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comparison datasets_gene.xml @ 17:da8260eba74b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
author iuc
date Fri, 21 Feb 2025 18:44:07 +0000
parents a6a475ed58cb
children
comparison
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16:a6a475ed58cb 17:da8260eba74b
73 #end if 73 #end if
74 74
75 ## unzip and rehydrate if any data is to be downloaded (include is not None) 75 ## unzip and rehydrate if any data is to be downloaded (include is not None)
76 #if $file_choices.kingdom_cond.include 76 #if $file_choices.kingdom_cond.include
77 ## unzip 77 ## unzip
78 && 7z x -y ncbi_dataset.zip > 7z.log 78 && unzip ncbi_dataset.zip
79 #end if 79 #end if
80 ]]></command> 80 ]]></command>
81 <inputs> 81 <inputs>
82 <section name="query" title="Query" expanded="true"> 82 <section name="query" title="Query" expanded="true">
83 <conditional name="subcommand"> 83 <conditional name="subcommand">
112 <add value=" " /> 112 <add value=" " />
113 <add value="-" /> 113 <add value="-" />
114 </valid> 114 </valid>
115 </sanitizer> 115 </sanitizer>
116 </param> 116 </param>
117 <param argument="--include-flanks-bp" type="integer" optional="true" min="0" label="Length of flanking nucleotides" help="WP accessions only"/> 117 <param argument="--include-flanks-bp" type="integer" optional="true" min="0" value="" label="Length of flanking nucleotides" help="WP accessions only"/>
118 </when> 118 </when>
119 <when value="taxon"> 119 <when value="taxon">
120 <expand macro="taxon_positional"/> 120 <expand macro="taxon_positional"/>
121 </when> 121 </when>
122 </conditional> 122 </conditional>
194 <filter>file_choices['kingdom_cond']['include'] and "product-report" in file_choices['kingdom_cond']['include']</filter> 194 <filter>file_choices['kingdom_cond']['include'] and "product-report" in file_choices['kingdom_cond']['include']</filter>
195 </data> 195 </data>
196 <data name="gene_fasta" label="NCBI Gene Datasets: Gene fasta" format="fasta" from_work_dir="ncbi_dataset/data/gene.fna"> 196 <data name="gene_fasta" label="NCBI Gene Datasets: Gene fasta" format="fasta" from_work_dir="ncbi_dataset/data/gene.fna">
197 <filter>file_choices['kingdom_cond']['include'] and "gene" in file_choices['kingdom_cond']['include']</filter> 197 <filter>file_choices['kingdom_cond']['include'] and "gene" in file_choices['kingdom_cond']['include']</filter>
198 </data> 198 </data>
199 <data name="gene_flanks" label="NCBI Gene Datasets: Flanking faste" format="fasta" from_work_dir="ncbi_dataset/data/gene_flank.fna">
200 <filter>query['subcommand']['download_by'] == "accession" and query['subcommand']['include_flanks_bp'] != ""</filter>
201 </data>
199 <data name="rna_fasta" label="NCBI Gene Datasets: RNA fasta" format="fasta" from_work_dir="ncbi_dataset/data/rna.fna"> 202 <data name="rna_fasta" label="NCBI Gene Datasets: RNA fasta" format="fasta" from_work_dir="ncbi_dataset/data/rna.fna">
200 <filter>file_choices['kingdom_cond']['include'] and "rna" in file_choices['kingdom_cond']['include']</filter> 203 <filter>file_choices['kingdom_cond']['include'] and "rna" in file_choices['kingdom_cond']['include']</filter>
201 </data> 204 </data>
202 <data name="protein_fasta" label="NCBI Gene Datasets: protein fasta" format="fasta" from_work_dir="ncbi_dataset/data/protein.faa"> 205 <data name="protein_fasta" label="NCBI Gene Datasets: protein fasta" format="fasta" from_work_dir="ncbi_dataset/data/protein.faa">
203 <filter>file_choices['kingdom_cond']['include'] and "protein" in file_choices['kingdom_cond']['include']</filter> 206 <filter>file_choices['kingdom_cond']['include'] and "protein" in file_choices['kingdom_cond']['include']</filter>
351 <output name="gene_product_report"> 354 <output name="gene_product_report">
352 <assert_contents> 355 <assert_contents>
353 <has_text text="house mouse"/> 356 <has_text text="house mouse"/>
354 <has_text text="XR_004936704.1"/> 357 <has_text text="XR_004936704.1"/>
355 <has_n_lines min="130"/> 358 <has_n_lines min="130"/>
356 <has_n_columns n="38"/> 359 <has_n_columns n="39"/>
357 </assert_contents> 360 </assert_contents>
358 </output> 361 </output>
359 <output name="threep_utr_fasta"> 362 <output name="threep_utr_fasta">
360 <assert_contents> 363 <assert_contents>
361 <has_text text=">"/> 364 <has_text text=">"/>
435 <has_n_columns n="8"/> 438 <has_n_columns n="8"/>
436 </assert_contents> 439 </assert_contents>
437 </output> 440 </output>
438 </test> 441 </test>
439 442
440 <!-- 9: datasets download gene accession WP_004675351.1 + include_flanks_bp 443 <!-- 9: datasets download gene accession WP_003249567.1 + include_flanks_bp -->
441 test broken at the moment https://github.com/ncbi/datasets/issues/328 444 <test expect_num_outputs="4">
442 -->
443 <test expect_failure="true"> <!-- expect_num_outputs="3" -->
444 <conditional name="query|subcommand"> 445 <conditional name="query|subcommand">
445 <param name="download_by" value="accession"/> 446 <param name="download_by" value="accession"/>
446 <conditional name="text_or_file"> 447 <conditional name="text_or_file">
447 <param name="text_or_file" value="text"/> 448 <param name="text_or_file" value="text"/>
448 <param name="accession" value="WP_004675351.1"/> 449 <param name="accession" value="WP_003249567.1"/>
449 </conditional> 450 </conditional>
450 <param name="include_flanks_bp" value="100"/> 451 <param name="include_flanks_bp" value="100"/>
451 </conditional> 452 </conditional>
452 <section name="file_choices"> 453 <section name="file_choices">
453 <conditional name="kingdom_cond"> 454 <conditional name="kingdom_cond">
454 <param name="kingdom_sel" value="prok-gene"/> 455 <param name="kingdom_sel" value="prok-gene"/>
455 <param name="include" value="gene,protein"/> 456 <param name="include" value="gene,protein"/>
456 </conditional> 457 </conditional>
457 </section> 458 </section>
458 <!-- <output name="gene_data_report"> 459 <output name="gene_data_report">
459 <assert_contents> 460 <assert_contents>
460 <has_text text="glcE"/> 461 <has_text text="WP_003249567.1"/>
462 <has_text text="menG"/>
461 <has_n_lines n="2"/> 463 <has_n_lines n="2"/>
462 <has_n_columns n="7"/> 464 <has_n_columns n="7"/>
463 </assert_contents> 465 </assert_contents>
464 </output> 466 </output>
465 <output name="gene_fasta"> 467 <output name="gene_fasta">
466 <assert_contents> 468 <assert_contents>
467 <has_text text=">"/> 469 <has_text text=">"/>
468 </assert_contents> 470 </assert_contents>
469 </output> 471 </output>
472 <output name="gene_flanks">
473 <assert_contents>
474 <has_text text=">"/>
475 </assert_contents>
476 </output>
470 <output name="protein_fasta"> 477 <output name="protein_fasta">
471 <assert_contents> 478 <assert_contents>
472 <has_text text=">"/> 479 <has_text text=">"/>
473 </assert_contents> 480 </assert_contents>
474 </output> --> 481 </output>
475 <assert_command> 482 <assert_command>
476 <has_text text="include-flanks-bp 100"/> 483 <has_text text="include-flanks-bp 100"/>
477 </assert_command> 484 </assert_command>
478 </test> 485 </test>
479 486
480 <!-- 10: datasets download gene taxon human --> 487 <!-- 10: datasets download gene taxon human -->
481 <test expect_num_outputs="1"> 488 <!-- <test expect_num_outputs="1">
482 <conditional name="query|subcommand"> 489 <conditional name="query|subcommand">
483 <param name="download_by" value="taxon"/> 490 <param name="download_by" value="taxon"/>
484 <param name="taxon_positional" value="human"/> 491 <param name="taxon_positional" value="human"/>
485 </conditional> 492 </conditional>
486 <section name="file_choices"> 493 <section name="file_choices">
493 <has_text text="human"/> 500 <has_text text="human"/>
494 <has_n_lines min="72000"/> 501 <has_n_lines min="72000"/>
495 <has_n_columns n="8"/> 502 <has_n_columns n="8"/>
496 </assert_contents> 503 </assert_contents>
497 </output> 504 </output>
498 </test> 505 </test> -->
499 <!-- 11: datasets download gene taxon human + \-\-fasta-filter --> 506 <!-- 11: datasets download gene taxon human + \-\-fasta-filter -->
500 <test expect_num_outputs="2"> 507 <!-- <test expect_num_outputs="2">
501 <conditional name="query|subcommand"> 508 <conditional name="query|subcommand">
502 <param name="download_by" value="taxon"/> 509 <param name="download_by" value="taxon"/>
503 <param name="taxon_positional" value="human"/> 510 <param name="taxon_positional" value="human"/>
504 </conditional> 511 </conditional>
505 <section name="file_choices"> 512 <section name="file_choices">
522 </output> 529 </output>
523 <output name="protein_fasta"> 530 <output name="protein_fasta">
524 <assert_contents> 531 <assert_contents>
525 <has_text text=">" n="1" /> 532 <has_text text=">" n="1" />
526 </assert_contents> 533 </assert_contents>
527 </output></test> 534 </output>
535 </test> -->
528 </tests> 536 </tests>
529 <help> 537 <help>
530 <![CDATA[ 538 <![CDATA[
531 **Download Gene Datasets from NCBI** 539 **Download Gene Datasets from NCBI**
532 540