# HG changeset patch
# User ebi-gxa
# Date 1627029170 0
# Node ID 8b0d6f6f44c8cc390b789966b6537fd551f067bd
# Parent  c4868b59cf7f571ddb8992a997883d3b93169f6d
"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 c4868b59cf7f -r 8b0d6f6f44c8 scanpy-run-tsne.xml
--- a/scanpy-run-tsne.xml	Thu Jul 22 20:56:08 2021 +0000
+++ b/scanpy-run-tsne.xml	Fri Jul 23 08:32:50 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
   <description>visualise cell clusters using tSNE</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -9,7 +9,7 @@
 #set embeddings_tsv='embeddings.tsv'
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-run-tsne
-#if $use_rep != "auto"
+#if $use_rep
     --use-rep '${use_rep}'
 #end if
 #if $embeddings
@@ -64,11 +64,7 @@
     <expand macro="output_object_params"/>
     <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
 
-    <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation">
-      <option value="X_pca">X_pca, use PCs</option>
-      <option value="X">X, use normalised expression values</option>
-      <option value="auto" selected="true">Automatically chosen based on problem size</option>
-    </param>
+    <param name="use_rep" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="Use the indicated representation. 'X' (for the content of .X, usuaally 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."/>
     <conditional name="settings">
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>