Mercurial > repos > iuc > ncbi_datasets
comparison datasets_genome.xml @ 15:198c75abbf55 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
author | iuc |
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date | Mon, 04 Mar 2024 17:27:59 +0000 |
parents | 75acf92c8fd5 |
children | a6a475ed58cb |
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14:75acf92c8fd5 | 15:198c75abbf55 |
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31 #end if | 31 #end if |
32 #if $filters.chromosomes: | 32 #if $filters.chromosomes: |
33 --chromosomes '$filters.chromosomes' | 33 --chromosomes '$filters.chromosomes' |
34 #end if | 34 #end if |
35 $filters.exclude_atypical | 35 $filters.exclude_atypical |
36 #if $filters.mag: | |
37 --mag '$filters.mag' | |
38 #end if | |
39 | |
36 @INCLUDE@ | 40 @INCLUDE@ |
37 @RELEASED_BEFORE@ | 41 @RELEASED_BEFORE@ |
38 @RELEASED_AFTER@ | 42 @RELEASED_AFTER@ |
39 #for search_term in $filters.search: | 43 #for search_term in $filters.search: |
40 --search '$filters.search_term' | 44 --search '$filters.search_term' |
104 <option value="all">All</option> | 108 <option value="all">All</option> |
105 </param> | 109 </param> |
106 <expand macro="assembly_source"/> | 110 <expand macro="assembly_source"/> |
107 <expand macro="chromosomes"/> | 111 <expand macro="chromosomes"/> |
108 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/> | 112 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/> |
113 <param argument="--mag" type="select" multiple="false" optional="true" label="Filter metagenome assembled genomes (MAGs)"> | |
114 <option value="only" selected="false">Limit to MAGs</option> | |
115 <option value="exclude" selected="false">Exclude MAGs</option> | |
116 </param> | |
109 <expand macro="released_options"/> | 117 <expand macro="released_options"/> |
110 <expand macro="released_options" before_or_after="after"/> | 118 <expand macro="released_options" before_or_after="after"/> |
111 | 119 |
112 <repeat name="search" title="Add search terms"> | 120 <repeat name="search" title="Add search terms"> |
113 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/> | 121 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/> |
330 <param name="include" value="seq-report,gff3,gbff"/> | 338 <param name="include" value="seq-report,gff3,gbff"/> |
331 <param name="decompress" value="true"/> | 339 <param name="decompress" value="true"/> |
332 </section> | 340 </section> |
333 <output name="genome_data_report"> | 341 <output name="genome_data_report"> |
334 <assert_contents> | 342 <assert_contents> |
335 <has_text text="GCF_000013305.1"/> | 343 <has_text text="GCF_000013305.1"/> |
336 <has_text text="GCF_000007445.1"/> | 344 <has_text text="GCF_000007445.1"/> |
337 <has_n_lines n="3"/> | 345 <has_n_lines n="3"/> |
338 <has_n_columns n="4"/> | 346 <has_n_columns n="4"/> |
339 </assert_contents> | 347 </assert_contents> |
340 </output> | 348 </output> |
341 <output_collection name="genomic_gff" type="list"> | 349 <output_collection name="genomic_gff" type="list"> |
347 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/> | 355 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/> |
348 </output_collection> | 356 </output_collection> |
349 </test> | 357 </test> |
350 | 358 |
351 <!-- should not fail https://github.com/ncbi/datasets/issues/194 --> | 359 <!-- should not fail https://github.com/ncbi/datasets/issues/194 --> |
352 <test expect_num_outputs="2"> <!-- expect_failure="true"> --> | 360 <test expect_num_outputs="2"> |
353 <conditional name="query|subcommand"> | 361 <conditional name="query|subcommand"> |
354 <param name="download_by" value="accession"/> | 362 <param name="download_by" value="accession"/> |
355 <conditional name="text_or_file"> | 363 <conditional name="text_or_file"> |
356 <param name="text_or_file" value="text"/> | 364 <param name="text_or_file" value="text"/> |
357 <param name="accession" value="GCF_000001405"/> | 365 <param name="accession" value="GCF_000001405"/> |
360 <param name="released_before" value="01/01/2015"/> | 368 <param name="released_before" value="01/01/2015"/> |
361 <param name="assembly_version" value="all"/> | 369 <param name="assembly_version" value="all"/> |
362 <section name="file_choices"> | 370 <section name="file_choices"> |
363 <param name="include" value="seq-report"/> | 371 <param name="include" value="seq-report"/> |
364 </section> | 372 </section> |
365 <!-- | 373 <output name="genome_data_report"> |
366 <output_collection name="sequence_report" type="list" count="4" > | 374 <!-- assert that we get at least the 16 versions available at the time of writing this test --> |
367 --> | 375 <assert_contents> |
376 <has_text text="GCF_000001405" min="16"/> | |
377 <has_n_lines min="16"/> | |
378 <has_n_columns n="4"/> | |
379 </assert_contents> | |
380 </output> | |
381 <!--not testing the collection output. the count will change over time | |
382 and this can't be tested for at the moment | |
383 <output_collection name="sequence_report" type="list" count="16"/> --> | |
368 </test> | 384 </test> |
369 <test expect_num_outputs="5"> | 385 <test expect_num_outputs="5"> |
370 <conditional name="query|subcommand"> | 386 <conditional name="query|subcommand"> |
371 <param name="download_by" value="accession"/> | 387 <param name="download_by" value="accession"/> |
372 <conditional name="text_or_file"> | 388 <conditional name="text_or_file"> |
411 </section> | 427 </section> |
412 <output_collection name="genome_fasta" type="list:list" count="1"> | 428 <output_collection name="genome_fasta" type="list:list" count="1"> |
413 <element name="GCF_000146045.2"> | 429 <element name="GCF_000146045.2"> |
414 <element name="GCF_000146045.2_R64" ftype="fasta.gz"> | 430 <element name="GCF_000146045.2_R64" ftype="fasta.gz"> |
415 <assert_contents> | 431 <assert_contents> |
416 <has_size value="3843460"/> | 432 <has_size value="3843460" delta="2000"/> |
417 </assert_contents> | 433 </assert_contents> |
418 </element> | 434 </element> |
419 </element> | 435 </element> |
420 </output_collection> | 436 </output_collection> |
421 <output_collection name="protein_fasta" type="list" count="1"> | 437 <output_collection name="protein_fasta" type="list" count="1"> |
422 <element name="GCF_000146045.2" ftype="fasta.gz"> | 438 <element name="GCF_000146045.2" ftype="fasta.gz"> |
423 <assert_contents> | 439 <assert_contents> |
424 <has_size value="1845038"/> | 440 <has_size value="1845038" delta="2000"/> |
425 </assert_contents> | 441 </assert_contents> |
426 </element> | 442 </element> |
427 </output_collection> | 443 </output_collection> |
428 <output_collection name="rna_fasta" type="list" count="1"> | 444 <output_collection name="rna_fasta" type="list" count="1"> |
429 <element name="GCF_000146045.2" ftype="fasta.gz"> | 445 <element name="GCF_000146045.2" ftype="fasta.gz"> |
430 <assert_contents> | 446 <assert_contents> |
431 <has_size value="2784899"/> | 447 <has_size value="2784899" delta="2000"/> |
432 </assert_contents> | 448 </assert_contents> |
433 </element> | 449 </element> |
434 </output_collection> | 450 </output_collection> |
435 </test> | 451 </test> |
436 <test expect_num_outputs="3"> | 452 <test expect_num_outputs="3"> |
449 <output_collection name="genome_fasta" type="list:list" count="2"> | 465 <output_collection name="genome_fasta" type="list:list" count="2"> |
450 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/> | 466 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/> |
451 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/> | 467 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/> |
452 </output_collection> | 468 </output_collection> |
453 </test> | 469 </test> |
454 <!-- tax_exact_match seems not able to filter out strains | 470 <!-- tax_exact_match should filter out strains |
455 https://github.com/ncbi/datasets/issues/187 | 471 https://github.com/ncbi/datasets/issues/187 --> |
456 hence we set expect_test_failure="true"--> | 472 <test expect_num_outputs="1"> |
457 <test expect_num_outputs="1" expect_test_failure="true"> | |
458 <conditional name="query|subcommand"> | 473 <conditional name="query|subcommand"> |
459 <param name="download_by" value="taxon"/> | 474 <param name="download_by" value="taxon"/> |
460 <param name="taxon_positional" value="4932"/> | 475 <param name="taxon_positional" value="4932"/> |
461 <param name="tax_exact_match" value="true"/> | 476 <param name="tax_exact_match" value="true"/> |
462 </conditional> | 477 </conditional> |