modules/krona_ktimporttaxonomy

KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.

plottaxonomyinteractivehtmlvisualisationkrona chart

https://github.com/nf-core/modules/[...]/modules/nf-core/krona/ktimporttaxonomy

Description

KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.

Input

name:type

description

pattern

`meta:map`

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

`report:file`

A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored.

*.{tsv}

`taxonomy:file`

Path to a Krona taxonomy .tab file normally downloaded and generated by krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but must end in .tab.

*tab

Output

name:type

description

pattern

`html`

`meta:file`

A html file containing an interactive krona plot.

*.{html}

`*.html:file`

A html file containing an interactive krona plot.

*.{html}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

krona

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

github.com/marbl/Krona/wiki/KronaTools http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1 10.1186/1471-2105-12-385