# HG changeset patch
# User ebi-gxa
# Date 1594138332 14400
# Node ID 3dd08eb96cf69618a69bf993e492702e600238fb
# Parent  d552332dff6d37a6552e89a1a8e38924617b9e4b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit ed7141cff329d11308fe2556eeb01d51bfaa6759"

diff -r d552332dff6d -r 3dd08eb96cf6 dropletutils-read-10x.xml
--- a/dropletutils-read-10x.xml	Mon Jul 06 10:52:50 2020 -0400
+++ b/dropletutils-read-10x.xml	Tue Jul 07 12:12:12 2020 -0400
@@ -1,23 +1,23 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy1">
+<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy2">
   <description>into SingleCellExperiment object</description>
   <macros>
     <import>dropletutils_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
-ln -s '${matrix}' matrix.mtx &&
-ln -s '${genes}' genes.tsv &&
-ln -s '${barcodes}' barcodes.tsv &&
-dropletutils-read-10x-counts.R
-    -s .
-    -c TRUE
-    -o '${output_rds}'
+    ln -s '${matrix}' matrix.mtx &&
+    ln -s '${genes}' genes.tsv &&
+    ln -s '${barcodes}' barcodes.tsv &&
+    dropletutils-read-10x-counts.R
+        -s .
+        -c TRUE
+        -o '${output_rds}'
 
-#if $add_metadata.add_metadata_file 
---metadata-files "${add_metadata.metadata_files}"
---cell-id-column "${add_metadata.cell_id_column}" 
-#end if
+    #if $add_metadata.add_metadata_file 
+    --metadata-files "${add_metadata.metadata_files}"
+    --cell-id-column "${add_metadata.cell_id_column}" 
+    #end if
 
 ]]></command>