">
+    <data name="output_tsv" format="tabular" from_work_dir="diffexp.tsv" label="${tool.name} on ${on_string}: Marker table">
       <filter>output_markers</filter>
     </data>
   </outputs>
 
   <tests>
     <test>
-      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_obj_file" value="louvain_1.0"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <param name="output_csv" value="true"/>
+      <param name="output_tsv" value="true"/>
       <param name="n_genes" value="50"/>
-      <param name="output_markers" value="false"/>
+      <param name="output_markers" value="true"/>
       <param name="default" value="false"/>
-      <param name="groupby" value="louvain"/>
+      <param name="groupby" value="INPUT_OBJ"/>
+      <param name="key_added" value="GROUPBY_marker"/>
       <param name="method" value="t-test_overestim_var"/>
       <param name="rankby_abs" value="false"/>
       <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
     </test>
   </tests>