| Previous changeset 16:a6a475ed58cb (2024-06-07) Next changeset 18:d951c5b0edd1 (2025-02-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b |
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modified:
datasets_gene.xml datasets_genome.xml macros.xml |
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| diff -r a6a475ed58cb -r da8260eba74b datasets_gene.xml --- a/datasets_gene.xml Fri Jun 07 14:19:58 2024 +0000 +++ b/datasets_gene.xml Fri Feb 21 18:44:07 2025 +0000 |
| [ |
| @@ -75,7 +75,7 @@ ## unzip and rehydrate if any data is to be downloaded (include is not None) #if $file_choices.kingdom_cond.include ## unzip - && 7z x -y ncbi_dataset.zip > 7z.log + && unzip ncbi_dataset.zip #end if ]]></command> <inputs> @@ -114,7 +114,7 @@ </valid> </sanitizer> </param> - <param argument="--include-flanks-bp" type="integer" optional="true" min="0" label="Length of flanking nucleotides" help="WP accessions only"/> + <param argument="--include-flanks-bp" type="integer" optional="true" min="0" value="" label="Length of flanking nucleotides" help="WP accessions only"/> </when> <when value="taxon"> <expand macro="taxon_positional"/> @@ -196,6 +196,9 @@ <data name="gene_fasta" label="NCBI Gene Datasets: Gene fasta" format="fasta" from_work_dir="ncbi_dataset/data/gene.fna"> <filter>file_choices['kingdom_cond']['include'] and "gene" in file_choices['kingdom_cond']['include']</filter> </data> + <data name="gene_flanks" label="NCBI Gene Datasets: Flanking faste" format="fasta" from_work_dir="ncbi_dataset/data/gene_flank.fna"> + <filter>query['subcommand']['download_by'] == "accession" and query['subcommand']['include_flanks_bp'] != ""</filter> + </data> <data name="rna_fasta" label="NCBI Gene Datasets: RNA fasta" format="fasta" from_work_dir="ncbi_dataset/data/rna.fna"> <filter>file_choices['kingdom_cond']['include'] and "rna" in file_choices['kingdom_cond']['include']</filter> </data> @@ -353,7 +356,7 @@ <has_text text="house mouse"/> <has_text text="XR_004936704.1"/> <has_n_lines min="130"/> - <has_n_columns n="38"/> + <has_n_columns n="39"/> </assert_contents> </output> <output name="threep_utr_fasta"> @@ -437,15 +440,13 @@ </output> </test> - <!-- 9: datasets download gene accession WP_004675351.1 + include_flanks_bp - test broken at the moment https://github.com/ncbi/datasets/issues/328 - --> - <test expect_failure="true"> <!-- expect_num_outputs="3" --> + <!-- 9: datasets download gene accession WP_003249567.1 + include_flanks_bp --> + <test expect_num_outputs="4"> <conditional name="query|subcommand"> <param name="download_by" value="accession"/> <conditional name="text_or_file"> <param name="text_or_file" value="text"/> - <param name="accession" value="WP_004675351.1"/> + <param name="accession" value="WP_003249567.1"/> </conditional> <param name="include_flanks_bp" value="100"/> </conditional> @@ -455,9 +456,10 @@ <param name="include" value="gene,protein"/> </conditional> </section> - <!-- <output name="gene_data_report"> + <output name="gene_data_report"> <assert_contents> - <has_text text="glcE"/> + <has_text text="WP_003249567.1"/> + <has_text text="menG"/> <has_n_lines n="2"/> <has_n_columns n="7"/> </assert_contents> @@ -467,18 +469,23 @@ <has_text text=">"/> </assert_contents> </output> + <output name="gene_flanks"> + <assert_contents> + <has_text text=">"/> + </assert_contents> + </output> <output name="protein_fasta"> <assert_contents> <has_text text=">"/> </assert_contents> - </output> --> + </output> <assert_command> <has_text text="include-flanks-bp 100"/> </assert_command> </test> <!-- 10: datasets download gene taxon human --> - <test expect_num_outputs="1"> + <!-- <test expect_num_outputs="1"> <conditional name="query|subcommand"> <param name="download_by" value="taxon"/> <param name="taxon_positional" value="human"/> @@ -495,9 +502,9 @@ <has_n_columns n="8"/> </assert_contents> </output> - </test> + </test> --> <!-- 11: datasets download gene taxon human + \-\-fasta-filter --> - <test expect_num_outputs="2"> + <!-- <test expect_num_outputs="2"> <conditional name="query|subcommand"> <param name="download_by" value="taxon"/> <param name="taxon_positional" value="human"/> @@ -524,7 +531,8 @@ <assert_contents> <has_text text=">" n="1" /> </assert_contents> - </output></test> + </output> + </test> --> </tests> <help> <![CDATA[ |
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| diff -r a6a475ed58cb -r da8260eba74b datasets_genome.xml --- a/datasets_genome.xml Fri Jun 07 14:19:58 2024 +0000 +++ b/datasets_genome.xml Fri Feb 21 18:44:07 2025 +0000 |
| [ |
| @@ -55,7 +55,7 @@ ## unzip and rehydrate if any data is to be downloaded (include is not None) #if $file_choices.include ## unzip - && 7z x -y ncbi_dataset.zip > 7z.log + && unzip ncbi_dataset.zip ## rehydrate && datasets rehydrate @@ -463,8 +463,8 @@ </section> <output_collection name="sequence_report" type="list" count="2"/> <output_collection name="genome_fasta" type="list:list" count="2"> - <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"/> - <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"/> + <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"/> + <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"/> </output_collection> </test> <!-- tax_exact_match should filter out strains |
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| diff -r a6a475ed58cb -r da8260eba74b macros.xml --- a/macros.xml Fri Jun 07 14:19:58 2024 +0000 +++ b/macros.xml Fri Feb 21 18:44:07 2025 +0000 |
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| b'@@ -1,5 +1,5 @@\n <macros>\n- <token name="@TOOL_VERSION@">16.20.0</token>\n+ <token name="@TOOL_VERSION@">16.41.0</token>\n <token name="@VERSION_SUFFIX@">0</token>\n <token name="@PROFILE@">23.0</token>\n <token name="@LICENSE@">MIT</token>\n@@ -11,8 +11,8 @@\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>\n- <requirement type="package" version="2024.2.2">ca-certificates</requirement>\n- <requirement type="package" version="16.02">p7zip</requirement>\n+ <requirement type="package" version="2025.1.31">ca-certificates</requirement>\n+ <requirement type="package" version="6.0">unzip</requirement>\n </requirements>\n </xml>\n <xml name="bio_tools">\n@@ -116,9 +116,28 @@\n none\n #end if\n ]]></token>\n+\n <xml name="tsv_report_columns">\n <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">\n <option value="accession">Assembly Accession</option>\n+ <option value="ani-best-ani-match-ani">ANI Best ANI match ANI</option>\n+ <option value="ani-best-ani-match-assembly">ANI Best ANI match Assembly</option>\n+ <option value="ani-best-ani-match-assembly_coverage">ANI Best ANI match Assembly Coverage</option>\n+ <option value="ani-best-ani-match-category">ANI Best ANI match Type Category</option>\n+ <option value="ani-best-ani-match-organism">ANI Best ANI match Organism</option>\n+ <option value="ani-best-ani-match-type_assembly_coverage">ANI Best ANI match Type Assembly Coverage</option>\n+ <option value="ani-best-match-status">ANI Best match status</option>\n+ <option value="ani-category">ANI Category</option>\n+ <option value="ani-check-status">ANI Check status</option>\n+ <option value="ani-comment">ANI Comment</option>\n+ <option value="ani-submitted-ani-match-ani">ANI Declared ANI match ANI</option>\n+ <option value="ani-submitted-ani-match-assembly">ANI Declared ANI match Assembly</option>\n+ <option value="ani-submitted-ani-match-assembly_coverage">ANI Declared ANI match Assembly Coverage</option>\n+ <option value="ani-submitted-ani-match-category">ANI Declared ANI match Type Category</option>\n+ <option value="ani-submitted-ani-match-organism">ANI Declared ANI match Organism</option>\n+ <option value="ani-submitted-ani-match-type_assembly_coverage">ANI Declared ANI match Type Assembly Coverage</option>\n+ <option value="ani-submitted-organism">ANI Submitted organism</option>\n+ <option value="ani-submitted-species">ANI Submitted species</option>\n <option value="annotinfo-busco-complete">Annotation BUSCO Complete</option>\n <option value="annotinfo-busco-duplicated">Annotation BUSCO Duplicated</option>\n <option value="annotinfo-busco-fragmented">Annotation BUSCO Fragmented</option>\n@@ -137,23 +156,29 @@\n <option value="annotinfo-pipeline">Annotation Pipeline</option>\n <option value="annotinfo-provider">Annotation Provider</option>\n <option value="annotinfo-release-date">Annotation Release Date</option>\n- <option value="annotinfo-release-version">Annotation Release Version</option>\n <option value="annotinfo-report-url">Annotation Report URL</option>\n <option value="annotinfo-software-version">Annotation Software Version</option>\n <option value="annotinfo-status">Annotation Status</option>\n+ <option value="assminfo-assembly-method">Assembly Assembly Method</option>\n <option value="assminfo-atypicalis-atypical">Assembly Atypical Is Atypical</option>\n <option value="assminfo-atypicalwarnings">Assembly Atypical Warnings</option>\n+ <option'..b'tation-release-date">Annotation Release Date</option>\n <option value="annotation-release-name">Annotation Release Name</option>\n@@ -260,12 +318,30 @@\n <option value="genomic-region-gene-range-range-start">Genomic Region Gene Range Start</option>\n <option value="genomic-region-gene-range-range-stop">Genomic Region Gene Range Stop</option>\n <option value="genomic-region-genomic-region-type">Genomic Region Genomic Region Type</option>\n+ <option value="go-assigned-by">Gene Ontology Assigned By</option>\n+ <option value="go-bp-evidence-code">Gene Ontology Biological Process Evidence Code</option>\n+ <option value="go-bp-id">Gene Ontology Biological Process Go ID</option>\n+ <option value="go-bp-name">Gene Ontology Biological Process Name</option>\n+ <option value="go-bp-qualifier">Gene Ontology Biological Process Qualifier</option>\n+ <option value="go-bp-reference-pmid">Gene Ontology Biological Process Reference PMID</option>\n+ <option value="go-cc-evidence-code">Gene Ontology Cellular Component Evidence Code</option>\n+ <option value="go-cc-id">Gene Ontology Cellular Component Go ID</option>\n+ <option value="go-cc-name">Gene Ontology Cellular Component Name</option>\n+ <option value="go-cc-qualifier">Gene Ontology Cellular Component Qualifier</option>\n+ <option value="go-cc-reference-pmid">Gene Ontology Cellular Component Reference PMID</option>\n+ <option value="go-mf-evidence-code">Gene Ontology Molecular Function Evidence Code</option>\n+ <option value="go-mf-id">Gene Ontology Molecular Function Go ID</option>\n+ <option value="go-mf-name">Gene Ontology Molecular Function Name</option>\n+ <option value="go-mf-qualifier">Gene Ontology Molecular Function Qualifier</option>\n+ <option value="go-mf-reference-pmid">Gene Ontology Molecular Function Reference PMID</option>\n <option value="group-id">Gene Group Identifier</option>\n <option value="group-method">Gene Group Method</option>\n+ <option value="locus-tag">Locus Tag</option>\n <option value="name-authority">Nomenclature Authority</option>\n <option value="name-id">Nomenclature ID</option>\n <option value="omim-ids">OMIM IDs</option>\n <option value="orientation">Orientation</option>\n+ <option value="protein-count">Proteins</option>\n <option value="ref-standard-gene-range-accession">Reference Standard Gene Range Sequence Accession</option>\n <option value="ref-standard-gene-range-range-order">Reference Standard Gene Range Order</option>\n <option value="ref-standard-gene-range-range-orientation">Reference Standard Gene Range Orientation</option>\n@@ -274,14 +350,19 @@\n <option value="ref-standard-genomic-region-type">Reference Standard Genomic Region Type</option>\n <option value="replaced-gene-id">Replaced NCBI GeneID</option>\n <option value="rna-type">RNA Type</option>\n+ <option value="summary-date">Summary Date</option>\n+ <option value="summary-description">Summary Description</option>\n+ <option value="summary-source">Summary Source</option>\n <option value="swissprot-accessions">SwissProt Accessions</option>\n <option value="symbol">Symbol</option>\n <option value="synonyms">Synonyms</option>\n <option value="tax-id">Taxonomic ID</option>\n <option value="tax-name">Taxonomic Name</option>\n+ <option value="transcript-count">Transcripts</option>\n <yield/>\n </param>\n </xml>\n+\n <xml name="prok_gene_tsv_report_columns">\n <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">\n <option value="accession">Accession</option>\n' |