diff --git a/tools/ena_upload/ena_upload.xml b/tools/ena_upload/ena_upload.xml
index 92f0ba7f62d..ca01a552752 100644
--- a/tools/ena_upload/ena_upload.xml
+++ b/tools/ena_upload/ena_upload.xml
@@ -2,7 +2,7 @@
     <description>Submission of (meta)data to the European Nucleotide Archive (ENA)</description>
     <macros>
         <token name="@TOOL_VERSION@">0.7.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <import>samples_macros.xml</import>
     </macros>
     <requirements>
@@ -196,7 +196,7 @@ ena-upload-cli
     --sample '$samples_table_path'
 #elif $action_options.input_format_conditional.input_format == "isa_json":
     --isa_json ./isa_json_input.json
-    --isa_assay_stream '$isa_assay_stream'
+    --isa_assay_stream '$action_options.input_format_conditional.isa_assay_stream'
 #end if
 #if $action_options.input_format_conditional.input_format == "build_tables":
     #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":