# HG changeset patch
# User ebi-gxa
# Date 1627028928 0
# Node ID bc9e8de21efbde8105c49f3558877c850924faf6
# Parent  a30d21fd5319b1d129434c4785356970376c1d99
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty"

diff -r a30d21fd5319 -r bc9e8de21efb scanpy-neighbours.xml
--- a/scanpy-neighbours.xml	Thu Jul 22 20:57:34 2021 +0000
+++ b/scanpy-neighbours.xml	Fri Jul 23 08:28:48 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>
@@ -31,7 +31,7 @@
     --method '${settings.method}'
     --metric '${settings.metric}'
     --random-state '${settings.random_seed}'
-    #if $settings.use_rep != "auto"
+    #if $settings.use_rep
         --use-rep '${settings.use_rep}'
     #end if
     #if $settings.n_pcs
@@ -55,11 +55,7 @@
         <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
         <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
                label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
-        <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="use_rep" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="'X' (for the content of .X, usually normalised expression values) or any key for .obsm (e.g. X_pca for PCA) is valid. If not set, the representation is chosen automatically: For .n_vars less than 50, .X is used, otherwise ‘X_pca’ is used. If ‘X_pca’ is not present, it’s computed with default parameters."/>
         <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"
                label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>