# HG changeset patch
# User ebi-gxa
# Date 1594138208 0
# Node ID 34d289e805b11ff7a04398eed6c78c889844ca82
# Parent  3fe8973bc205d75fa2892bd5b3fb18df0ed4f9e1
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit ed7141cff329d11308fe2556eeb01d51bfaa6759"

diff -r 3fe8973bc205 -r 34d289e805b1 dropletutils-read-10x.xml
--- a/dropletutils-read-10x.xml	Mon Jul 06 14:51:42 2020 +0000
+++ b/dropletutils-read-10x.xml	Tue Jul 07 16:10:08 2020 +0000
@@ -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>