diff samples_macros.xml @ 7:6f6537780379 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"

--- a/samples_macros.xml	Mon Nov 15 11:47:13 2021 +0000
+++ b/samples_macros.xml	Thu Feb 24 18:20:40 2022 +0000
@@ -1,4 +1,48 @@
 <macros>
+    <xml name="checklist_input_macro">
+        <param type="select" name="checklist_id" label="Select the metadata checklist" help="You can find metadata templates for each checklist at: https://github.com/ELIXIR-Belgium/ENA-metadata-templates">
+            <option value="ERC000011">ENA default sample checklist (ERC000011)</option>
+            <option value="ERC000012">GSC MIxS air (ERC000012)</option>
+            <option value="ERC000013">GSC MIxS host associated (ERC000013)</option>
+            <option value="ERC000014">GSC MIxS human associated (ERC000014)</option>
+            <option value="ERC000015">GSC MIxS human gut (ERC000015)</option>
+            <option value="ERC000016">GSC MIxS human oral (ERC000016)</option>
+            <option value="ERC000017">GSC MIxS human skin (ERC000017)</option>
+            <option value="ERC000018">GSC MIxS human vaginal (ERC000018)</option>
+            <option value="ERC000019">GSC MIxS microbial mat biolfilm (ERC000019)</option>
+            <option value="ERC000020">GSC MIxS plant associated (ERC000020)</option>
+            <option value="ERC000021">GSC MIxS sediment (ERC000021)</option>
+            <option value="ERC000022">GSC MIxS soil (ERC000022)</option>
+            <option value="ERC000023">GSC MIxS wastewater sludge (ERC000023)</option>
+            <option value="ERC000024">GSC MIxS water (ERC000024)</option>
+            <option value="ERC000025">GSC MIxS miscellaneous natural or artificial environment (ERC000025)</option>
+            <option value="ERC000027">ENA Micro B3 (ERC000027)</option>
+            <option value="ERC000028">ENA prokaryotic pathogen minimal sample checklist (ERC000028)</option>
+            <option value="ERC000029">ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1 (ERC000029)</option>
+            <option value="ERC000030">ENA Tara Oceans (ERC000030)</option>
+            <option value="ERC000031">GSC MIxS built environment (ERC000031)</option>
+            <option value="ERC000032">ENA Influenza virus reporting standard checklist (ERC000032)</option>
+            <option value="ERC000033">ENA virus pathogen reporting standard checklist (ERC000033)</option>
+            <option value="ERC000034">ENA mutagenesis by carcinogen treatment checklist (ERC000034)</option>
+            <option value="ERC000035">ENA Crop Plant sample enhanced annotation checklist (ERC000035)</option>
+            <option value="ERC000036">ENA sewage checklist (ERC000036)</option>
+            <option value="ERC000037">ENA Plant Sample Checklist (ERC000037)</option>
+            <option value="ERC000038">ENA Shellfish Checklist (ERC000038)</option>
+            <option value="ERC000039">ENA parasite sample checklist (ERC000039)</option>
+            <option value="ERC000040">ENA UniEuk_EukBank Checklist (ERC000040)</option>
+            <option value="ERC000041">ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist (ERC000041)</option>
+            <option value="ERC000043">ENA Marine Microalgae Checklist (ERC000043)</option>
+            <option value="ERC000044">COMPARE-ECDC-EFSA pilot human-associated reporting standard (ERC000044)</option>
+            <option value="ERC000045">COMPARE-ECDC-EFSA pilot food-associated reporting standard (ERC000045)</option>
+            <option value="ERC000047">GSC MIMAGS (ERC000047)</option>
+            <option value="ERC000048">GSC MISAGS (ERC000048)</option>
+            <option value="ERC000049">GSC MIUVIGS (ERC000049)</option>
+            <option value="ERC000050">ENA binned metagenome (ERC000050)</option>
+            <option value="ERC000051">PDX Checklist (ERC000051)</option>
+            <option value="ERC000052">HoloFood Checklist (ERC000052)</option>
+            <option value="ERC000053">Tree of Life Checklist (ERC000053)</option>
+        </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/" />
@@ -23,17 +67,19 @@
     <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?">
-                <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option>
+                <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="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
             </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="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" />
+                <!--<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"/>
+                <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" />
                 <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="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"/>
@@ -161,7 +207,7 @@
             <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="text" label="Enter the taxonomic ID corresponding to the sample species" />
+            <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" />