# HG changeset patch
# User ebi-gxa
# Date 1599483952 0
# Node ID f6291dbb3afc11139e4e4f5cf98919c7892870b7
# Parent  af9cf232d6c92ae90e94282653eb074f4b2c005d
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

diff -r af9cf232d6c9 -r f6291dbb3afc scanpy-find-markers.xml
--- 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>
diff -r af9cf232d6c9 -r f6291dbb3afc scanpy_macros2.xml
--- a/scanpy_macros2.xml	Fri Jun 05 09:12:18 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 13:05:52 2020 +0000
@@ -1,10 +1,13 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.4.3</token>
+  <token name="@TOOL_VERSION@">1.6.0</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
   <token name="@PROFILE@">18.01</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/
+
 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
 
 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
@@ -46,7 +49,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.2.10">scanpy-scripts</requirement>
+      <requirement type="package" version="0.3.0">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>