--- a/samples_macros.xml	Thu Nov 10 15:18:00 2022 +0000
+++ b/samples_macros.xml	Fri Oct 27 19:44:40 2023 +0000
@@ -44,9 +44,9 @@
         </param>
     </xml>
     <xml name="test_submit_section">
-        <section name="test_submit_parameters" expanded="true" title="Testing options">
-            <param name="submit_dev" type="boolean" truevalue="true" falsevalue="false" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" />
-            <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
+        <section name="test_submit_parameters" expanded="True" title="Testing options">
+            <param name="submit_dev" type="boolean" truevalue="True" falsevalue="False" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" />
+            <param name="dry_run" type="boolean" truevalue="True" falsevalue="False" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
         </section>
     </xml>
     <xml name="run_inputs_macro">
@@ -57,7 +57,7 @@
             </param>
             <when value="multiple_selection_list">
                 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
-                <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
+                <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
             </when>
             <when value="paired_list">
                 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" />
@@ -68,7 +68,7 @@
         <conditional name="input_format_conditional">
             <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
                 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option>
-                <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>
+                <option value="build_tables" selected="False">Interactive generation of the study structure (only recommended for small studies)</option>
                 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
             </param>
             <when value="excel_tables">
@@ -81,19 +81,22 @@
                 <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
                 <expand macro="checklist_input_macro"/>
                 <expand macro="run_inputs_macro" />
-                <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/>
-                <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
-                <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
-                <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
+                <param name="studies_users_table" type="data" format="tabular" multiple="False" label="Studies table" help="Studies metadata file"/>
+                <param name="samples_users_table" type="data" format="tabular" multiple="False" label="Samples table" help="Samples metadata file"/>
+                <param name="experiments_users_table" type="data" format="tabular" multiple="False" label="Experiments table" help="Experiments metadata file"/>
+                <param name="runs_users_table" type="data" format="tabular" multiple="False" label="Runs table" help="Runs metadata file"/>
             </when>
             <when value="build_tables">
-                <param name="add_extension" type="boolean" checked="false" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
+                <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
                 <conditional name="conditional_viral_metadata">
-                    <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
-                    <when value="true">
+                    <param name="viral_sample" type="select" label="Select your sample type" help="Non-viral interactive submissions lack specific sample checklist attributes and are suboptimal. It's highly recommended to use Excel or TSV templates as input for a more comprehensive submission.">
+                        <option value="True" selected="True">Viral</option>
+                        <option value="False" selected="False">Non viral</option>
+                    </param>
+                    <when value="True">
                         <expand macro="viral_samples" />
                     </when>
-                    <when value="false">
+                    <when value="False">
                         <expand macro="nonviral_samples" />
                     </when>
                 </conditional>
@@ -106,9 +109,9 @@
             <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
             <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
             <param name="study_type" type="select" label="Please select the type of study">
-                    <options from_data_table="study_type">
-                        <column name="value" index="0"/>
-                    </options>
+                <options from_data_table="study_type">
+                    <column name="value" index="0"/>
+                </options>
             </param>
             <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
             <repeat name="rep_sample" title="Samples associated with this study" min="1" >
@@ -146,17 +149,17 @@
                 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
                     <param name="experiment_title" type="text" label="Specify an experiment title" />
                     <param name="experiment_design" type="text" label="Describe the experiment design" />
-                    <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
+                    <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
                         <options from_data_table="library_strategy">
                             <column name="value" index="0"/>
                         </options>
                     </param>
-                    <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
+                    <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
                         <options from_data_table="library_source">
                             <column name="value" index="0"/>
                         </options>
                     </param>
-                    <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
+                    <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
                         <options from_data_table="library_selection">
                             <column name="value" index="0"/>
                         </options>
@@ -169,16 +172,9 @@
                     <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
                     <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
                     <param name="platform" type="select" label="Select the sequencing platform used">
-                        <option value="LS454">LS454</option>
-                        <option value="ILLUMINA">Illumina</option>
-                        <option value="HELICOS">Helicos</option>
-                        <option value="ABI_SOLID">ABI Solid</option>
-                        <option value="COMPLETE_GENOMICS">Complete Genomics</option>
-                        <option value="BGISEQ">BGI Seq</option>
-                        <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
-                        <option value="PACBIO_SMRT">PacBio</option>
-                        <option value="ION_TORRENT">Ion Torrent</option>
-                        <option value="CAPILLARY">Capillary sequencing</option>
+                        <options from_data_table="platform">
+                            <column name="value" index="0"/>
+                        </options>
                     </param>
                     <param name="instrument_model" type="select" label="Instrument model">
                         <options from_data_table="instrument_model">
@@ -187,75 +183,79 @@
                     </param>
                     <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
                         <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
-                        <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
+                        <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="File(s) associated with this run"/>
                     </repeat>
                 </repeat>
             </repeat>
         </repeat>
     </xml>
     <xml name="nonviral_samples">
-    <repeat name="rep_study" title="Study" min="1">
-        <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
-        <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
-        <param name="study_type" type="select" label="Please select the type of study">
-                <options from_data_table="study_type">
-                    <column name="value" index="0"/>
-                </options>
-        </param>
-        <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
-        <repeat name="rep_sample" title="Samples associated with this study" min="1" >
-            <param name="sample_title" type="text" label="Sample title"/>
-            <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
-            <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
-            <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
-            <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
-                <param name="experiment_title" type="text" label="Specify an experiment title" />
-                <param name="experiment_design" type="text" label="Describe the experiment design" />
-                <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
-                    <options from_data_table="library_strategy">
+        <repeat name="rep_study" title="Study" min="1">
+            <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
+            <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
+            <param name="study_type" type="select" label="Please select the type of study">
+                    <options from_data_table="study_type">
                         <column name="value" index="0"/>
                     </options>
+            </param>
+            <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
+            <repeat name="rep_sample" title="Samples associated with this study" min="1" >
+                <param name="sample_title" type="text" label="Sample title"/>
+                <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
+                <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
+                <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
+                <param name="collection_date" type="text" label="Collection date" optional="True" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
+                    <option value="not collected">not collected</option>
+                    <option value="restricted access">restricted access</option>
+                    <option value="not provided">not provided</option>
+                    <validator type="regex"  message="Data format is not valid">(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)</validator>
                 </param>
-                <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
-                    <options from_data_table="library_source">
-                        <column name="value" index="0"/>
-                    </options>
-                </param>
-                <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
-                    <options from_data_table="library_selection">
+                <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
+                    <options from_data_table="geographic_location_1">
                         <column name="value" index="0"/>
                     </options>
                 </param>
-                <param name="library_layout" type="select" label="Library layout">
-                    <options from_data_table="library_layout">
-                        <column name="value" index="0"/>
-                    </options>
-                </param>
-                <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
-                <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
-                <param name="platform" type="select" label="Select the sequencing platform used">
-                    <option value="LS454">LS454</option>
-                    <option value="ILLUMINA" selected="True">Illumina</option>
-                    <option value="HELICOS">Helicos</option>
-                    <option value="ABI_SOLID">ABI Solid</option>
-                    <option value="COMPLETE_GENOMICS">Complete Genomics</option>
-                    <option value="BGISEQ">BGI Seq</option>
-                    <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
-                    <option value="PACBIO_SMRT">PacBio</option>
-                    <option value="ION_TORRENT">Ion Torrent</option>
-                    <option value="CAPILLARY">Capillary sequencing</option>
-                </param>
-                <param name="instrument_model" type="select" label="Instrument model">
-                    <options from_data_table="instrument_model">
-                        <column name="value" index="0"/>
-                    </options>
-                </param>
-                <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
-                    <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
-                    <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
+                <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
+                    <param name="experiment_title" type="text" label="Specify an experiment title" />
+                    <param name="experiment_design" type="text" label="Describe the experiment design" />
+                    <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
+                        <options from_data_table="library_strategy">
+                            <column name="value" index="0"/>
+                        </options>
+                    </param>
+                    <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
+                        <options from_data_table="library_source">
+                            <column name="value" index="0"/>
+                        </options>
+                    </param>
+                    <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
+                        <options from_data_table="library_selection">
+                            <column name="value" index="0"/>
+                        </options>
+                    </param>
+                    <param name="library_layout" type="select" label="Library layout">
+                        <options from_data_table="library_layout">
+                            <column name="value" index="0"/>
+                        </options>
+                    </param>
+                    <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
+                    <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
+                    <param name="platform" type="select" label="Select the sequencing platform used">
+                        <options from_data_table="platform">
+                            <column name="value" index="0"/>
+                        </options>
+                    </param>
+                    <param name="instrument_model" type="select" label="Instrument model">
+                        <options from_data_table="instrument_model">
+                            <column name="value" index="0"/>
+                        </options>
+                    </param>
+                    <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
+                        <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
+                        <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="File(s) associated with this run"/>
+                    </repeat>
                 </repeat>
             </repeat>
         </repeat>
-    </repeat>
     </xml>
 </macros>