--- a/scanpy-find-markers.xml	Fri Jun 05 09:12:18 2020 -0400
+++ b/scanpy-find-markers.xml	Mon Sep 07 13:05:52 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -22,7 +22,8 @@
     #end if
     --reference '${settings.reference}'
     --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}'
-#end if
+    #end if
+    $settings.pts $settings.tie_correct
     @INPUT_OPTS@
     @OUTPUT_OPTS@
 ]]></command>
@@ -55,6 +56,8 @@
                help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/>
         <param name="min_fold_change" type="float" value="2" label="Minimum fold change"
                help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
+        <param name="pts" argument="--pts"  type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
+        <param name="tie_correct" argument="--tie-correct"  type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/>
       </when>
     </conditional>
   </inputs>