changeset 13:c46750e2e4a4 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

--- a/scanpy-find-cluster.xml	Fri Jun 05 08:55:05 2020 -0400
+++ b/scanpy-find-cluster.xml	Mon Sep 07 13:06:07 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@">
+<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>based on community detection on KNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -10,7 +10,10 @@
 PYTHONIOENCODING=utf-8 scanpy-find-cluster
     ${method}
 #if $settings.default == "false"
-    --use-graph '${settings.use_graph}'
+    --neighbors-key '${settings.neighbors_key}'
+    #if $settings.layer
+        --layer '${settings.layer}'
+    #end if
     #if $settings.key_added
         --key-added '${settings.key_added}'
     #end if
@@ -49,8 +52,10 @@
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>
       <when value="false">
-        <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
+        <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
             label="Name of the slot that holds the KNN graph"/>
+        <param name="layer" argument="--layer" value="" type="text"
+            label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/>
         <param name="key_added" argument="--key-added" type="text" optional="true"
             label="Additional suffix to the name of the slot to save the calculated clustering"/>
 

--- a/scanpy_macros2.xml	Fri Jun 05 08:55:05 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 13:06:07 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>