# HG changeset patch
# User ebi-gxa
# Date 1591909115 0
# Node ID cc47d8df79ebcbc0a165315c86ea3a8cba2ebead
# Parent  92a98e92907fe273611e14876c7aa60939288162
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit f12604f7ae850f2269a924f95a442c668948a61a"

diff -r 92a98e92907f -r cc47d8df79eb cell-browser.xml
--- a/cell-browser.xml	Fri May 29 11:09:28 2020 +0000
+++ b/cell-browser.xml	Thu Jun 11 20:58:35 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy1" profile="18.01">
+<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.7.10+galaxy0" profile="18.01">
   <description>displays single-cell clusterized data in an interactive web application.</description>
   <requirements>
-    <requirement type="package" version="0.5.43">ucsc-cell-browser</requirement>
+    <requirement type="package" version="0.7.10">ucsc-cell-browser</requirement>
   </requirements>
 <stdio>
 <exit_code range="1:" />
@@ -42,6 +42,11 @@
      --markerField '${input_type.marker_field}'
    #end if
 
+   #if $input_type.cluster_field:
+     --clusterField '${input_type.cluster_field}'
+   #end if
+
+
      -o outdir -n sample --htmlDir '$html_file.extra_files_path';
    cp '$__tool_directory__/redirect.html' '$html_file';
 
@@ -65,6 +70,7 @@
     <when value="scanpy">
       <param name="input_anndata_file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/>
       <param name="marker_field" argument="--markerField" type="text" value="rank_genes_groups" label="Marker genes field" help="Scanpy marker genes field to use, optional, if not set 'rank_genes_groups' will be used."/>
+      <param name="cluster_field" argument="--clusterField" type="text" label="Cluster field" help="Scanpy cluster field to use. Optional, if not set 'louvain' will be used. If the AnnData object doesn't not have 'louvain' among its clustering fields, then this NEEDS to be set or UCSC CellBrowser will fail."/>
     </when>
   </conditional>
 </inputs>