From 2fc11f2d7417db9403a2562eea5e02808dd22cdf Mon Sep 17 00:00:00 2001
From: bedroesb <bert.droesbeke@vib.be>
Date: Wed, 27 Mar 2024 15:17:19 +0100
Subject: [PATCH 1/2] ena upload fix

---
 tools/ena_upload/ena_upload.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ena_upload/ena_upload.xml b/tools/ena_upload/ena_upload.xml
index 92f0ba7f62d..61564e1f54b 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":

From e23721cde824ef8ccef325fa75eb2b7227dd7330 Mon Sep 17 00:00:00 2001
From: bedroesb <bert.droesbeke@vib.be>
Date: Wed, 27 Mar 2024 15:19:03 +0100
Subject: [PATCH 2/2] no double dolar sign

---
 tools/ena_upload/ena_upload.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ena_upload/ena_upload.xml b/tools/ena_upload/ena_upload.xml
index 61564e1f54b..ca01a552752 100644
--- a/tools/ena_upload/ena_upload.xml
+++ b/tools/ena_upload/ena_upload.xml
@@ -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 '$$action_options.input_format_conditional.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":