# HG changeset patch
# User ebi-gxa
# Date 1593450247 14400
# Node ID 058a4137929137bcef3ca9d9991161ef41a3be0a
# Parent  48c1e7b396759a5f31fac6531c662495e6b06303
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit e1ed5cbba4d1c042b91cefec41f98e7c736dfbe2"

diff -r 48c1e7b39675 -r 058a41379291 dropletutils-read-10x.xml
--- a/dropletutils-read-10x.xml	Mon Mar 16 10:35:03 2020 -0400
+++ b/dropletutils-read-10x.xml	Mon Jun 29 13:04:07 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy0">
+<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy1">
   <description>into SingleCellExperiment object</description>
   <macros>
     <import>dropletutils_macros.xml</import>
@@ -13,12 +13,26 @@
     -s .
     -c TRUE
     -o '${output_rds}'
+
+#if $add_metadata_file 
+--metadata-files "${metadata_files}" 
+--cell-id-column "${cell_id_column}" 
+#end if
+
+
 ]]></command>
 
   <inputs>
     <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/>
     <param name="genes" type="data" format="tsv,tabular" label="Gene table"/>
     <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/>
+    <conditional name="add_metadata">
+        <param name="add_metadata_file" type="boolean" checked="false" label="Should metadata file be added?" />
+        <when value="true" >
+          <param name="metadata_files" type="data" label="Metadata file" help="Provide metadata file e.g. containing cell types"/>
+          <param name="cell_id_column" type="text" label="Cell ID column" help="Cell ID column. Values must match those provided in the expression matrix." />
+        </when>
+      </conditional>
   </inputs>
 
   <outputs>
diff -r 48c1e7b39675 -r 058a41379291 dropletutils_macros.xml
--- a/dropletutils_macros.xml	Mon Mar 16 10:35:03 2020 -0400
+++ b/dropletutils_macros.xml	Mon Jun 29 13:04:07 2020 -0400
@@ -18,6 +18,7 @@
   <xml name="citations">
     <citations>
       <citation type="doi">10.1101/234872</citation>
+      <citation type="doi">10.1101/2020.04.08.032698</citation>
     </citations>
   </xml>
 </macros>