diff samples_macros.xml @ 1:57251c760cab draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"

--- a/samples_macros.xml	Sat Nov 28 09:45:44 2020 +0000
+++ b/samples_macros.xml	Fri Apr 30 12:09:25 2021 +0000
@@ -1,5 +1,24 @@
 <macros>
-
+    <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>
+    </xml>
+    <xml name="run_inputs_macro">
+        <conditional name="run_input_format_conditional">
+            <param name="run_input_format" type="select" label="Select runs input format">
+                <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
+                <option value="paired_list" selected="False">Input from a paired collection</option>
+            </param>
+            <when value="multiple_selection_list">
+                <param name="data" type="data" format="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="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" />
+            </when>
+        </conditional>
+    </xml>
     <xml name="table_inputs_macro">
         <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?">
@@ -9,22 +28,20 @@
             </param>
             <when value="excel_tables">
                 <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)" />
-                <param name="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
-                <param name="xlsx_file" type="data" format="xlsx" />
-                <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/>
+                <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" />
+                <expand macro="run_inputs_macro" />
             </when>
             <when value="user_generated_tables">
                 <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)" />
-                <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/>
+                <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"/>
             </when>
             <when value="build_tables">
-                <param name="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
                 <conditional name="conditional_viral_metadata">
-                    <param name="viral_sample" type="boolean" label="Does your submission contains viral samples?" />
+                    <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
                     <when value="true">
                         <expand macro="viral_samples" />
                     </when>
@@ -51,8 +68,11 @@
                 <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="text" 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 leave blank">
-                    <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})?)?)?)?)?$)|(^not colected$)|(^not provided$)|(^restricted access$)</validator>
+                <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="geo_location_country" type="select" label="Select the country where the sample was obtained">
                     <options from_data_table="geographic_location_1">
@@ -118,6 +138,7 @@
                         </options>
                     </param>
                     <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
+                        <param name="run_base_name" type="text" optional="False" default="" 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="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
                     </repeat>
                 </repeat>
@@ -166,7 +187,7 @@
                 <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="ILLUMINA" selected="True">Illumina</option>
                     <option value="HELICOS">Helicos</option>
                     <option value="ABI_SOLID">ABI Solid</option>
                     <option value="COMPLETE_GENOMICS">Complete Genomics</option>
@@ -182,6 +203,7 @@
                     </options>
                 </param>
                 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
+                    <param name="run_base_name" type="text" optional="False" default="" 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="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
                 </repeat>
             </repeat>