diff --git a/tools/graphlan/export2graphlan/Snakefile b/tools/graphlan/export2graphlan/Snakefile
index 3377b9c8733be9a50134a5ae2d1740d3dbf5f8c3..448fcf072da3d3c1defeca1d1af2873e4298017e 100644
--- a/tools/graphlan/export2graphlan/Snakefile
+++ b/tools/graphlan/export2graphlan/Snakefile
@@ -6,9 +6,9 @@ rule export2graphlan:
         __export2graphlan_input
     output:
         tree = __export2graphlan_output_tree,
-        annot = __export2graphlan_output_annot
+        annot = __export2graphlan_output_annotation
     params:
         exec_command = __export2graphlan_exec_command,
         options = __export2graphlan_options
     shell:
-        "{params.exec_command} {params.options} -i {input} -tree {output.tree} --annotation {output.annot}"
+        "{params.exec_command} {params.options} -i {input} --tree {output.tree} --annotation {output.annot}"
diff --git a/tools/graphlan/graphlan_annotate/Snakefile b/tools/graphlan/graphlan_annotate/Snakefile
index c7aa660cea430766b5a6f5e9c25cf6788a4db6a4..6a1b11736878fdfe639a2b686a8515f601357a5b 100644
--- a/tools/graphlan/graphlan_annotate/Snakefile
+++ b/tools/graphlan/graphlan_annotate/Snakefile
@@ -3,8 +3,8 @@ __graphlan_annotate_options = config['graphlan_annotate'].get('options', "")
 
 rule graphlan_annotate:
     input:
-        tree = __graphlan_annotate_input_tree
-        annot = __graphlan_annotate_input_annot
+        tree = __graphlan_annotate_input_tree,
+        annot = __graphlan_annotate_input_annotation
     output:
         __graphlan_annotate_output
     params: