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comparison ena_upload.xml @ 15:89329e428dc6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
author iuc
date Mon, 27 Jan 2025 18:12:42 +0000
parents 5cb6146337d8
children 440074098911
comparison
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14:5cb6146337d8 15:89329e428dc6
1 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT"> 1 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT">
2 <description>Submission of (meta)data to the European Nucleotide Archive (ENA)</description> 2 <description>Submission of (meta)data to the European Nucleotide Archive (ENA)</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.7.3</token> 4 <token name="@TOOL_VERSION@">0.7.5</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <import>samples_macros.xml</import> 6 <import>samples_macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement>
356 </output> 356 </output>
357 <output name="runs_table_out"> 357 <output name="runs_table_out">
358 <assert_contents> 358 <assert_contents>
359 <has_n_lines n="5"/> 359 <has_n_lines n="5"/>
360 <has_n_columns n="8"/> 360 <has_n_columns n="8"/>
361 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> 361 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date\tstatus"/>
362 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> 362 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
363 </assert_contents> 363 </assert_contents>
364 </output> 364 </output>
365 </test> 365 </test>
366 <!--Test 2: excel input of VIRAL samples with extended columns--> 366 <!--Test 2: excel input of VIRAL samples with extended columns-->
407 </output> 407 </output>
408 <output name="runs_table_out"> 408 <output name="runs_table_out">
409 <assert_contents> 409 <assert_contents>
410 <has_n_lines n="5"/> 410 <has_n_lines n="5"/>
411 <has_n_columns n="8"/> 411 <has_n_columns n="8"/>
412 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> 412 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date\tstatus"/>
413 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> 413 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/>
414 </assert_contents> 414 </assert_contents>
415 </output> 415 </output>
416 <output name="output"> 416 <output name="output">
417 <assert_contents> 417 <assert_contents>
466 </output> 466 </output>
467 <output name="runs_table_out"> 467 <output name="runs_table_out">
468 <assert_contents> 468 <assert_contents>
469 <has_n_lines n="2"/> 469 <has_n_lines n="2"/>
470 <has_n_columns n="8"/> 470 <has_n_columns n="8"/>
471 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> 471 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date\tstatus"/>
472 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/> 472 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/>
473 </assert_contents> 473 </assert_contents>
474 </output> 474 </output>
475 </test> 475 </test>
476 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection --> 476 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection -->
610 </output> 610 </output>
611 <output name="runs_table_out"> 611 <output name="runs_table_out">
612 <assert_contents> 612 <assert_contents>
613 <has_n_lines n="3"/> 613 <has_n_lines n="3"/>
614 <has_n_columns n="8"/> 614 <has_n_columns n="8"/>
615 <has_line_matching expression="alias\tstatus\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tfile_checksum"/> 615 <has_line_matching expression="alias\tstatus\texperiment_alias\tfile_name\tfile_format\tfile_checksum\taccession\tsubmission_date"/>
616 </assert_contents> 616 </assert_contents>
617 </output> 617 </output>
618 </test> 618 </test>
619 <!--Test 6: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples 619 <!--Test 6: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples
620 also tests compression of uncompressed inputs and adding the .gz suffix --> 620 also tests compression of uncompressed inputs and adding the .gz suffix -->
841 </output> 841 </output>
842 <output name="runs_table_out"> 842 <output name="runs_table_out">
843 <assert_contents> 843 <assert_contents>
844 <has_n_lines n="4"/> 844 <has_n_lines n="4"/>
845 <has_n_columns n="10"/> 845 <has_n_columns n="10"/>
846 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_type\tfile checksum\taccession\tsubmission date\tstatus\tsubmission_date\tfile_checksum"/> 846 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_type\tfile checksum\taccession\tsubmission date\tstatus\tfile_checksum\tsubmission_date"/>
847 </assert_contents> 847 </assert_contents>
848 </output> 848 </output>
849 </test> 849 </test>
850 </tests> 850 </tests>
851 <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 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. 851 <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 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.