# HG changeset patch
# User ebi-gxa
# Date 1599484211 0
# Node ID 820493156c4a3da10c0a36d5bb204dfa56d461a3
# Parent  1ab80fc6f66716aae1ffc95c6f08e399ddaee800
"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 1ab80fc6f667 -r 820493156c4a scanpy-run-dpt.xml
--- a/scanpy-run-dpt.xml	Fri Jun 05 09:11:11 2020 -0400
+++ b/scanpy-run-dpt.xml	Mon Sep 07 13:10:11 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@">
+<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>diffusion pseudotime inference</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -15,11 +15,14 @@
     --min-group-size ${min_group_size}
 #end if
 #if $use_graph
-    --use-graph '${use_graph}'
+    --neighbors-key '${use_graph}'
 #end if
 #if $key_added
     --key-added '${key_added}'
 #end if
+#if not $allow_kendall_tau_shift
+    --disallow-kendall-tau-shift
+#end if
     @INPUT_OPTS@
     @OUTPUT_OPTS@
 ]]></command>
@@ -39,10 +42,11 @@
            label="Name of attribute that defines clustering"/>
     <param name="root_value" argument="--root attr {value}" type="text"
            label="Name of the clustering that defines the root cell type"/>
-    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
+    <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
            label="Name of the slot that holds the KNN graph"/>
     <param name="key_added" argument="--key-added" type="text" optional="true"
            label="Additional suffix to the name of the slot to save the calculated pseudo-time"/>
+    <param name="allow_kendall_tau_shift" type="boolean" checked="true" label="Allow Kendall Tau shift" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of [Haghverdi16] to stabilize the splitting" />
   </inputs>
 
   <outputs>
@@ -55,10 +59,10 @@
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="n_dcs" value="10"/>
-      <param name="root_attr" value="leiden"/>
+      <param name="root_attr" value="louvain"/>
       <param name="root_value" value="1"/>
       <param name="use_graph" value="neighbors"/>
-      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" file="dpt.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>
 
diff -r 1ab80fc6f667 -r 820493156c4a scanpy_macros2.xml
--- a/scanpy_macros2.xml	Fri Jun 05 09:11:11 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 13:10:11 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>