Mercurial > repos > iuc > ncbi_datasets

comparison datasets_genome.xml @ 17:da8260eba74b draft default tip

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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
equal deleted inserted replaced
16:a6a475ed58cb 17:da8260eba74b
53 > genome_data_report.tsv 53 > genome_data_report.tsv
54 54
55 ## unzip and rehydrate if any data is to be downloaded (include is not None) 55 ## unzip and rehydrate if any data is to be downloaded (include is not None)
56 #if $file_choices.include 56 #if $file_choices.include
57 ## unzip 57 ## unzip
58 && 7z x -y ncbi_dataset.zip > 7z.log 58 && unzip ncbi_dataset.zip
59 59
60 ## rehydrate 60 ## rehydrate
61 && datasets rehydrate 61 && datasets rehydrate
62 --directory ./ 62 --directory ./
63 #if not $file_choices.decompress 63 #if not $file_choices.decompress
461 <param name="include" value="seq-report,genome"/> 461 <param name="include" value="seq-report,genome"/>
462 <param name="decompress" value="true"/> 462 <param name="decompress" value="true"/>
463 </section> 463 </section>
464 <output_collection name="sequence_report" type="list" count="2"/> 464 <output_collection name="sequence_report" type="list" count="2"/>
465 <output_collection name="genome_fasta" type="list:list" count="2"> 465 <output_collection name="genome_fasta" type="list:list" count="2">
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"/> 466 <expand macro="genome_fasta_assert" el1="GCF_000002945.2" el2="GCF_000002945.2_ASM294v3" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe.*" expression_n="4"/>
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"/> 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].*" expression_n="17"/>
468 </output_collection> 468 </output_collection>
469 </test> 469 </test>
470 <!-- tax_exact_match should filter out strains 470 <!-- tax_exact_match should filter out strains
471 https://github.com/ncbi/datasets/issues/187 --> 471 https://github.com/ncbi/datasets/issues/187 -->
472 <test expect_num_outputs="1"> 472 <test expect_num_outputs="1">