Mercurial > repos > iuc > ncbi_datasets
changeset 24:94e32337ba54 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb
| author | iuc |
|---|---|
| date | Fri, 26 Dec 2025 17:17:02 +0000 |
| parents | 95be88b49f4e |
| children | |
| files | datasets_gene.xml datasets_genome.xml macros.xml |
| diffstat | 3 files changed, 139 insertions(+), 54 deletions(-) [+] |
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--- a/datasets_gene.xml Mon Aug 04 08:51:59 2025 +0000 +++ b/datasets_gene.xml Fri Dec 26 17:17:02 2025 +0000 @@ -209,7 +209,7 @@ <filter>file_choices['kingdom_cond']['include'] and "cds" in file_choices['kingdom_cond']['include']</filter> </data> <data name="threep_utr_fasta" label="NCBI Gene Datasets: 3' UTR fasta" format="fasta" from_work_dir="ncbi_dataset/data/3p_utr.fna"> - <filter>file_choices['kingdom_cond']['include'] and "5p-utr" in file_choices['kingdom_cond']['include']</filter> + <filter>file_choices['kingdom_cond']['include'] and "3p-utr" in file_choices['kingdom_cond']['include']</filter> </data> <data name="fivep_utr_fasta" label="NCBI Gene Datasets: 5' UTR fasta" format="fasta" from_work_dir="ncbi_dataset/data/5p_utr.fna"> <filter>file_choices['kingdom_cond']['include'] and "5p-utr" in file_choices['kingdom_cond']['include']</filter> @@ -513,15 +513,60 @@ </output> </test> --> </tests> - <help> -<![CDATA[ -**Download Gene Datasets from NCBI** + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Downloads gene data from NCBI using the `datasets`_ command-line tool. +Retrieve gene sequences, transcripts, proteins, and annotation reports. + +**Query Options** + +============= ================================================================ +Method Description +============= ================================================================ +Gene ID NCBI Gene ID (e.g., 672 for BRCA1) +Symbol Gene symbol with taxon (e.g., TP53 in human) +Accession RefSeq nucleotide (NM\_) or protein (NP\_/WP\_) accession +Taxon All genes for a taxon (large downloads) +============= ================================================================ + +---- + +**Key Options** + +- **Ortholog retrieval**: Get orthologous genes across taxa (vertebrates/insects) +- **Taxon filter**: Limit WP\_ accession results to specific organisms +- **Flanking sequence**: Include nucleotides upstream/downstream (WP\_ only) +- **FASTA filter**: Subset output to specific accessions -Download a gene dataset (gene sequence, transcipt, amino acid sequences, -nucleotide coding sequences, 5'-UTR, 3'-UTR) as well as gene and gene -product reports. Genes can be referred by gene id, symbol, accession, -or taxon. -]]> - </help> +**Outputs (Eukaryote)** + +- **Gene Data Report**: Tabular metadata (ID, symbol, description, coordinates) +- **Gene Product Report**: Detailed transcript/protein information +- **Sequences**: Gene, RNA, protein, CDS, 5'/3' UTR FASTA files + +**Outputs (Prokaryote)** + +Prokaryotic genes (WP\_ accessions) use a different report format with: +accession, description, EC number, gene symbol, protein info. + +**Examples** + +Download human BRCA1:: + + Query by: Gene ID + Gene ID: 672 + +Download TP53 orthologs in rodents:: + + Query by: Symbol + Symbol: tp53 + Ortholog: rodentia + + +.. _datasets: https://www.ncbi.nlm.nih.gov/datasets/ +]]></help> <expand macro="citations"/> </tool>
--- a/datasets_genome.xml Mon Aug 04 08:51:59 2025 +0000 +++ b/datasets_genome.xml Fri Dec 26 17:17:02 2025 +0000 @@ -46,7 +46,7 @@ @RELEASED_BEFORE@ @RELEASED_AFTER@ #for search_term in $filters.search: - --search '$filters.search_term' + --search '$search_term.search' #end for --no-progressbar --dehydrated @@ -191,18 +191,18 @@ <output name="genome_data_report"> <assert_contents> <has_text text="Assembly Accession	Assembly Name	Assembly Submitter	Organism Name"/> - <has_n_lines n="142"/> + <has_n_lines min="140"/> <has_n_columns n="4"/> </assert_contents> </output> - <output_collection name="rna_fasta" type="list" count="2"> + <output_collection name="rna_fasta" type="list"> <element name="GCF_000306695.2" decompress="true"> <assert_contents> <has_text text=">"/> </assert_contents> </element> </output_collection> - <output_collection name="genomic_gff" type="list" count="12"> + <output_collection name="genomic_gff" type="list"> <element name="GCF_000306695.2"> <assert_contents> <has_n_lines min="1000000"/> @@ -218,29 +218,25 @@ <test expect_num_outputs="2"> <conditional name="query|subcommand"> <param name="download_by" value="taxon"/> - <param name="taxon_positional" value="human"/> + <param name="taxon_positional" value="Norway rat"/> </conditional> <section name="filters"> - <param name="chromosomes" value="21"/> - <param name="assembly_level" value="chromosome,complete"/> - <param name="released_before" value="01/01/2018"/> + <param name="chromosomes" value="MT"/> </section> <section name="file_choices"> <param name="include" value="genome"/> <param name="decompress" value="true"/> </section> - <output_collection name="genome_fasta" type="list:list" count="11"> - <expand macro="genome_fasta_assert" el1="GCA_000002115.2" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_000002125.2" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_000212995.1" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_000306695.2" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_000365445.1" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_001292825.2" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_001524155.4" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_001712695.1" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCA_022833125.2" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/> - <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/> + <output_collection name="genome_fasta" type="list:list" count="9"> + <expand macro="genome_fasta_assert" el1="GCA_000001895.4" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCA_015227675.2" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCA_036323735.1" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCA_041222355.1" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCA_045687965.1" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCA_045687995.1" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCA_045688005.1" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCF_000001895.5" el2="chrMT" expression=">"/> + <expand macro="genome_fasta_assert" el1="GCF_015227675.2" el2="chrMT" expression=">"/> <!-- According to https://github.com/ncbi/datasets/issues/188, the following should not be included among the returned results anymore 09/2023 --> <!-- <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/> @@ -249,7 +245,7 @@ </output_collection> <output name="genome_data_report"> <assert_contents> - <has_text text="Homo sapiens"/> + <has_text text="Rattus norvegicus"/> <has_n_columns n="4"/> </assert_contents> </output> @@ -495,25 +491,72 @@ </assert_contents> </output> </test> + <!-- test search filter --> + <test expect_num_outputs="1"> + <conditional name="query|subcommand"> + <param name="download_by" value="taxon"/> + <param name="taxon_positional" value="Streptococcus"/> + </conditional> + <section name="filters"> + <repeat name="search"> + <param name="search" value="pyogenes"/> + </repeat> + </section> + <section name="file_choices"> + <param name="include" value_json="null"/> + </section> + <output name="genome_data_report"> + <assert_contents> + <has_text text="pyogenes"/> + </assert_contents> + </output> + </test> </tests> - <help> -<![CDATA[ -**Download Genome Datasets from NCBI** + <help><![CDATA[ +.. class:: infomark -Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report. -Genome datasets can be specified by NCBI Assembly or BioProject accession(s) or by taxon. +**What it does** + +Downloads genome assemblies from NCBI using the `datasets`_ command-line tool. +Retrieve genome sequences, annotations, and metadata by accession or taxon. -The download is a three step process: +**Query Options** + +- **By Accession**: NCBI Assembly (GCF\_/GCA\_) or BioProject accession +- **By Taxon**: Taxonomy ID, scientific name, or common name -1. A "dehydrated" zip file is downloaded which includes the metadata and the download URL) -2. The metadata is transformed into a tabular (TSV) file -3. The data is hydrated (the actual data is downloaded) +**Filters** + +==================== =============================================== +Filter Description +==================== =============================================== +Reference only Limit to reference/representative assemblies +Annotated only Include only genomes with annotations +Assembly level Chromosome, complete, contig, or scaffold +Assembly source RefSeq (GCF\_) or GenBank (GCA\_) +Exclude atypical Remove atypical assemblies (e.g., partial) +MAG filter Include/exclude metagenome-assembled genomes +Date range Filter by release date +==================== =============================================== + +---- -The 3rd step can be skipped by unselecting all output types in the `Include` parameter. -Thereby its possible to inspect the metadata prior to the actual data download. Also this -allows to use the tool for querying data sets (and their accessions) of interest which -can then be downloaded in a second call using the accessions. -]]> - </help> +.. class:: warningmark + +**Note**: The "Reference only" filter returns only RefSeq (GCF\_) assemblies. +If a taxon has only GenBank (GCA\_) assemblies, this filter will return no results +with a misleading error message. It is a NCBI datasets bug (not a Galaxy bug). + +**Outputs** + +- **Data Report**: Tabular metadata for matching assemblies +- **Genome FASTA**: Genomic sequences (nested collection by accession) +- **Annotation files**: GFF3, GTF, GenBank flat files +- **Protein/RNA/CDS**: Amino acid and nucleotide sequences +- **Sequence Report**: Per-sequence metadata (chromosome, length, etc.) + +.. _datasets: https://www.ncbi.nlm.nih.gov/datasets/ + +]]></help> <expand macro="citations"/> </tool>
--- a/macros.xml Mon Aug 04 08:51:59 2025 +0000 +++ b/macros.xml Fri Dec 26 17:17:02 2025 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">18.5.1</token> + <token name="@TOOL_VERSION@">18.13.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.0</token> <token name="@LICENSE@">MIT</token> @@ -95,7 +95,7 @@ <xml name="genome_includes"> <option value="genome" selected="true">genomic sequence (genome)</option> <option value="rna">transcript (rna)</option> - <option value="protein">amnio acid sequences (protein)</option> + <option value="protein">amino acid sequences (protein)</option> <option value="cds">nucleotide coding sequences (cds)</option> <option value="gff3">general feature file (gff3)</option> <option value="gtf">gene transfer format (gtf)</option> @@ -105,7 +105,7 @@ </xml> <xml name="gene_includes"> <option value="gene">gene sequence (gene)</option> - <option value="protein" selected="true">amnio acid sequences (protein)</option> + <option value="protein" selected="true">amino acid sequences (protein)</option> <yield/> </xml> @@ -402,11 +402,8 @@ </xml> <xml name="citations"> <citations> - <citation type="bibtex">@misc{NCBI, - author = "{NCBI}", - title = "NCBI Datasets", - year = "2022", - url = "https://github.com/ncbi/datasets"} + <citation type="doi"> + 10.1038/s41597-024-03571-y </citation> </citations> </xml>