Description

Queries an NCBI database using an UID

Input

Name (Type)
Description
Pattern

meta (map)

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

]

xml_input (file)

XML text file containing query results from database.

pattern (value)

String in xml_input that encloses element to search.

element (value)

Space-delimited strings that will be converted to columns.

sep (value)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

xtract_table (file)

TXT file containing columns searched from element.

*.txt
maintainer
Github user alxndrdiaz
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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