Description

Queries an NCBI database using an UID

Input

name:type
description
pattern

meta{:bash}

:map

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

xml_input{:bash}

:file

XML text file containing query results from database.

pattern{:bash}

:string

String in xml_input that encloses element to search.

element{:bash}

:string

Space-delimited strings that will be converted to columns.

sep{:bash}

:string

Separator/delimiter between columns (for instance ”,” or “\t”).

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Text file

*.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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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