diff ena_upload.xml @ 10:480d9e9d156b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3

--- a/ena_upload.xml	Thu Nov 10 15:18:00 2022 +0000
+++ b/ena_upload.xml	Fri Oct 27 19:44:40 2023 +0000
@@ -1,10 +1,11 @@
-<tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT">
+<tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT">
     <macros>
-        <token name="@VERSION@">0.6.1</token>
+        <token name="@TOOL_VERSION@">0.6.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
         <import>samples_macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement>
     </requirements>
     <stdio>
         <regex match="Oops" source="stderr" level="fatal"/>
@@ -47,7 +48,7 @@
 #if $action_options.input_format_conditional.input_format == "excel_tables":
     ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx &&
 #end if
-#if $action_options.test_submit_parameters.dry_run == "false" and $action_options.test_submit == "False":
+#if $action_options.test_submit_parameters.dry_run == "False" and $action_options.test_submit == "False":
     webin_id=`grep 'username' $credentials`;
     if [ "\$webin_id" = "" ]; then
       ## No credentials in user defined preferences    
@@ -57,7 +58,7 @@
           credentials_path=\${GALAXY_ENA_SECRETS};     
           webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`;
           if [ "\$webin_id" = "" ]; then
-              echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
+                echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
               exit 1;
           fi;
       #else:
@@ -80,7 +81,7 @@
           #for $run in $experiment.rep_runs:
             #for $file in $run.upload_files:
                 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
-                #if $action_options.input_format_conditional.add_extension == "true":
+                #if $action_options.input_format_conditional.add_extension == "True":
                     #set $extension = '.fastq'
                 #else
                     #set $extension = ''
@@ -90,7 +91,7 @@
                     #set $safename_reads_file = $safename_reads_file + $extension + '.gz'
                     gzip -c '$file' > $safename_reads_file &&
                 #else:
-                    #if $action_options.input_format_conditional.add_extension == "true":
+                    #if $action_options.input_format_conditional.add_extension == "True":
                         #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
                             #set $compression = '.gz' 
                         #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
@@ -148,14 +149,14 @@
             #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
             #if $file.is_of_type('fastq', 'fastqsanger'):
                 ## always compress add the gz extension
-                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
+                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
                     #set $safename_reads_file = $safename_reads_file + '.fastq.gz'
                 #else
                     #set $safename_reads_file = $safename_reads_file + '.gz'
-                #end if   
+                #end if
                 gzip -c '$file' > $safename_reads_file &&
             #else
-                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "true":
+                #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True":
                     #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'):
                         #set $extension = '.fastq.gz'
                     #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'):
@@ -172,7 +173,7 @@
 
 #if $action_options.action == "add":
 ena-upload-cli
-    --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
+    --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy'
     --action '$action_options.action'
     --center '$action_options.center'
     --secret \${credentials_path}
@@ -180,7 +181,7 @@
     #for $dataset in $files_to_upload:
         '$dataset'
     #end for
-#if $action_options.test_submit_parameters.dry_run == "true":
+#if $action_options.test_submit_parameters.dry_run == "True":
     --draft
 #end if
 #if $action_options.input_format_conditional.input_format != "excel_tables":
@@ -196,17 +197,17 @@
         --checklist $action_options.input_format_conditional.checklist_id
 #else:
     #if $action_options.input_format_conditional.input_format == "build_tables":
-        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
+        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
           --checklist ERC000033
         #end if
     #else:
           --checklist $action_options.input_format_conditional.checklist_id
     #end if
 #end if
-#if $action_options.idempotent == "true":
+#if $action_options.idempotent == "True":
     --auto_action
 #end if
-#if $action_options.test_submit_parameters.submit_dev == "true":
+#if $action_options.test_submit_parameters.submit_dev == "True":
     -d
 #end if
     >> '$output';
@@ -216,7 +217,7 @@
 
 #if $action_options.action == "modify":
     ena-upload-cli
-    --tool 'ena-upload-cli v@VERSION@ @ Galaxy'
+    --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy'
     --action '$action_options.action'
     --center '$action_options.center'
     --secret \${credentials_path}
@@ -224,7 +225,7 @@
     #for $dataset in $files_to_upload:
         '$dataset'
     #end for
-#if $action_options.test_submit_parameters.dry_run == "true":
+#if $action_options.test_submit_parameters.dry_run == "True":
     --draft
 #end if
 #if $action_options.input_format_conditional.input_format != "excel_tables":
@@ -241,7 +242,7 @@
         --checklist $action_options.input_format_conditional.checklist_id
 #else:
     #if $action_options.input_format_conditional.input_format == "build_tables":
-        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
+        #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
           --checklist ERC000033
         #end if
     #else:
@@ -251,7 +252,7 @@
     >> '$output';
 #end if
 
-#if $action_options.test_submit_parameters.dry_run == "false":
+#if $action_options.test_submit_parameters.dry_run == "False":
     echo -e 'center_name\t$action_options.center' >> '$output';
     echo -e 'action_option\t$action_options.action' >> '$output';
 #end if
@@ -305,12 +306,10 @@
     
 $experiments.append({'title':str($experiment.experiment_title),'experiment_design':str($experiment.experiment_design),'library_strategy':str($experiment.library_strategy),'library_source':str($experiment.library_source),'library_selection':str($experiment.library_selection),'library_layout':str($experiment.library_layout),'insert_size':str($experiment.insert_size),'library_construction_protocol':str($experiment.library_construction_protocol),'platform':str($experiment.platform),'instrument_model':str($experiment.instrument_model),'runs':$runs})
       #end for
-      #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "true":
-
+      #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True":
 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'host_common_name':str($sample.host_common_name),'host_subject_id':str($sample.host_subject_id),'host_health_state':str($sample.host_health_state),'host_sex':str($sample.host_sex),'host_scientific_name':str($sample.host_scientific_name),'collector_name':str($sample.collector_name),'collecting_institution':str($sample.collecting_institution),'isolate':str($sample.isolate),'experiments':$experiments})
       #else:
-
-$samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'experiments':$experiments})
+$samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'experiments':$experiments})
       #end if
     #end for
     $studies.append({'title':str($study.study_title),'type':str($study.study_type),'abstract':str($study.study_abstract),'pubmed_id':str($study.study_pubmed_id),'samples':$samples})
@@ -326,7 +325,7 @@
                 <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"/>
+                <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" />
@@ -355,19 +354,19 @@
     </outputs>
     <tests>
        <!--Test 1:  excel input of VIRAL samples -->
-        <test>
+        <test expect_num_outputs="5">
             <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="true" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="True" />
                 </section>
                 <conditional name="input_format_conditional">
                     <param name="input_format" value="excel_tables"/>
                     <param name="checklist_id" value="ERC000033"/>
                     <param name="xlsx_file" value="metadata_test_viral.xlsx"/>
                     <conditional name="run_input_format_conditional">
-                        <param name="add_extension" value="false"/>
+                        <param name="add_extension" value="False"/>
                         <param name="run_input_format" value="multiple_selection_list"/>
                         <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
                     </conditional>
@@ -405,19 +404,19 @@
             </output>
         </test>
         <!--Test 2: excel input of VIRAL samples with extended columns-->
-        <test>
+        <test expect_num_outputs="5">
             <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="true" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="True" />
                 </section>
                 <conditional name="input_format_conditional">
                     <param name="input_format" value="excel_tables"/>
                     <param name="checklist_id" value="ERC000033"/>
                     <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/>
                     <conditional name="run_input_format_conditional">
-                        <param name="add_extension" value="false"/>
+                        <param name="add_extension" value="False"/>
                         <param name="run_input_format" value="multiple_selection_list"/>
                         <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/>
                     </conditional>
@@ -465,19 +464,19 @@
             </output>
         </test>
         <!--Test 3: excel input of NON-VIRAL samples-->
-        <test>
+        <test expect_num_outputs="5">
             <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="true" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="True" />
                 </section>
                 <conditional name="input_format_conditional">
                     <param name="input_format" value="excel_tables"/>
                     <param name="checklist_id" value="ERC000011"/>
                     <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/>
                     <conditional name="run_input_format_conditional">
-                        <param name="add_extension" value="true"/>
+                        <param name="add_extension" value="True"/>
                         <param name="run_input_format" value="multiple_selection_list"/>
                         <param name="data" value="sample_no_extension"/>
                     </conditional>
@@ -501,8 +500,8 @@
             <output name="samples_table_out">
                 <assert_contents>
                     <has_n_lines n="2"/>
-                    <has_n_columns n="8"/>
-                    <has_line_matching expression="alias\ttitle\tscientific_name\tsample_description\taccession\tsubmission_date\tstatus\ttaxon_id"/>
+                    <has_n_columns n="10"/>
+                    <has_line_matching expression="s_20201007_026\tC026\tSaccharomyces cerevisiae\tSample from beer\t2020-03-25\tAntarctica\t\t\tADDED\t"/>
                 </assert_contents>
             </output>
             <output name="runs_table_out">
@@ -515,15 +514,15 @@
             </output>
         </test>
         <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
-        <test expect_failure="true">
+        <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" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="False" />
                 </section>
                 <conditional name="input_format_conditional">
-                    <param name="add_extension" value="true"/>
+                    <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"/>
@@ -550,16 +549,16 @@
             </assert_command>
         </test>
         <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection + Idempotent submission -->
-        <test expect_failure="true">
+        <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" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="False" />
                 </section>
-                <param name="idempotent" value="true"/>
+                <param name="idempotent" value="True"/>
                 <conditional name="input_format_conditional">
-                    <param name="add_extension" value="true"/>
+                    <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"/>
@@ -587,16 +586,16 @@
             </assert_command>
         </test>
         <!--Test 5: build tables from user input fields NON-VIRAL samples-->
-        <test>
+        <test expect_num_outputs="5">
             <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="true" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="True" />
                 </section>
                 <conditional name="input_format_conditional">
                     <param name="input_format" value="build_tables"/>
-                    <param name="add_extension" value="false"/>
+                    <param name="add_extension" value="False"/>
                     <conditional name="conditional_viral_metadata">
                         <param name="viral_sample" value="False"/>
                         <repeat name="rep_study">
@@ -609,6 +608,8 @@
                                 <param name="sample_description" value="Test Sample description"/>
                                 <param name="scientific_name" value="Test Sample scientific name"/>
                                 <param name="tax_id" value="2697049"/>
+                                <param name="collection_date" value="2020"/>
+                                <param name="geo_location_country" value="Belgium"/>
                                 <repeat name="rep_experiment">
                                     <param name="experiment_title" value="Test experiment title"/>
                                     <param name="experiment_design" value="Test experiment design description"/>
@@ -646,7 +647,7 @@
             <output name="samples_table_out">
                 <assert_contents>
                     <has_n_lines n="2"/>
-                    <has_n_columns n="8"/>
+                    <has_n_columns n="10"/>
                 </assert_contents>
             </output>
             <output name="runs_table_out">
@@ -657,19 +658,21 @@
                 </assert_contents>
             </output>
         </test>
-        <!--Test 6: RUN failing build tables from user input fields NON-VIRAL samples-->
-        <test expect_failure="true">
+        <!--Test 6: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
+            also tests compression of uncompressed inputs and adding the .gz suffix -->
+        <test expect_failure="False" expect_num_outputs="5">
             <conditional name="action_options">
                 <param name="action" value="add"/>
                 <section name="test_submit_parameters">
-                    <param name="submit_dev" value="true" />
-                    <param name="dry_run" value="false" />
+                    <param name="submit_dev" value="True" />
+                    <param name="dry_run" value="True" />
                 </section>
+                <param name="test_submit" value="True"/>
                 <conditional name="input_format_conditional">
+                    <param name="add_extension" value="False"/>
                     <param name="input_format" value="build_tables"/>
-                    <param name="add_extension" value="true"/>
                     <conditional name="conditional_viral_metadata">
-                        <param name="viral_sample" value="false"/>
+                        <param name="viral_sample" value="False"/>
                         <repeat name="rep_study">
                             <param name="study_title" value="Test study title"/>
                             <param name="study_abstract" value="Test study abstract"/>
@@ -680,56 +683,8 @@
                                 <param name="sample_description" value="Test Sample description"/>
                                 <param name="scientific_name" value="Test Sample scientific name"/>
                                 <param name="tax_id" value="2697049"/>
-                                <repeat name="rep_experiment">
-                                    <param name="experiment_title" value="Test experiment title"/>
-                                    <param name="experiment_design" value="Test experiment design description"/>
-                                    <param name="library_strategy" value="CTS"/>
-                                    <param name="library_source" value="GENOMIC"/>
-                                    <param name="library_selection" value="PCR"/>
-                                    <param name="library_layout" value="SINGLE"/>
-                                    <param name="insert_size" value="150"/>
-                                    <param name="library_construction_protocol" value="Test library construction"/>
-                                    <param name="platform" value="ILLUMINA"/>
-                                    <param name="instrument_model" value="Illumina HiSeq 4000"/>
-                                    <repeat name="rep_runs">
-                                        <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger"/>
-                                    </repeat>
-                                </repeat>
-                            </repeat>
-                        </repeat>
-                    </conditional>
-                </conditional>
-            </conditional>
-            <param name="center" value="Some research center"/>
-            <assert_stdout>
-                <has_text_matching expression="No ENA credentials defined"/>
-            </assert_stdout>
-        </test>
-        <!--Test 7: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
-            also tests compression of uncompressed inputs and adding the .gz suffix -->
-        <test expect_failure="false">
-            <conditional name="action_options">
-                <param name="action" value="add"/>
-                <section name="test_submit_parameters">
-                    <param name="submit_dev" value="true" />
-                    <param name="dry_run" value="true" />
-                </section>
-                <param name="test_submit" value="True"/>
-                <conditional name="input_format_conditional">
-                    <param name="add_extension" value="false"/>
-                    <param name="input_format" value="build_tables"/>
-                    <conditional name="conditional_viral_metadata">
-                        <param name="viral_sample" value="false"/>
-                        <repeat name="rep_study">
-                            <param name="study_title" value="Test study title"/>
-                            <param name="study_abstract" value="Test study abstract"/>
-                            <param name="study_type" value="Epigenetics"/>
-                            <param name="study_pubmed_id" value="Test study pubmedID"/>
-                            <repeat name="rep_sample">
-                                <param name="sample_title" value="Test Sample title"/>
-                                <param name="sample_description" value="Test Sample description"/>
-                                <param name="scientific_name" value="Test Sample scientific name"/>
-                                <param name="tax_id" value="2697049"/>
+                                <param name="collection_date" value="2020"/>
+                                <param name="geo_location_country" value="Belgium"/>
                                 <repeat name="rep_experiment">
                                     <param name="experiment_title" value="Test experiment title"/>
                                     <param name="experiment_design" value="Test experiment design description"/>
@@ -759,20 +714,20 @@
                 <not_has_text text="modify" />
             </assert_command>
         </test>
-        <!--Test 8: viral submission - User input metadata - Add extension = False-->
-        <test expect_failure="false">
+        <!--Test 7: viral submission - User input metadata - Add extension = False-->
+        <test expect_failure="False" expect_num_outputs="5">
             <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="true" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="True" />
                 </section>
                 <param name="test_submit" value="True"/>
                 <conditional name="input_format_conditional">
-                    <param name="add_extension" value="false"/>
+                    <param name="add_extension" value="False"/>
                     <param name="input_format" value="build_tables"/>
                     <conditional name="conditional_viral_metadata">
-                        <param name="viral_sample" value="true"/>
+                        <param name="viral_sample" value="True"/>
                         <repeat name="rep_study">
                             <param name="study_title" value="Test study title"/>
                             <param name="study_abstract" value="Test study abstract"/>
@@ -822,17 +777,17 @@
                 <has_text_matching expression="--checklist ERC000033"/>
             </assert_command>
         </test>
-        <!--Test 9: modify option and auto compression - viral submission - User input metadata-->
-        <test expect_failure="false">
+        <!--Test 8: modify option and auto compression - viral submission - User input metadata-->
+        <test expect_failure="False" expect_num_outputs="5">
             <conditional name="action_options">
                 <param name="action" value="modify"/>
                 <section name="test_submit_parameters">
-                    <param name="submit_dev" value="false" />
-                    <param name="dry_run" value="true" />
+                    <param name="submit_dev" value="False" />
+                    <param name="dry_run" value="True" />
                 </section>
                 <param name="test_submit" value="True"/>
                 <conditional name="input_format_conditional">
-                    <param name="add_extension" value="fasle"/>
+                    <param name="add_extension" value="False"/>
                     <param name="input_format" value="build_tables"/>
                     <conditional name="conditional_viral_metadata">
                         <param name="viral_sample" value="True"/>
@@ -869,7 +824,7 @@
                                     <param name="instrument_model" value="Illumina HiSeq 4000"/>
                                     <repeat name="rep_runs">
                                         <param name="run_base_name" value="run_from_hospital_X"/>
-                                        <param name="upload_files" value="1.fastqsanger.gz" ftype="fastqsanger.gz"/>
+                                        <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/>
                                     </repeat>
                                 </repeat>
                             </repeat>
@@ -880,7 +835,7 @@
             <param name="center" value="Some research center"/>
             <assert_command>
                 <has_text_matching expression="ena-upload-cli"/>
-                <has_text_matching expression="--data '1.fastqsanger.gz'"/>
+                <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
                 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
                 <has_text_matching expression="--checklist ERC000033"/>
                 <not_has_text text="add" />
@@ -889,9 +844,9 @@
     </tests>
     <help><![CDATA[
         This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli
-        The input metadata can be submitted following the tabular format of the templates in https://github.com/usegalaxy-eu/ena-upload-cli/tree/master/example_tables
-        It is also possible to submit an excel file by following the template in https://github.com/ELIXIR-Belgium/ENA-metadata-templates
+        The input metadata can be submitted following the tabular format of the templates or their excel spreadsheet equivalent in https://github.com/ELIXIR-Belgium/ENA-metadata-templates. This template repo provides ready to use sheets for every ENA sample checklist and is automatically updated.
     ]]></help>
     <citations>
+        <citation type="doi">doi:10.1093/bioinformatics/btab421</citation>
     </citations>
 </tool>