diff --git a/tools/rna_tools/sortmerna/macros.xml b/tools/rna_tools/sortmerna/macros.xml
index 99c88fd7cb..ccefc0de84 100644
--- a/tools/rna_tools/sortmerna/macros.xml
+++ b/tools/rna_tools/sortmerna/macros.xml
@@ -8,8 +8,8 @@
-
-
+
+
diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
index 112fa8cce6..6d84f0a687 100644
--- a/tools/rna_tools/sortmerna/sortmerna.xml
+++ b/tools/rna_tools/sortmerna/sortmerna.xml
@@ -30,6 +30,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
mkdir -p './aligned' &&
mkdir -p './kvdb_folder' &&
+ mkdir -p './idx_folder' &&
+ mkdir -p './readb_folder' &&
sortmerna
#for $i, $reference in enumerate($ref)
@@ -80,6 +82,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
--threads \${GALAXY_SLOTS:-1}
-m \${GALAXY_MEMORY_MB:-8192}
--kvdb 'kvdb_folder'
+ --idx-dir 'idx_folder'
+ --readb 'readb_folder'
#if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
--out2
#end if
@@ -100,8 +104,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
-
-
+
+
@@ -136,7 +140,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
-
+