Mercurial > repos > iuc > ena_upload

comparison ena_upload.xml @ 8:d147d6455873 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
author iuc
date Wed, 04 May 2022 17:06:42 +0000
parents 6f6537780379
children a62c4a11a67d
comparison
equal deleted inserted replaced
7:6f6537780379 8:d147d6455873
1 <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT"> 1 <tool id="ena_upload" name="ENA Upload tool" version="@VERSION@" profile="20.01" license="MIT">
2 <macros> 2 <macros>
3 <token name="@VERSION@">0.5.3</token> 3 <token name="@VERSION@">0.6.0</token>
4 <import>samples_macros.xml</import> 4 <import>samples_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement> 7 <requirement type="package" version="@VERSION@">ena-upload-cli</requirement>
8 </requirements> 8 </requirements>
201 #end if 201 #end if
202 #else: 202 #else:
203 --checklist $action_options.input_format_conditional.checklist_id 203 --checklist $action_options.input_format_conditional.checklist_id
204 #end if 204 #end if
205 #end if 205 #end if
206 206 #if $action_options.idempotent == "true":
207 --auto_action
208 #end if
207 #if $action_options.test_submit_parameters.submit_dev == "true": 209 #if $action_options.test_submit_parameters.submit_dev == "true":
208 -d 210 -d
209 #end if 211 #end if
210 >> '$output'; 212 >> '$output';
211 #end if 213 #end if
322 <param name="action" type="select" label="Action to execute"> 324 <param name="action" type="select" label="Action to execute">
323 <option value="add" selected="True">Add new data</option> 325 <option value="add" selected="True">Add new data</option>
324 <option value="modify">Modify metadata</option> 326 <option value="modify">Modify metadata</option>
325 </param> 327 </param>
326 <when value="add"> 328 <when value="add">
329 <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"/>
327 <expand macro="test_submit_section"/> 330 <expand macro="test_submit_section"/>
328 <param name="test_submit" type="hidden" value="False" /> 331 <param name="test_submit" type="hidden" value="False" />
329 <expand macro="table_inputs_macro" /> 332 <expand macro="table_inputs_macro" />
330 </when> 333 </when>
331 <when value="modify"> 334 <when value="modify">
542 <param name="center" value="Some research center"/> 545 <param name="center" value="Some research center"/>
543 <assert_command> 546 <assert_command>
544 <has_text_matching expression="ena-upload-cli"/> 547 <has_text_matching expression="ena-upload-cli"/>
545 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/> 548 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
546 <has_text_matching expression="--action 'add' --center 'Some research center'"/> 549 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
550 </assert_command>
551 </test>
552 <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection + Idempotent submission -->
553 <test expect_failure="true">
554 <conditional name="action_options">
555 <param name="action" value="add"/>
556 <section name="test_submit_parameters">
557 <param name="submit_dev" value="false" />
558 <param name="dry_run" value="false" />
559 </section>
560 <param name="idempotent" value="true"/>
561 <conditional name="input_format_conditional">
562 <param name="add_extension" value="true"/>
563 <param name="input_format" value="excel_tables"/>
564 <param name="checklist_id" value="ERC000011"/>
565 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/>
566 <conditional name="run_input_format_conditional">
567 <param name="run_input_format" value="paired_list"/>
568 <param name="paired_end_collection">
569 <collection type="list:paired">
570 <element name="paired_run_name">
571 <collection type="paired">
572 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" />
573 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" />
574 </collection>
575 </element>
576 </collection>
577 </param>
578 </conditional>
579 </conditional>
580 </conditional>
581 <param name="center" value="Some research center"/>
582 <assert_command>
583 <has_text_matching expression="ena-upload-cli"/>
584 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/>
585 <has_text_matching expression="--action 'add' --center 'Some research center'"/>
586 <has_text_matching expression="--auto_action"/>
547 </assert_command> 587 </assert_command>
548 </test> 588 </test>
549 <!--Test 5: build tables from user input fields NON-VIRAL samples--> 589 <!--Test 5: build tables from user input fields NON-VIRAL samples-->
550 <test> 590 <test>
551 <conditional name="action_options"> 591 <conditional name="action_options">