# HG changeset patch
# User ebi-gxa
# Date 1620660499 0
# Node ID 5ec3b715809cfcf02ade7bc83ad05bf61e63be10
# Parent  c42c2b540ceddc6b1ca8b9cdab5699d46c1e9ff3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 21707e9160aa5028dcf8fb762506790f8e085153-dirty"

diff -r c42c2b540ced -r 5ec3b715809c scanpy-neighbours.xml
--- a/scanpy-neighbours.xml	Wed May 05 12:11:28 2021 +0000
+++ b/scanpy-neighbours.xml	Mon May 10 15:28:19 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
   <description>to derive kNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -58,6 +58,7 @@
         <param name="use_rep" type="select" label="Use the indicated representation">
           <option value="X_pca" selected="true">X_pca, use PCs</option>
           <option value="X">X, use normalised expression values</option>
+          <option value="X_diffmap"> X_diffmap, use diffusion map</option>
         </param>
         <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
         <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"