--- a/ena_upload.xml	Thu Feb 24 18:20:40 2022 +0000
+++ b/ena_upload.xml	Wed May 04 17:06:42 2022 +0000
@@ -1,6 +1,6 @@
 <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT">
     <macros>
-        <token name="@VERSION@">0.5.3</token>
+        <token name="@VERSION@">0.6.0</token>
         <import>samples_macros.xml</import>
     </macros>
     <requirements>
@@ -203,7 +203,9 @@
           --checklist $action_options.input_format_conditional.checklist_id
     #end if
 #end if
-
+#if $action_options.idempotent == "true":
+    --auto_action
+#end if
 #if $action_options.test_submit_parameters.submit_dev == "true":
     -d
 #end if
@@ -324,6 +326,7 @@
                 <option value="modify">Modify metadata</option>
             </param>
             <when value="add">
+                <param type="boolean" name="idempotent" checked="False" label="Idempotent submissions: only add the elements that were not submitted before" help="NOTE: this feature is based on a beta parameter of the CLI that checks the remote ENA repository for entries using the alias. This remote detection can have false positives, i.e assumes that it's present in the repository but it's not"/>
                 <expand macro="test_submit_section"/>    
                 <param name="test_submit" type="hidden" value="False" />
                 <expand macro="table_inputs_macro" />
@@ -546,6 +549,43 @@
                 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
             </assert_command>
         </test>
+        <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection + Idempotent submission -->
+        <test expect_failure="true">
+            <conditional name="action_options">
+                <param name="action" value="add"/>
+                <section name="test_submit_parameters">
+                    <param name="submit_dev" value="false" />
+                    <param name="dry_run" value="false" />
+                </section>
+                <param name="idempotent" value="true"/>
+                <conditional name="input_format_conditional">
+                    <param name="add_extension" value="true"/>
+                    <param name="input_format" value="excel_tables"/>
+                    <param name="checklist_id" value="ERC000011"/>
+                    <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
+                    <conditional name="run_input_format_conditional">
+                        <param name="run_input_format" value="paired_list"/>
+                        <param name="paired_end_collection">
+                            <collection type="list:paired">
+                                <element name="paired_run_name">
+                                    <collection type="paired">
+                                        <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" />
+                                        <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" />
+                                    </collection>
+                                </element>
+                            </collection>
+                        </param>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <param name="center" value="Some research center"/>
+            <assert_command>
+                <has_text_matching expression="ena-upload-cli"/>
+                <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
+                <has_text_matching expression="--action 'add' --center 'Some research center'"/>
+                <has_text_matching expression="--auto_action"/>
+            </assert_command>
+        </test>
         <!--Test 5: build tables from user input fields NON-VIRAL samples-->
         <test>
             <conditional name="action_options">