Description

Queries an NCBI database using Unique Identifier(s)

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

uid{:bash}

:string

Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file

uids_file{:bash}

:file

Text file containing multiple UIDs. Cannot be used at the same time as uid.

database{:bash}

:string

Value must be a valid Entrez database name (‘assembly’, etc).

Output

name:type
description
pattern

xml{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.xml{:bash}

:file

Query result in XML format

*.xml

versions_esummary{:bash}

${task.process}{:bash}

:string

The name of the process

ENTREZDIRECT{:bash}

:string

The name of the tool

esummary -version 2>&1{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

ENTREZDIRECT{:bash}

:string

The name of the tool

esummary -version 2>&1{:bash}

:eval

The expression to obtain the version of the tool

Tools

entrezdirect
PUBLIC DOMAIN

Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

ncbi.nlm.nih.gov/books/NBK179288 ncbi.nlm.nih.gov/books/NBK25501 https://www.ncbi.nlm.nih.gov/books/NBK25498/ 10.1016/S0076-6879(96)66012-1
maintainer
Github user alxndrdiaz
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